bluuebunny/crossref_metadata_2025 huggingface dataset:
Basic characteristics and features of the molecular genetic test systems designed for non-invasive diagnostics and prognosis of prostate cancer and bladder cancer
Authors: Mikhaylenko D. S. , Sergienko S. A. , Alekseev B. Ya. , Kaprin A. D. , Nemtsova M. V.
Published: January 2020

Improving the laboratory diagnosis of prostate cancer and bladder cancer are still an actual problem in modern urologic oncology. Test systems for DNA or RNA alterations that occurred during carcinogenesis and associated with the malignant tumor and the prognosis of disease have been actively developed in recent years. Here we reviewed the data published mainly in the last 5 years about the molecular genetic kits for diagnosis (Progensa, SelectMDx, ExoDx Prostate Test, Prosta-Test, Confirm MDx) and assessment of prognosis (Prolaris, Decipher, Oncotype DX) in patients with prostate cancer, discussed their sensitivity and specificity. The characteristics of analogous kits and panels for bladder cancer (UroVysion, CertNDx Bladder Cancer Assay, UroSEEK, mutations in the FGFR3 and TERT genes, and the Cxbladder Monitor/Detect/Triage kit's line) were systematized. Particularly we focused on the description of the patient cohorts for whom kits mentioned above have greater diagnostic accuracy, described limitations of these test systems in consequence both a methodological and registration aspects, and their use in combination with other tumor markers. This review is aimed at oncologists, urologists, laboratory geneticists and specialists in related professions.
Current advances in kidney cancer immunotherapy
Authors: Korotaeva A. A. , Apanovich N. V. , Braga E. A. , Matveev V. B. , Karpukhin A. V.
Published: January 2020

In Russia, among tumors of the genitourinary system, renal cell carcinoma takes the 2nd place after prostate cancer. In 25 % of patients at the time of diagnosis, metastases are detected. Treatment of advanced stages of renal cell carcinoma is often not effective enough. The introduction into clinical practice of modern immunotherapeutic drugs based on inhibition of immune check points has changed the prognosis of the disease for many patients with various malignant neoplasms, including kidney cancer. In this article, we described the results of recent clinical trials on the use of immunotherapy in the treatment of kidney cancer. The most effective is combination of drugs that inhibit different immune check points, and a combination of a check point inhibitor with a targeted drug. This approach is likely to be a major one in the treatment of renal cell carcinoma in the short term. Combinations of control point inhibitors with radiation therapy and immunomodulatory drugs, the role of miRNAs in the regulation of expression of immune control points, the significance and characteristics of the microbiome in connection with the success of immunotherapy for kidney cancer, gene expression profiles as biomarkers of the immune response, and other biomarkers are considered. A better understanding of the mechanisms that limit the effectiveness of immune control point inhibitors will improve future treatment.
Pancreatic metastases from renal cancer: comparing surgery and pharmacotherapy efficacy
Authors: Kotelnikov A. G. , Kriger A. G. , Podluzhny D. V. , Proskuryakov I. S. , Galkin G. V. , Patyutko Yu. I. , Fainstein I. A.
Published: January 2020

Background. Today, targeted therapy is a standard treatment in advanced renal cell carcinoma, while the surgical method plays the role of a possible approach in a select category of patients with solitary and single metastases.

The study objective to compare the effectiveness of two alternative treatment approaches: the surgical method and modern pharmacotherapy in achieving long-term overall survival of patients with pancreatic metastases of renal cell carcinoma.

Materials and methods. A retrospective two-center study was conducted. The cohort of surgical treatment included patients (n = 56) who underwent surgery for pancreatic metastases from renal cell carcinoma at the N.N. Blokhin National Medical Research Center of Oncology and A.V. Vishnevsky National Medical Research Center of Surgery in the period from 1990 to 2019. Operations were performed for all types of pancreatic lesions: synchronous/metachronous, solitary/single and multiple, isolated/combined with lesions of other organs. Postoperative mortality rate was 5 % (3 patients). The pharmacotherapy cohort (n = 28) included patients with potentially resectable pancreatic metastases from clear cell renal cell carcinoma who underwent targeted therapy. Survival was assessed using the Kaplan–Mayer method. The Mantel–Cox test was used to test null hypothesis.

Results. The 5-year overall survival rate was 68 % in the surgery group compared to 35 % for the pharmacotherapy group. Median overall survival for surgical and non-surgical patients was 82 months and 43 months, respectively (p = 0.01). The advantage of the surgical method was also found in a subgroup survival analysis of patients with extrapancreatic disease (p = 0.037). In this case, the 5-year overall survival rate was 66 % in the surgery subgroup (n = 25) compared to 35 % for the pharmacotherapy subgroup (n = 24). Conclusion. Radical surgical treatment in comparison with modern pharmacotherapy allows to achieve significantly higher rates of overall survival in patients with pancreatic metastases of renal cell carcinoma and can be considered as a priority.
QUALITY EVALUATION METHOD OF THE CITY ENVIRONMENT
Authors: Mikhno O. , Patrakeiev I.
Published: January 2020

The approach to the estimation of the condition of the surrounding anthropogenically-transformed environment, based on the metabolic concept of the urban environment is proposed. Improvement of existing and development of new indicators are an important stage in the implementation of the geoinformational monitoring of the forecasting of the state of the city environment in practice, which will realize in practice the concept of sustainable development of the urban environment, which is today the development of V.I. Vernadsky's doctrine of the noosphere. Keywords: energy balance, entropy, free energy, Takagi-Sugeno-Kang algorithm, material-energy flows, geoinformational monitoring.
Solvent-based Extrusion 3D Printing for the Fabrication of Tissue Engineering Scaffolds
Authors: Zhang Bin , Cristescu Rodica , B. Chrisey Douglas , J. Narayan Roger
Published: January 2020

Three-dimensional (3D) printing has been emerging as a new technology for scaffold fabrication to overcome the problems associated with the undesirable microstructure associated with the use of traditional methods. Solvent-based extrusion (SBE) 3D printing is a popular 3D printing method, which enables incorporation of cells during the scaffold printing process. The scaffold can be customized by optimizing the scaffold structure, biomaterial, and cells to mimic the properties of natural tissue. However, several technical challenges prevent SBE 3D printing from translation to clinical use, such as the properties of current biomaterials, the difficulties associated with simultaneous control of multiple biomaterials and cells, and the scaffold-to-scaffold variability of current 3D printed scaffolds. In this review paper, a summary of SBE 3D printing for tissue engineering (TE) is provided. The influences of parameters such as ink biomaterials, ink rheological behavior, crosslinking mechanisms, and printing parameters on scaffold fabrication are considered. The printed scaffold structure, mechanical properties, degradation, and biocompatibility of the scaffolds are summarized. It is believed that a better understanding of the scaffold fabrication process and assessment methods can improve the functionality of SBE-manufactured 3D printed scaffolds.
Perfil de Uso do Espaço Virtual como Estratégia Pedagógica para a Práxis Educativa Online
Authors: Santo Eniel do Espirito , Cardoso Ariston de Lima , Santos Adilson Gomes dos , Barros Daniela Melaré Vieira , Moreira Jose António Marques
Published: January 2020

Neste artigo analisamos o perfil de uso do espaço virtual dos estudantes como estratégia pedagógica para a práxis educativa nos ambientes virtuais de aprendizagem. Decorrente da teoria dos estilos de aprendizagem, a abordagem teórica do perfil de uso do espaço virtual pressupõe quatro estilos básicos: 1) participativo; 2) de busca e pesquisa; 3) de estruturação e planejamento; e 4) de ação concreta e produção. O estudo configura-se como um relato de experiência, realizado com a aplicação do questionário de identificação desse perfil com 159 estudantes em um curso de pós-graduação lato sensu a distância. Os dados revelaram predomínio do estilo de estruturação e planejamento no espaço virtual (40,7%), com resultados equilibrados nos estilos de busca e pesquisa (36,4%), uso participativo (36,4%) e de ação concreta e de produção (34,9%). Diante disso, os docentes do curso foram orientados a priorizar estratégias pedagógicas capazes de sequenciar a aprendizagem, partindo do estilo predominante e avançando pelos demais estilos menos desenvolvidos. O relato conclui apontando a pertinência do diagnóstico dos estilos de uso do espaço virtual para a práxis educativa online, recomendando a sua realização no início do período letivo, visando nortear o trabalho docente e elaboração das atividades didáticas.
Palavras-chave: Estilos de uso do espaço virtual. Estratégias pedagógicas.
Para além da Oferta de Unidades Curriculares: Uma Possibilidade Inclusiva para Estudantes Aspies por meio de Plataformas Virtuais
Authors: Moreira Jonathan Rosa , Barros Everson da Silva , Ribeiro Jefferson Bruno Pereira
Published: January 2020

As instituições de educação superior ofertam as unidades curriculares por semestre em função do quantitativo de estudantes e de sua infraestrutura física. Quando o enfoque está nas instituições privadas, é razoável que esse controle seja ainda mais persistente e com processos definidos porque afeta diretamente sua sustentabilidade. Considerando as unidades curriculares que utilizam salas de aula convencionais, a quantidade de estudantes alocados por turma é feita sobre o quantitativo convencionado, e não necessariamente pelo perfil dos estudantes. No processo de ensino e aprendizagem, os professores precisam planejar sua organização didático-pedagógica em função do perfil e da pluralidade diagnosticada na turma. Há, portanto, uma dualidade de processos acadêmicos, cada um com sua importância. Por um lado, há de se garantir a situação financeira da instituição. Por outro lado, há de primar pela qualidade do processo de ensino e aprendizagem, considerando a diversidade e os diferentes estilos de aprendizagem. O objetivo deste estudo foi apresentar uma proposta de itinerário formativo, considerando as particularidades do caso de um estudante acometido por síndrome de Asperger no curso de graduação da Faculdade Projeção de Ceilândia, Distrito Federal. Para tanto, optou-se por uma abordagem mista, do tipo documental e descritivo, com cinco etapas definidas para a construção de um itinerário formativo com base na tipologia de conteúdos, taxonomia de Bloom e aprendizagem adaptativa, mediado por ambiente virtual de aprendizagem. Uma estratégia metodológica mediada por educação a distância pode ser viável para mitigar as limitações e dificuldades características da síndrome de Asperger.

Palavras-chave: Oferta Acadêmica. Educação Inclusiva. Síndrome de Asperger.
Eficacia y seguridad de la liraglutida como tratamiento coadyuvante para disminuir el índice de masa corporal
Authors: Hernández-Rodríguez Diana Carolina
Published: January 2020

Introducción. El sobrepeso y la obesidad son condiciones que vienen en aumento en Colombia y en el mundo, lo cual es preocupante ya que generan predisposición para enfermedades que causan alta morbimortalidad. El tratamiento para estas enfermedades necesita un enfoque multidisciplinario que incluya hábitos saludables con cambios en la dieta, aumento de la actividad física y, en ocasiones, uso de fármacos y cirugía bariátrica como tratamiento coadyuvante. Algunos medicamentos GLP-1 han demostrado eficacia en la pérdida de peso, en especial la liraglutida, un medicamento usado como complemento de la dieta y el ejercicio para lograr mayor control glucémico en adultos con diabetes mellitus tipo 2 que también tienen enfermedad cardiovascular.
Objetivo. Evaluar la eficacia y seguridad de la liraglutida como medicamento coadyuvante para disminuir el índice de masa corporal (IMC) en personas con sobrepeso (IMC=25-30 kg/m2) y obesidad (IMC>30 kg/m2).
Materiales y métodos. Se realizó una búsqueda en las bases de datos Trip Database, Embase, PubMed, Scopus y Clinical Key sobre estudios que cumplieran los criterios de inclusión y que evaluaran la disminución de peso con el uso de liraglutida.
Conclusiones. La liraglutida es un medicamento que reduce el IMC en personas con sobrepeso y obesidad; sin embargo, presenta efectos adversos que deben ser evaluados, razón por la cual es necesario ampliar la literatura y las líneas de investigación para, de esta manera, tener evidencia clara con la cual sea posible discutir su eficacia y seguridad como tratamiento coadyuvante en personas con sobrepeso.
Popularyzacja języka i kultury rosyjskiej wśród dzieci. Fenomen serialu animowanego Masza i Niedźwiedź
Authors: Olechno-Wasiluk Joanna
Published: January 2020

W niniejszym artykule autorka koncentruje się na możliwościach wykorzystania serialu animowanego Masza i Niedźwiedź w nauczaniu języka rosyjskiego dzieci w wieku przedszkolnym i wczesnoszkolnym. Zwraca uwagę na bogactwo elementów kultury rosyjskiej zawartych w serialu i przekazywanych widzowi „przy okazji” narracji. Autorka dokonuje analizy stereotypów ulokowanych w animacji, szczególnie tych o treści poznawczej, tj. związanych z dniem powszednim Rosjan, ich zainteresowaniami, tradycjami, ubiorem. Publikacja niniejsza oparta jest na doświadczeniach autorki z realizacji własnego projektu pod hasłem: „Zrozumieć Maszę. Wesoło, kolorowo i ciekawie o języku i kulturze Rosji”. Zakłada on popularyzację języka i kultury rosyjskiej wśród dzieci oraz przygotowanie ich do uczestnictwa w dialogu międzykulturowym.
HIV and human endogenous retroviruses: an hypothesis with therapeutic implications.
Authors: McIntosh E M , Haynes R H
Published: January 2020

The enzyme dUTP pyrophosphatase (dUTPase, EC 3.6.1.23) is essential for cellular DNA replication and cell viability by virtue of its role in reducing the availability of dUTP as a substrate for DNA polymerases. Several members of the onco- and lentivirus families of retroviruses encode dUTPases and mutant strains of these viruses defective in this enzyme exhibit suboptimal replication kinetics. Among the lentiviruses there exists a surprising phylogenetic discontinuity in the distribution of dUTPase genes: non-primate viruses (EIAV, CAEV, FIV, visna) contain such genes whereas the primate viruses (HIVs, SIVs) do not. The reason for this difference is unknown. We suggest the following explanation: (1) the nuclear and mitochondrial compartmentalization of the mammalian dUTPase, combined with the cytoplasmic location of ribonucleotide reductase, leads to the net synthesis of dUTP, together with dCTP, dGTP and dATP in the cytoplasm; (2) this combination of dNTPs serves as a "toxic cocktail" for viral replication by virtue of its ability to promote the synthesis of uracil-substituted DNA; (3) many viruses have adapted to this challenge by encoding dUTPases that are free of normal cellular regulatory constraints; and (4) the fortuitous expression of a dUTPase encoded by one or more human endogenous retroviruses (HERVs) has led to the evolutionary loss of the putative ancestral dUTPase gene of primate lentiviruses. Thus, we propose that efficient replication of HIV in humans depends upon expression of a dUTPase encoded by an endogenous retrovirus. If this proposal is correct, then the entry of HIV into target cells is necessary, but not sufficient, for replication of the virus in humans.
Influence of low temperature on the synthesis of some Galleria mellonella proteins.
Authors: Kłudkiewicz B , Godlewski J , Grzelak K , Cymborowski B , Lassota Z
Published: January 2020

In developing Galleria mellonella larvae (reared at 30 degrees C) three proteins of 74, 76 and 81/82 kDa were identified. They represent a group of storage proteins (LHP proteins). In Galleria larvae, the development of which is arrested by low temperature (18 degrees C), accumulation of the 74, 76 and 81/82 kDa proteins was detected in the hemolymph. The synthesis of 74 kDa and 76 kDa proteins started after 24 h, and that of about 80 kDa after 96 h following the transfer of larvae from 30 degrees C to 18 degrees C. 20-Hydroxyecdysone inhibited synthesis of the 74 and 76 kDa proteins in larvae exposed to low temperature. The arrest of development of Galleria larvae is associated with the synthesis and accumulation of storage proteins, and ecdysteroids are involved in these processes.
Proteinases from pollen and pests.
Authors: Travis J , Whitworth T , Matheson N , Bagarozzi D
Published: January 2020

An examination of the proteinases present in two very different systems is described, in order to illustrate the diversity in function of this class of enzymes. In the first case we have noted the importance of gut proteinases from the fire ant Solenopsis invicta in relation to the nutritional requirements of the entire colony. In the second we have investigated the properties of endoproteases from both ragweed and mesquite pollen, relative to their role in the development of allergies and asthma. If the function of each type of enzyme(s) is correct, then it is clear that addition of exogenous inhibitors might be useful in a) controlling the infestation associated with the fire ant, and b) reducing the deleterious effects associated with the development of asthma.
The intracellular serpin family.
Authors: Korpula-Mastalerz R , Dubin A
Published: January 2020

The serpins are widely distributed, structurally related family of proteins with diverse functions. Most of the known serpins are proteinase inhibitors, the majority being found as secreted species, however, there are a few that occur intracellularly and their physiological role remains unknown. Most of the intracellularly occurring serpins have been classified into the ovalbumin subfamily. The possible phytogenetic tree of 14 intracellular serpins is presented.
The use of sequential affinity chromatography for separation of human neutrophil elastase, cathepsin G and azurocidin.
Authors: Watorek W , Polanowski A , Wilusz T
Published: January 2020

Elastase, cathepsin G and azurocidin from human neutrophils are key components of body inflammatory defense. Perturbations in regulation of their activities lead to many serious pathological states. The paper describes a simple, fast and efficient method of joint purification of these proteins with the use of sequential affinity chromatography on squash trypsin inhibitor (CMTI I) and bovine pancreatic trypsin inhibitor (BPTI).
Gastrin activates tyrosine kinase and phospholipase C in isolated rat colonocytes.
Authors: Małecka-Panas E , Tureaud J , Majumdar A P
Published: January 2020

Postreceptor regulation of the trophic action of gastrin is not fully elucidated. Tyrosine kinase (Tyr-kinase) has been associated with receptors of a number of growth factors and plays an important role in regulation of cellular growth within the gastrointestinal tract. The aim of this study was to determine, whether Tyr-kinase plays a role in mediating the growth promoting action of gastrin and whether phospholipase C (PLC) is involved in the signal transduction pathway. Colonocytes isolated from Fischer 344 rats were incubated for 2 min with gastrin (10(-8) M) and assayed for Tyr-kinase and PLC activities. Incubations with gastrin resulted in 60%-70% rise in Tyr-kinase and 150%-200% rise in PLC activities over the corresponding basal levels. When processed separately, in proximal colon Tyr-kinase activation by gastrin was 15%-20%, while in distal colon 70%-80% as compared to the buffer control. Gastrin activation of both Tyr-kinase and PLC was abolished by Tyr-kinase inhibitor, tyrphostin-25 (3.2 microM) and was not affected by staurosporine (20 ng/ml). We conclude that Tyr-kinase is involved in the mechanism of trophic action of gastrin, and PLC activation appears to be the next step in the signal transduction pathway.
New approaches to the mapping of chromosomal domains.
Authors: Filipski J , Svetlova E , Avril-Fournout N , Deschavanne P , Bellis M
Published: January 2020

Although it is generally accepted that the chromosome is divided into elementary subunits, the structural and functional domains, the organisation of these structures at the molecular level is not well understood. In particular, the domain boundaries are not easily identifiable. Several possible candidates such as MARs/SARs, insulators, LCRs, palindromic sequences, or easily melting sequences have been found in the regions having properties one would except for boundaries. None of these elements, however, has been found in all of the constructs functioning as boundaries in tests in vivo. Recent work suggests that the common denominator might be the presence og GC-rich oligonucleotide stretches and the formation of the chromatin hypersensitive sites. A model is discussed in which "unusual" structures, in particular the four-stranded DNA sequence elements containing unpaired bases, play the role of domain boundaries.
On the strategy of using nonviral carriers in cancer gene therapy.
Authors: Sochanik A , Szala S
Published: January 2020

Effectiveness and mode of therapeutic gene delivery in vivo as well as biological safety of such transfer must be improved before widespread application of gene therapy in the clinic becomes possible. Most research has so far focused on recombinant viral delivery systems. Clinical future seems to belong, however, to nonviral delivery systems. Such systems feature DNA complexed to lipid, protein, peptide or polymeric carriers with ligands allowing in vivo tissue targeting by the complex and nuclear translocation of the exogene. Nonviral gene carrier systems are discussed together with strategies of destroying cancer cells.
Applications of impedance spectroscopy in biochemistry and biophysics.
Authors: Janshoff A , Wegener J , Steinem C , Sieber M , Galla H J
Published: January 2020

The present study is intended to demonstrate the application of impedance spectroscopy to two very different fields of biophysical research. The core component of our measuring setup is a self-constructed continuous wave impedance spectrometer together with special measuring chambers which are individually designed for the systems under investigation. We directed our attention towards: i) the investigation of solid supported lipid bilayers in general, especially systems which are suitable for protein reconstitution such as dimethyldioctadecylammonium bromide (DODAB) immobilized onto a gold electrode, precovered with a negatively charged monolayer of 3-mercaptopropionic acid. Impedance spectroscopy allows to study the stability, the thickness and the electrode coverage of those artificial membranes as well as the observation of ion transport mediated by ionophores like gramicidin D incorporated into a DODAB-bilayer. ii) The characterization of the passive electrical properties of epithelial and endothelial cell monolayers in general and especially the determination of their transepithelial (transendothelial) electrical resistances as a measure for epithelial barrier function. From impedance spectra, as reported here, we are able to follow the formation and modulation of cell layer permeability to small ions.
Mitochondrial metabolite carrier family, topology, structure and functional properties: an overview.
Authors: Sluse F E
Published: January 2020

A set of metabolite carriers operates the traffic of numerous molecules consumed or produced in mitochondrial matrix and/or cytosolic compartments. As their existence has been predicted by the chemiosmotic theory, the first challenge, in the late sixties, was to prove their presence in the inner mitochondrial membrane and to describe the various transports carried out. The second challenge was to understand their mechanisms by the kinetic approach in intact mitochondria (seventies). The third challenge (late seventies-eighties) was to isolate and to reconstitute the carriers in liposomes in order to characterize the proteins and to establish the concept of a structural and a functional family as well as some structure-function relationship with the help of primary sequences. Genetics, molecular biology and genomic sequencing bring the fourth challenge (nineties): a raising number of putative carriers becomes known only by their primary sequences but their functions have to be discovered. The actual challenge of the future is the elucidation of the ternary structure of carrier proteins that together with site-directed mutagenesis and kinetic mechanism will permit to advance in the understanding of molecular mechanisms of transport processes.
Halogenated benzimidazole inhibitors of phosphorylation, in vitro and in vivo, of the surface acidic proteins of the yeast ribosomal 60S subunit by endogenous protein kinases CK-II and PK60S.
Authors: Szyszka R , Boguszewska A , Shugar D , Grankowski N
Published: January 2020

Several halogeno benzimidazoles and 2-azabenzimidazoles, previously shown to be relatively selective inhibitors of protein kinases CK-I and/or CK-II from various sources, including CK-II from yeast [Szyszka et al. (1995) Biochem. Biophys. Res. Commun. 208, 418-424] inhibit also the yeast ribosomal protein kinase PK60S. The most effective inhibitor of CK-II and PK60S was tetrabromo-2-azabenzimidazole ](TetraBr-2-azaBz), which was competitive with respect to ATP (and GTP in the case of CK-II) with Ki values of 0.7 microM for CK-II, and 0.1 microM for PK60S PK60S phosphorylates only three (YP1 beta', YP2 alpha) out of five polypeptides of pp13 kDa acidic proteins of 60S subunit phosphorylated by CK-II [Szyszka et al. (1995) Acta Biochim. Polon. 42, 357-362]. Accordingly, TetraBr-2-azaBz inhibits phosphorylation only of these polypeptides, catalysed by PK60S . Addition of TetraBr-2-azaBz to cultures of yeast cells, at concentrations which were without effect on cell growth, led to inhibition of intracellular phosphorylation of ribosomal acidic proteins, paralleling that observed in vitro. TetraBr-2-azaBz is shown to be a useful tool for studies on the intracellular regulation of phosphorylation of the ribosomal 60S acidic proteins, which are involved in formation of active ribosomes.
Protective effect of pantothenic acid and related compounds against permeabilization of Ehrlich ascites tumour cells by digitonin.
Authors: Slyshenkov V S , Rakowska M , Wojtczak L
Published: January 2020

Preincubation of Ehrlich ascites tumour cells with millimolar concentrations of pantothenic acid, pantothenol or pantethine, but not with homopantothenic acid, at 22 degrees C or 32 degrees C, but not at 0 degrees C, makes the plasma membrane more resistant to the damaging effect of submillimolar concentrations of digitonin. It is proposed that this increased resistance is due to the increased rate of cholesterol biosynthesis. In fact, incorporation of [14C]acetate into cholesterol is by 45% increased in the cells preincubated with pantothenic acid; this probably reflects elevation of the content of CoA in such cells [Slyshenkov, V.S., Rakowska, M., Moiseenok, A.G. & Wojtczak, L. (1995) Free Radical Biol. Med. 19, 767-772].
Synthesis, physicochemical and biological properties of poly-alpha-amino acids--the simplest of protein models.
Authors: Katchalski-Katzir E
Published: January 2020

During the 1950s, linear and multichain poly-alpha-amino acids were synthesized by polymerization of the corresponding N-carboxy-amino acid anhydrides in solution in the presence of suitable catalysts. The resulting homo- and heteropolymers have since been widely employed as simple protein models. Under appropriate conditions, poly-alpha-amino acids, in the solid state and in solution, were found to acquire conformations of an alpha-helix and of beta-parallel and antiparallel pleated sheets, or to exist as random coils. Their use in experimental and theoretical investigations of helix-coil transitions helped to shed new light on the mechanisms involved in protein denaturation. Poly-alpha-amino acids played an important role in the deciphering of the genetic code. In addition, analysis of the antigenicity of poly-alpha-amino acids led to the elucidation of the factors determining the antigenicity of proteins and peptides. Interest in the biological and physicochemical characteristics of poly-alpha-amino acids was recently renewed because of the reported novel findings that some copolymers of amino acids are effective as drugs in multiple sclerosis, and that glutamine repeats and reiteration of other amino acids occur in inherited neurodegenerative diseases. The presence of repeating sequences of amino acids in proteins, and of nucleotides in DNA, raises many interesting questions about their respective roles in determining protein structure and function, and gene performance and regulation.
Synthetic and biological applications of tricyclic analogues of guanosine.
Authors: Golankiewicz B
Published: January 2020

Tricyclic nucleosides incorporating the 9-oxo-imidazo [1,2-a]purine (1,N2-ethenoguanine) system, natural prototypes of which occur in tRNA(Phe) as nucleosides of the wyosine series, were used for synthetic, structural and biological purposes. 1,N2-(Prop-1-ene-1,2-diyl)guanosine derivatives used as intermediates allowed to enforce on guanosine the substitution at the N-3 position and at the N2 exo-amino group, not possible to be performed directly. Wyosine and 2'-deoxywyosine together with 4,5'-anhydro-4-desmethylwyosine and its congeners were used as, respectively, 100% anti and 100% syn conformation standards in a new graphical method for the syn-anti conformational analysis of nucleosides by 1D 1H NOE difference spectroscopy. Substitution at the appended third ring allowed to modify the biological and physical properties of antiviral agents acyclovir and ganciclovir, e.g. to develop their fluorescent analogues.
New insights regarding the potential of the pronucleotide approach in antiviral chemotherapy.
Authors: Gosselin G , Girardet J L , Périgaud C , Benzaria S , Lefebvre I , Schlienger N , Pompon A , Imbach J L
Published: January 2020

The rationale for a pronucleotide approach based on the use of phosphotriesters which incorporate enzyme-mediated bio-labile protection is discussed in detail. Among the studied bio-labile phosphate protecting groups, the S-acyl-2-thioethyl (SATE) groups appeared the most promising as exemplified in cell culture systems in the case of the pronucleotides of 3'-azido-3'-deoxythymidine, 2',3'-didehydro-3'-deoxythymidine, 2',3'-dideoxyadenosine and acyclovir In vivo implementations of such bis(SATE) pronucleotides have been planned for future animal studies.
Effect of reversed orientation and length of An.Tn DNA bending sequences in the -35 and spacer domains of a consensus-like Escherichia coli promoter on its strength in vivo and gross structure of the open complex in vitro.
Authors: Loziński T , Wierzchowski K L
Published: January 2020

In continuation of an earlier study (Loziński et al., 1991 Nucleic Acids Res. 19, 2947-2953) a series of consensus-like E. coli promoters with bending An.Tn sequences of different length (n = 3-8) and orientation in the -35 and spacer domains was constructed, cloned into the plasmid pDS3 and their strength in vivo measured in relation to an internal transcriptional standard. Gel mobilities of free DNA restriction fragments carrying these promoters and of open transcriptional complexes with cognate RNA polymerase were determined by polyacrylamide gel electrophoresis and the gross structure of the complexes interpreted in terms of the theoretically predicted superstructure of DNA restriction fragments. The results obtained together with those reported earlier show that bending of the DNA helix axis immediately upstream of the -35 domain generally lowers the promoter strength in vivo and brings about shortening of the mean square end-to-end distance between free DNA ends in the open complex in vitro. T4(-34 ...-37) and T5(-34 ...-38) tracts located in the nontemplate DNA strand had the largest and comparable effect on the promoter strength, while the A5.T5(-37 ... -41) sequence in either orientation (A5 tract in the template or nontemplate strand) exerted a much smaller effect. Promoters with the spacer bent by about 40 degrees but in different directions, by two A(n) (n = 5 or 6) tracts aligned in phase with the B-DNA repeat and located either in the template or nontemplate strands, had somewhat lower strength in vivo but the gross geometry of the respective open complexes was the same as that of a control promoter with straight spacer. Implications of these findings are discussed in connection with the existing model of E. coli transcriptional open complex.
Effects of exon sequences on splicing of model pre-mRNA substrates in vitro.
Authors: Dominski Z , Kole R
Published: January 2020

We used several related pre-mRNA substrates consisting of two introns and three exons to study effects of exon sequences on in vitro splicing. By varying the sequence of the internal exon and measuring the frequency of its skipping we confirmed that 26-nucleotide exon element naturally existing in beta-globin gene and previously analysed in vivo, has a strong stimulatory effect on splicing. Sequence analysis of this element suggests that it belongs to a family of purine-rich splicing elements found in exons of several alternatively spliced pre-mRNAs. The 26-nucleotide element can efficiently function in enhancing inclusion of internal exons regardless of their size and sequence composition, suggesting that it plays a role of a general exon recognition element. The purine-rich element is dispensable in exons flanked by strong splice sites, which promote efficient inclusion of otherwise poorly recognized exons. A row of six cytidines inserted into the internal exon (GC2 mutation) initially considered to stimulate exon inclusion to a similar extent as the purine-rich element (Dominski & Kole, 1994, J. Biol. Chem. 269, 23590-23596), appears not to affect splice site selection in vitro, and in vivo it is likely to act by stabilizing mRNA that includes the internal exon against rapid cytoplasmic degradation.
Human lipoprotein lipase deficiency: does chronic dyslipidemia lead to increased oxidative stress and mitochondrial DNA damage in blood cells?
Authors: Ven Murthy M R , Julien P , Singh P , Levy E
Published: January 2020

Lipoprotein lipase (LPL) is a key enzyme in the metabolism of lipoproteins and their balanced distribution in the plasma. A deficiency of this enzyme due to gene mutations leads to severe dyslipidemia. In this report, we describe the major LPL gene mutations that are prevalent in the French-Canadian population of Québec and the nature of dyslipidemia caused by the resulting enzyme deficiency. We discuss the possibility that dyslipidemia caused by LPL deficiency may enhance oxidative stress in the blood cells, bring about increased fluidity of the membrane components of these cells and increase the susceptibility of their mitochondrial DNA to structural alterations. Some preliminary experimental results in verification of this hypothesis are presented.
Strategic Analysis of Turbine Manufacturing Development in Achieving Required Local Content
Authors: Sitompul Rislima F.
Published: January 2020

The government of Indonesia has set up an electricity development program of 35,000 Mega Watt (MW) to provide adequate electricity infrastructure so that the 100% electrification ratio can be achieved. The construction of the development of power infrastructure has implications for the demand for reliable electrical components, which supports upstream to downstream industries.  The turbine is one of the major components in electricity infrastructure which requires the supply of mechanical energy as the driving force. Despite its market potential, the turbine is a relatively high imported component, and this indicates the importance of fostering the development of turbine technology in Indonesia. The main objective of this study is to examine the capability of national turbine industries and research institutions in formulating policy recommendations to increase the use of the local content, called Tingkat Kemampuan Dalam Negeri (TKDN), in turbine manufacturing industries following the provisions stipulated in the Ministerial Decree No.54/M-IND/PER/03/2012 on Guidelines for Use of Products of State for Infrastructure Development in Electricity. This study applies SWOT and Balanced Scorecard, focusing on the analysis of capabilities of the turbine industry and identifying the mastery of turbine technology by various research and development institutions in Indonesia. The result of the study shows that the degree of BSC performance level in implementing the TKDN improvement strategy in the turbine industry is considered as less successful, therefore, short-term and long-term policy recommendation needs to be implemented to expedite the increase of TKDN.
Feature Selection Method using Genetic Algorithm for Medical Dataset
Authors: Jothi Neesha , Husain Wahidah , Abdul Rashid Nur’Aini , Syed-Mohamad Sharifah Mashita
Published: January 2020

There is a massive amount of high dimensional data that is pervasive in the healthcare domain. Interpreting these data continues as a challenging problem and it is an active research area due to their nature of high dimensional and low sample size. These problems produce a significant challenge to the existing classification methods in achieving high accuracy. Therefore, a compelling feature selection method is important in this case to improve the correctly classify different diseases and consequently lead to help medical practitioners. The methodology for this paper is adapted from KDD method. In this work, a wrapper-based feature selection using the Genetic Algorithm (GA) is proposed and the classifier is based on Support Vector Machine (SVM). The proposed algorithms was tested on five medical datasets naming the Breast Cancer, Parkinson’s, Heart Disease, Statlog (Heart), and Hepatitis. The results obtained from this work, which apply GA as feature selection yielded competitive results on most of the datasets. The accuracies of the said datasets are as follows: Breast Cancer - 72.71%, Parkinson’s - 88.36%, Heart Disease - 86.73%, Statlog (Heart) - 85.48 %, and Hepatitis - 76.95%. This prediction method with GA as feature selection will help medical practitioners to make better diagnose with patient’s disease.
An Unscented Kalman Filter-based Synchronization Control Approach for Communication-Based Train Control Systems
Authors: Faruqi Ismail , Waluya M. Brahma , Nazaruddin Yul Yunazwin , Tamba Tua Agustinus , Widyotriatmo Augie
Published: January 2020

Communication-based train control (CBTC) system is an advanced train signalling and control technology which is developed using the moving block signalling (MBS) framework. The CBTC system has been shown to be capable of improving the operational efficiency, line capacity and safety of the railway operation. The main objective in implementing the MBS framework in CBTC system is to minimize the train headways through the utilization of an inter-train continuous communication system that determine and control the position of each train more precisely. One important challenge in such an implementation is the fulfillment of the necessary requirement of having highly accurate train localization method to ensure the safety of the short headway operation. This paper describes the results from experimental examination and application of a synchronization control strategy for the CBTC system using an unscented Kalman filter (UKF)-based sensor fusion approach as the localization method. In the proposed approach, the train localization task is performed using an UKF-based sensor fusion method which fuses measurement data from speed sensors and radio frequency identification tags. A synchronization control approach to ensure the safety movement of the train convoy in curved railway tracks under the MBS scheme is then proposed. The results presented in this paper show that the proposed localization and synchronization control methods can significantly improve the localization accuracy and reduce the inter-train headways.
Digital Human Modeling to Predict Passenger Comfort: A Case of Indonesian Angkot
Authors: Prasetyo Ridwan Aji Budi , Lawson Glyn
Published: January 2020

This paper presents an evaluation of angkot, which was conducted to address ergonomic issues related to this mode of transport and to support the development of design recommendations for angkot use by the Indonesian population. This was achieved by carefully investigating the way people sit inside the angkot, modeling and running simulation to assess comfort, and finally proposing a design recommendation that is likely to be more ergonomic and healthy based on the simulation. A contextual inquiry method using video observation was applied to investigate sitting postures that appear most often among passengers. The analysis revealed that the most common sitting postures were sitting fairly upright, with the head facing down to the floor or facing front to the direction of travel; meanwhile, both arms were supported, and both legs were free on the floor. JACK Digital Human Modelling (DHM) software was used to perform Rapid Upper-Limb Assessment (RULA) analysis, which revealed a number of commonly adopted postures that require correction. A new seating layout is proposed based on the analysis and best practices from literature. RULA analysis was reapplied to the design changes to check the anticipated postures that would emerge i.e. passengers are facing towards the front of the bus, which is more likely to be ergonomically better for their comfort and health. This paper also discussed its limitations and potential future works. Future study of similar phenomena is still wide-open to obtain a more thorough comprehension of angkot microbus.
Influence of Acoustic Waves on the Shelf Life Quality of White Oyster Mushroom (Pleurotus Florida)
Authors: Ceejay O Paclibare , Lavarias Jeffrey A. , Tuates Jr Andres M. , Somera Carolyn Grace G. , G. Peneyra Ruel
Published: January 2020

Mushrooms are seasonal and highly perishable crops and contain about 90% (w.b) moisture. The moisture content of fresh mushrooms is 70 - 95% (w.b), depending upon the harvest time and environmental conditions, while that of dried mushrooms is close to 10% (w.b).  Due to their high moisture content, they cannot be stored for more than 24 hours at ambient conditions. Hence, they need to be preserved by some methods. Moisture transportation and distribution in products are key factors for the development of the product quality. To control quality development, an understanding of the moisture content at a certain time of the product is required. The objective of the study was to extend the shelf life of fresh harvest of White oyster mushroom without compromising the quality by applying the acoustic wave with various exposure time. White oyster mushroom samples were exposed to acoustic waves (1kHz, 100 dB) inside a soundproof chamber at three levels of exposure time (1, 2, 3) hours. Subsequently, white oyster mushrooms sample stored in a refrigerator at 10 oC. The effects of acoustic waves application were determined by measuring the surface color, flesh firmness, and shelf-life extension every other day at cold storage. Results of the study indicated that white oyster mushroom samples exposed to acoustic waves for 2 hours exhibited the slowest to effect change in surface color for 13 days compared to 1 hour and 3 hours of exposure time at 11 and 12 days, respectively. Moreover, flesh firmness of white oyster mushroom samples exposed to acoustic waves for 2 hours was proved to exhibits the slowest to effect change for 13 days compared to 1 hour and 3 hours of exposure time at 11 and 12 days, respectively. The acoustic waves have a potential benefit of extending the shelf life of white oyster mushroom up to 13 days at 10 oC without altering the quality.
New Method for Estimating Fractal Dimension in 3D Space and Its Application to Complex Surfaces
Authors: Babic Matej , Miliaresis George Ch. , Mikos Matjaz , Ambu Rita , Calì Michele
Published: January 2020

The concept of “surface modeling” generally describes the process of representing a physical or artificial surface by a geometric model, namely a mathematical expression. Among the existing techniques applied for the characterization of a surface, terrain modeling relates to the representation of the natural surface of the Earth. Cartographic terrain or relief models as three-dimensional representations of a part of the Earth's surface convey an immediate and direct impression of a landscape and are much easier to understand than two-dimensional models. This paper addresses a major problem in complex surface modeling and evaluation consisting in the characterization of their topography and comparison among different textures, which can be relevant in different areas of research. A new algorithm is presented that allows calculating the fractal dimension of images of complex surfaces. The method is used to characterize different surfaces and compare their characteristics. The proposed new mathematical method computes the fractal dimension of the 3D space with the average space component of Hurst exponent H, while the estimated fractal dimension is used to evaluate, compare and characterize complex surfaces that are relevant in different areas of research. Various surfaces with both methods were analyzed and the results were compared. The study confirms that with known coordinates of a surface, it is possible to describe its complex structure. The estimated fractal dimension is proved to be an ideal tool for measuring the complexity of the various surfaces considered.
Evaluating Food Waste Handling Using Trios Monitoring System on Soy Industry in Bali, Indonesia
Authors: Irianto I Ketut , Arygunartha Gede Yohanes
Published: January 2020

The purpose of this paper is to analyze a series of operational systems for biofilter technology. The object of research is an area of Wastewater Treatment in the food industry Denpasar, Bali. The Trios System Monitoring Method can be analyzed in three stages of the process of pre-treatment, treatment, stabilization, and three treatments. Biology analyzes settings (giving oxygen, feeding the number of food microorganisms F/M/ ratio, speed of waste flow). The analysis shows that biofilter technology is a technology that uses physical and biological treatment without using chemicals.  Physical treatment is carried out by filtration, flotation, sedimentation. Biological treatment is carried out by regulating oxygen delivery with aeration period of 24 hours/day, microorganism feeding F/Mg/ BOD/MLSS/day ratio 0.05-0.2 with 100% proven waste flow BOD decreases by 80% pre-stage treatment.  The wastewater is forwarded to the biofilter pond and given physical treatment, biological, and tricking filter in speed regulation, treatment process stage, liquid waste originating from conventional ponds is inserted into the aeration pond with aeration period of 6.0-9.0/hour. Feeding microorganisms F/Mg/BOD/day/MLSS ratio 0.2-0.5 with the waste flow 50%, BOD decreased by 85%. Feeding microorganisms F/Mg/BOD/day/MLSS ratio 0.2 - 0.5 oxygen administration with aeration period of 6.0-9.0/hour, BOD decreased by 85-90%.