bluuebunny/crossref_metadata_2025 huggingface dataset:
Colony Formation Titering Assay for Lentivirus v2
Authors: The Nonprofit Plasmid Repository Addgene
Published: December 2019

This protocol is for running a colony formation titering assay for Lentivirus. To see the full abstract and additional resources, visit the Addgene protocol page. Sample Data
2018 Fen Lisesi Kimya Dersi Öğretim Programı Kazanımlarının Yenilenmiş Bloom Taksonomisine Göre İncelenmesi ve 2018 Kimya Dersi Öğretim Programı ile Karşılaştırılması
Authors: AYDIN Abdullah , AYYILDIZ Yildizay , NAKİBOĞLU Canan
Published: December 2019

– Bu çalışmada, Fen Lisesi Kimya Dersi Öğretim Programı kazanımları ile Lise Kimya Dersi Öğretim Program kazanımlarının Yenilenmiş Bloom Taksonomisine göre aralarında bir farklılık olup olmadığının ve varsa hangi açılardan farklılık olduğunun belirlenmesi amaçlanmıştır. Çalışmada, nitel araştırma yöntemlerinden biri olan doküman incelemesi kullanılmıştır. Fen Lisesi Kimya Dersi kazanımlarının Yenilenmiş Bloom Taksonomisinin bilişsel süreç boyutuna göre dağılımının %44,44’ünün anlamak, %34,08’inin çözümlemek, %8,89’unun uygulamak, %5,19’unun hatırlamak, %3,70’inin değerlendirmek ve %3,70’inin de yaratmak bilişsel süreç boyutlarından oluştuğu sonucuna ulaşılmıştır. Adı geçen programın kazanımları Yenilenmiş Bloom Taksonomisinin bilgi boyutuna göre analiz edildiğinde ise %71,85 ile ağırlıklı dağılımın kavramsal bilgi basamağında olduğu; %13,33 ile işlemsel ve %8,89 ile olgusal bilgi basamaklarındaki kazanımların oldukça az olduğu; %5,93 ile üstbilişsel bilgi basamağındaki kazanımların da çok az olduğu sonucu elde edilmiştir. Adı geçen programın kazanımlarının Kavramsal Bilgi boyutunda yoğunlaştığı görülmektedir. Yeni tasarlanacak ve hazırlanacak programda, işaret edilen yoğunluğun üst düzey bilgi boyutlarına kaydırılması önerilebilir.
Family conflict, stress, and coping as predictors of violence
Authors: Gómez-Acosta Andrés , Castro Muñoz John Alexander
Published: December 2019

Introduction. Violence research has prioritized stress as a consequence, even though it would be suggested that it could be considered as a trigger for violent behavior; additionally, there are no models in Colombia from an empirical-analytical perspective that demonstrate which are the psychosocial factors that allow predicting interpersonal violence. Objective. To determine from the structural-equations model (SEM) the extent to which variables such as family conflict, in association with the perception of stress and coping strategies, predict the presence of violent behavior. Method. Cross-sectional descriptive-correlational investigation, with multivariate analysis. Results. The SEM obtained reports that the average of expressions of violence in the family, family conflict, perceived stress, and coping strategies explain the variance of violence by 68%, with optimal adjustment goodness of fit indicators. Discussion and conclusion. The situations of family conflict and the expression of manifestations of violence of any kind in the family scenario, added to stress of people can seem to trigger, if there are no adequate coping resources, the intention to inflict harm on people or things that are immersed in such contexts. However, it is necessary to develop new studies, in order to consolidate the explanatory potential of the formulated model.
The Regularized Trace Formula Of A Second Order Differentıal Equation Given With Anti-Perıodic Boundary Conditions
Authors: KIZILBUDAK ÇALIŞKAN Seda , ÖZEN Leyla
Published: December 2019

In this study, we examined the formula of the regularized
trace of the self-adjoint operator which is formed bydifferential
expression and 

anti-periodic boundary condition.
CT and MRI Medical Image Fusion Using Discrete Wavelet Transform
Authors: MOSHANTAT Molham , KARAMZADEH Saeid
Published: December 2019

In these days, using medical image is very important in
hospitals. These medical images give a lot of data about human body for example
Computed Tomography (CT) identifies the bone structure, Magnetic Resonance
Image (MRI) image gives information about tissue data, Positron on Emission
Tomography (PET) and Single photon release computed tomography (SPECT) give
human body functionality data. but these images can't give clear data image for
disease diagnosis and treatment planning. So, these different modality complementary
data for effective disease analysis is required. In this work we fused two
images (CT and MRI) by using discrete wavelet transform then applied this
transform on all types of wavelets (haar, Daubechies, Mexican Hat, Symlets,
Morlet, Shannon).
Inverse Nodal Problems for Dirac-Type Integro-Differential System with Boundary Conditions Polynomially Dependent on the Spectral Parameter
Authors: KESKİN Baki , TEL Hediye Dilara
Published: December 2019

In this work, we study the inverse nodal problem
for Dirac type integro-differential operator with the boundary conditions
dependent spectral parameter polynomially. We prove that dense subset of the
nodal points determines the coefficients of differential part of operator and
gives partial information for integral part of it.
A Dynamic Network Model For Population Growth And Urbanization
Authors: HALİKİ Emir
Published: December 2019

Dynamic networks imply those states of which change over time and such
changes are generally associated with the topology of a network. Dynamic models
are currently needed for numerous systems which could be defined as a network
model. Those related to the propagation of living organisms are also a typical
example. The study has examined a sample space which has been defined in the
network topology of human population as the way in which it will spread with
population growth and correlated with various variables in the modeled dynamic
network.
Half-Inverse Problem For Dirac Operator With Boundary And Transmission Conditions Dependent Spectral Parameter Polynomially
Authors: GÜLDÜ Yalçin , ARSLANTAŞ Merve
Published: December 2019

In this paper, half-inverse problem is considered
for Dirac equations with boundary and finite number of transmission conditions
depending polynomially on the spectral parameter, if the potential is given
over the half of the considered interval and if one spectrum is known then,
potential function  on the whole
interval and the other coefficients of the considered problem can be determined
uniquely.
Comparative Analysis of the Feature Extraction Performance of Augmented Reality Algorithms
Authors: TOSUN Umut
Published: December 2019

The algorithms that extract keypoints
and descriptors in augmented reality applications are getting more and more
important  in terms of performance.
Criterions like time and correct matching of points gain more impact according
to the type of application. In this paper, the performance of the algorithms
used to identify an image using keypoint and descriptor extraction is  studied. In the context of this research,
main criterion like the number of keypoints and descriptors that the algorithms
extract, algorithm execution time, and the quality of keypoints and descriptors
extracted are considered as the performance metrics. Same data stacks were used
for obtaining comparison results. In addition to comparisons for a group of
well-known augmented reality applications, the best performing algorithms for
varying applications were also suggested. C++ language and OpenCV library were
used for the implementation of the augmented reality algorithms compared.
Energy loss analysis from RBS spectrum of thin Cu2ZnSnS4 (CZTS) film
Authors: USTA Metin
Published: December 2019

The goal of this work is to
offer an alternative method to the available literature on determining the
energy loss of CZTS thin films. For this purpose, thin CZTS film structures
were first produced by sol-gel method and then the RBS spectrum was received
with RBS detector irradiating this structure with 3.034 MeV proton beams in a
microbeam chamber. The energy calibration was implemented to this spectrum,
where the it was fitted with SIMNRA program. In the RBS spectrum of the thin
film generated, a method for the calculation of energy loss was used for the
position and energy width analysis of the corresponding peaks and a polynomial
fit was obtained from the stopping power of the CZTS thin film by making
certain approaches. Also, the effective charge approach that we used in our
previous studies for the stopping power was employed with atomic natural
orbitals and it was founded that the results were close to each other at
certain error rates.  The data obtained
from this study will inspire the future studies on the interaction of radiation
with matter.
Ground-Motion Analysis of Hydraulic-Fracturing Induced Seismicity at Close Epicentral Distance
Authors: Rodríguez-Pradilla Germán , Eaton David W.
Published: December 2019

The application of seismic hazard analysis methods developed for natural earthquakes can provide an effective framework for managing risks of induced seismicity (IS) sequences, particularly for assessment of potential risk to nearby infrastructure. Among various factors, the reliability of these methods depends on the accuracy of the ground-motion prediction equation (GMPE)—especially at close epicentral distances where ground motions are expected to be highest. In addition, potential impacts on local infrastructure can be assessed based on ground-motion-derived intensity values, which provide a basis for some traffic-light protocols that are used for managing fluid IS. GMPEs in many areas of the world, however, are poorly calibrated at close epicentral distances, because the availability of near-source seismograph stations is generally very sparse. This study investigates ground motions generated by an IS sequence, up to local magnitude (ML) 3.77 that occurred during a hydraulic-fracturing stimulation in the Duvernay shale play in central Alberta, western Canada. The sequence was monitored using a near-surface array that was located directly above the hydraulically fractured horizontal wells, providing accurate ground-motion measurements at hypocentral distances <10  km. The local array consisted of a combination of geophones cemented in shallow wellbores to depth of ∼27  m, shallow buried broadband seismometers, and a strong-motion accelerometer. This configuration enabled direct measurement of near-surface seismic velocities in the top 27 m, which provided robust VS30 data used to correct observed ground motions for local site-amplification effects. Our data set extends previous analyses in this region by providing new measurements very close to the epicenters of moderate earthquakes and shows that a recently developed GMPE provides accurate near-source ground-motion estimates.
Indonesia 5G Channel Model Under Foliage Effect
Authors: Anwar Khoirul , Christy Evander , Astuti Rina Pudji
Published: December 2019

Abstract The performance of communications is determined by the channel, therefore knowledge of channel model of a country is important. This paper proposes (i) the fifth telecommunication generation (5G) Indonesia channel model and (ii) a framework to derive the channel model of any locations in Indonesia. We consider operating frequency of 3.3 GHz with bandwidth of 40 MHz with real-field parameters of several cities in Indonesia. We also present a theoretical outage performance evaluated for the proposed Indonesia 5G channel model validated by block error rate (BLER) performances of cyclic-prefix orthogonal frequency division multiplexing (CP-OFDM) numerology zero with 5G complex binary phase shift keying (C-BPSK) and Polar coding scheme. Sub-optimal Polar codes are used in this research, where better performances are expected in the future. We found that the Indonesia 5G channel model has 17 paths for the case of without foliage effect and has less than 15 paths for the case of with foliage effect. The results show that foliage attenuation causes performance degradations indicated by smaller number of paths and worse theoretical outage performances. The obtained outage performances from the proposed Indonesia 5G channel model in this paper are expected to be a reference for 5G implementations in Indonesia. Abstrak Kinerja sistem komunikasi ditentukan oleh kanal, sehingga pengetahuan model kanal suatu negara menjadi penting. Makalah ini mengusulkan (i) model kanal telekomunikasi generasi ke-lima (5G) Indonesia dan (ii) kerangka kerja untuk menghitung model kanal di lokasi lain di Indonesia. Model kanal dalam makalah ini diciptakan untuk bandwidth 40 MHz pada frekuensi 3,3 GHz dengan parameter riil lapangan. Makalah ini juga menampilkan teori outage performance yang diperoleh dari model kanal 5G Indonesia, kemudian memvalidasi teori outage performance tersebut menggunakan block error rate (BLER) pada cyclic-prefix orthogonal frequency division multiplexing (CP-OFDM) numerology zero dengan complex binary phase shift keying (C-BPSK) standard 5G dan Polar coding. Semua hasil numerik diperoleh dari simulasi komputer menggunakan parameter riil lapangan untuk alam Indonesia. Makalah ini menemukan bahwa kanal 5G Indonesia dapat dimodelkan power delay profile (PDP) dengan 17 path untuk kanal tanpa efek dedaunan dan kurang dari 15 path untuk kanal dengan dedaunan. Hasil tersebut menunjukkan bahwa redaman daun menyebabkan penurunan kinerja, yang ditandai dengan penurunan jumlah path dan memburuknya outage performance. Kurva outage performance yang diperoleh dari model kanal 5G Indonesia diharapkan menjadi referensi untuk implementasi sistem 5G di Indonesia dalam pengembangan 5G di Indonesia secara optimal, terutama untuk lokasi yang memiliki dedaunan lebat.
Döviz balonlarının tespitine yönelik bir analiz: Türkiye örneği
Authors: AFŞAR Muharrem , AFŞAR Aslı , DOĞAN Emrah
Published: December 2019

Varlık fiyatlarındaki keskin
artışların finansal piyasalarda oluşturduğu balonlar büyük ölçüde volatiliteden
kaynaklanmaktadır. Günümüz küresel finans düzeninde, finansal varlıkların
günden güne ön plana çıkması finansal varlıklıkların fiyatlarında aşırı
şişkinlik yaratmakta ve reel ekonomiyi zorlamaktadır. Öte yandan aşırı şişkin
fiyatlara sahip finansal varlıkların oluşturduğu balonların patlaması da
ekonomik istikrarı tehdit eder hale gelmektedir. Bu bağlamda, finansal
gidişatta günlük dalgalanmaların yansıması niteliğindeki döviz piyasalarında
balonların varlığının analizi ve tespiti daha önemli hale gelmektedir. Bu
çalışmada, 2005:01 ile 2018:11 dönemi için USD/TL ve EURO/TL döviz kuru
verilerinden hareketle, Türkiye döviz piyasalarında balonunun var olup olmadığı
araştırılmıştır. Bu amaçla, balonların varlığının tespit edilmesi için
Genelleştirilmiş SADF (GSADF) testi kullanılmıştır. Elde edilen sonuçlar,
Türkiye döviz piyasasında USD/TL ve EURO/TL döviz kurlarında spekülatif
balonların oluştuğunu destekleyen güçlü ampirik kanıtlar olduğunu
göstermektedir.
Finansal istikrarı sağlamada uluslararası rezervler önemli bir araç mıdır?
Authors: BAYAT Tayfur , TAŞ Şebnem
Published: December 2019

1990’larda yaşanan finansal krizlerin sonrasında ülkeler, uluslararası rezervleri finansal küreselleşmeden kaynaklanan oynaklığa karşı bir garanti mekanizması olarak görmeye başlamış ve bu nedenle uluslararası rezervlerin gayri safi yurt içi hasıladaki payını arttırmaya yönelmişlerdir. Bu çalışmada, yaşanan küresel krizlerin ardından edinilen tecrübeler doğrultusunda ulusal ekonomiler için makro ekonomik istikrarın önemli bir koşulu olan finansal istikrarın sağlanmasında rezervlerin etkili bir araç olup olmadığı Türkiye örneği için araştırılmaktadır. Bu kapsamda, Türkiye ekonomisinde 2005:Q4-2018:Q3 dönemi için finansal istikrar endeksi ile merkez bankası resmi rezervleri arasındaki ilişki ele alınmaktadır. Ampirik analiz periyodunun tamamında rezervlerin finansal istikrar üzerinde negatif etkisinin olduğu, her bir frekans alanında ise rezervlerin finansal istikrar üzerinde 2009:Q3-2012:Q2 arası pozitif, 2012:Q3-2016:Q4 arası negatif ve 2017:Q1-2018:Q3 arası tekrar pozitif etki yarattığı sonucuna ulaşılmıştır.
Postmodern Dini Düşüncenin Teknoloji Karşıtı Kodları ve Üretim Ekonomisi
Authors: CESUR Ertuğrul
Published: December 2019

İslam dünyasının Batı karşısındaki geri kalmışlık sorunu Osmanlı’nın son dönemlerinden beri defaatle tartışılmış ve modern bilim tekniğin benimsenmesi konusu vurgulanmıştır. Ancak aradan geçen onca zamana rağmen bu yönde kayda değer bir başarı gösterildiğini söylemek mümkün görünmemektedir. Bunda da çoğunlukla tartışmayı bile gerektirmeyecek kadar aksi bir durum yokmuş gibi geçiştirilse muhafazakâr aklın bilimsel düşünceye bakışı ve maddi dünya algısının rolü inkar edilemez. Nitekim 1970’lerden itibaren “modernite” kavramı etrafında geliştirilen söylem, toplumsal ana gövdeyi temsil eden muhafazakâr kitlelerin kanaat oluşturucuları için sanayi ve teknoloji kavramlarının hiç de müspet çağrışımları olmadığını göstermektedir. İşin daha garibi, teknik geri kalmışlığın ağır sonuçlarına rağmen en büyük iddiası “Batı karşıtlığı” olan bu çevreyi böyle bir din tasavvuruna sevk eden asıl saikın bizzat kendisinin Batılı olmasıdır: Postmodernizm.
Supramolecularity creates nonstandard protein ligands.
Authors: Piekarska B , Rybarska J , Stopa B , Zemanek G , Król M , Roterman I , Konieczny L
Published: December 2019

Congo red and a group of structurally related dyes long used to stain amyloid proteins are known to associate in water solutions. The self-association of some dyes belonging to this group appears particularly strong. In water solutions their molecules are arranged in ribbon-like micellar forms with liquid crystalline properties. These compounds have recently been found to form complexes with some native proteins in a non-standard way. Gaps formed by the local distribution of beta-sheets in proteins probably represent the receptor sites for these dye ligands. They may result from higher structural instability in unfolding conditions, but also may appear as long range cooperative fluctuations generated by ligand binding. Immunoglobulins G were chosen as model binding proteins to check the mechanism of binding of these dyes. The sites of structural changes generated by antigen binding in antibodies, believed to act as a signal propagated to distant parts of the molecule, were assumed to be suitable sites for the complexation of liquid-crystalline dyes. This assumption was confirmed by proving that antibodies engaged in immune complexation really do bind these dyes; as expected, this binding affects their function by significantly enhancing antigen binding and simultaneously inhibiting C1q attachment. Binding of these supramolecular dyes by some other native proteins including serpins and their natural complexes was also shown. The strict dependence of the ligation properties on strong self-assembling and the particular arrangement of dye molecules indicate that supramolecularity is the feature that creates non-standard protein ligands, with potential uses in medicine and experimental science.
Kinetic studies on the oxidation of nitrite by horseradish peroxidase and lactoperoxidase.
Authors: Gebicka L
Published: December 2019

The reaction of nitrite (NO2-) with horseradish peroxidase and lactoperoxidase was studied. Sequential mixing stopped-flow measurements gave the following values for the rate constants of the reaction of nitrite with compounds II (oxoferryl heme intermediates) of horseradish peroxidase and lactoperoxidase at pH 7.0, 13.3 +/- 0.07 mol(-1) dm3 s(-1) and 3.5 +/- 0.05 x 10(4) mol(-1) dm3 s(-1), respectively. Nitrite, at neutral pH, influenced measurements of activity of lactoperoxidase with typical substrates like 2,2'-azino-bis[ethyl-benzothiazoline-(6)-sulphonic acid] (ABTS), guaiacol or thiocyanate (SCN-). The rate of ABTS and guaiacol oxidation increased linearly with nitrite concentration up to 2.5-5 mmol dm(-3). On the other hand, two-electron SCN- oxidation was inhibited in the presence of nitrite. Thus, nitrite competed with the investigated substrates of lactoperoxidase. The intermediate, most probably nitrogen dioxide (*NO2), reacted more rapidly with ABTS or guaiacol than did lactoperoxidase compound II. It did not, however, effectively oxidize SCN- to OSCN-. NO2- did not influence the activity measurements of horseradish peroxidase by ABTS or guaiacol method.
Identification of actin from hepatoma Morris 5123 cells.
Authors: Nowak D , Kochman A , Malicka-Błaszkiewicz M
Published: December 2019

The hepatoma Morris 5123 tumor growth is accompanied by changes in actin content and polymerization (Malicka-Błaszkiewicz et al. (1995) Mat. Med. Pol., 27, 115-118; Nowak et al. (1995) J. Exp. Cancer Res. 14, 37-40). Presently actin isoforms from cytosol and cytoskeleton fractions were separated by SDS/PAGE and identified with antibodies directed against different actin isoforms. Actin isolated from the cytosol by affinity chromatography on DNase I bound to agarose shows the presence of only one protein spot on 2D gel electrophoresis corresponding to the mobility of the rabbit a skeletal muscle actin (Mr 43,000) and isoelectric point equal to 5.3. It interacts only with monoclonal anti beta actin isoform antibodies, posing the question of differential affinity of actin isoforms to DNase I.
Elevation of plasma fibrinogen in silent myocardial ischaemia.
Authors: Grzywacz A , Psuja P , Zozulińska M , Elikowski W , Zawilska K
Published: December 2019

High plasma levels of fibrinogen and plasminogen activator inhibitor (PAI-1) are reported to be correlated with coronary heart disease. Therefore the level of fibrinogen concentration in plasma was examined and verified for the possible correlation with the previously explored PAI-1 antigen and PAI-1 activity in the pathogenesis of premature atherosclerosis (Grzywacz et al., 1998, Blood Coagul Fibrinol. 9, 245-249). Examination included only men, aged 33-46 years, who were in a stable condition for at least six months after the acute event. They were divided into two subgroups: group A (n = 14) with and group B (n = 15) without ischaemic changes in 24 h Holter electrocardiogram. The number of involved vessels visible on the coronarography picture was similar in both groups. In the patients of group A the mean level of fibrinogen (3.92 vs 3.23 g/l, P < 0.05) was higher than in the controls (n = 15). No statistically differences were found between group B and control healthy subjects in any of the parameters measured. There were no correlation between fibrinogen concentration and PAI-1 antigen and activity levels, which were elevated in both groups of patients according to our previous study. Our results indicate that elevated levels of plasma fibrinogen and PAI-1 appeared in the group of patients with more severe disease, as revealed by silent myocardial ischaemia.
Peptide nucleic acids and their structural modifications.
Authors: Falkiewicz B
Published: December 2019

Peptide (polyamide) analogues of nucleic acids (PNAs) make very promising groups of natural nucleic acid (NA) ligands and show many other interesting properties. Two types of these analogues may be highlighted as particularly interesting: the first, containing a polyamide with alternating peptide/pseudopeptide bonds as its backbone, consisting of N-(aminoalkyl)amino-acid units (type I), with nucleobases attached to the backbone nitrogen with the carboxyalkyl linker; and the second, containing a backbone consisting of amino-acid residues carrying the nucleobases in their side chains (type II). So far, these two groups have been studied most intensively. The paper describes main groups of peptide nucleic acids, as well as various other amino acid-derived nucleobase monomers or their oligomers, which were either studied in order to determine their hybridisation to nucleic acids, or only discussed with respect to their potential usefulness in the oligomerisation and nucleic acids binding.
Protein inhibitors of serine proteinases.
Authors: Otlewski J , Krowarsch D , Apostoluk W
Published: December 2019

Serine proteinases and their natural protein inhibitors belong to the most intensively studied models of protein-protein recognition. Protein inhibitors do not form a single group but can be divided into about 20 different families. Global structures of proteins representing different inhibitor families are completely different and comprise alpha-helical proteins, beta-sheet proteins, alpha/beta-proteins and different folds of small disulfide-rich proteins. Three different types of inhibitors can be distinguished: canonical (standard mechanism) inhibitors, non-canonical inhibitors, and serpins. The canonical inhibitor binds to the enzyme through the exposed and convex binding loop, which is complementary to the active site of the enzyme. The mechanism of inhibition in this group is consistently very similar and resembles that of an ideal substrate. Non-canonical inhibitors, originating from blood sucking organisms, specifically block enzymes of the blood clotting cascade. The interaction is mediated through inhibitor N-terminus which binds to the proteinase forming a parallel beta-sheet. There are also extensive secondary interactions which provide an additional buried area and contribute significantly to the strength and specificity of recognition. Serpins are major proteinase inhibitors occurring in plasma. Similarly to canonical inhibitors, serpins interact with their target proteinases in a substrate-like manner. However, in the case of serpins, cleavage of a single peptide bond in a flexible and exposed binding loop leads to dramatic structural changes.
Modelling of insulin receptor tyrosine kinase in its active form: a case study for validation of theoretical methods.
Authors: Ginalski K , Wojciechowski M , Lesyng B
Published: December 2019

An active form of an insulin receptor tyrosine kinase (IRK) catalytic core was modelled based on its experimentally known inactive form and the active form of a serine/threonine kinase, protein kinase A (PKA). This theoretical model was compared with the crystallographic structure of the active form of IRK reported later. The structures are very similar, which shows that all the most important features and interactions have been taken into account in the modelling procedure. The elaborated procedure can be applied to other tyrosine kinases. This would allow designing of a wide class of tyrosine kinase inhibitors, very important potential anti-cancer and/or anti-viral drugs.
Fluorescence decay time distribution analysis of cyclic enkephalin analogues. Influence of the solvents and configuration of amino acids in position 2 and 3 on changes in conformation.
Authors: Malicka J , Groth M , Czaplewski C , Liwo A , Wiczk W
Published: December 2019

The lifetime distribution calculations were applied to study the influence of configuration of amino-acid residues in positions 2 and 3 on changes in conformation of the peptide chain of cyclic analogues of enkephalins containing a fluorescence energy donor and acceptor in different solvents. In all the solvents studied the lifetime distributions were bimodal. This testified to the presence of two families of conformations. In this paper the relationship between the population of each conformation and configuration of the residues in position 2 and 3, and the solvent used is discussed.
Application of aqueous hydrazine solution for beta-elimination of O-glycans from gastric mucin.
Authors: Kisiel D , Gindzieński A , Gadek A
Published: December 2019

O-Glycans from pig gastric mucin were released by beta-elimination in 0.2 M triethylamine and 50% aqueous hydrazine solution. The released glycan hydrazides were isolated using Centricon 10 separators, brought to their reducing form and reductive by labelled with p-aminobenzoic acid ethyl ester (ABEE). Labelled products were fractionated into neutral and acid fractions on a Bio-Gel P4 column, calibrated with a mixture of dextran oligosaccharides, labelled according to the same procedure.
Structure of yellow lupine genes coding for mitotic cyclins.
Authors: Jeleńska J , Zaborowska Z , Legocki A B
Published: December 2019

Cell cycle progression in eukaryotes is controlled by complexes of p34 protein kinases and cyclins. For the first time in plants, we have established the sequence of four yellow lupine mitotic cyclin B1 genes. Their coding regions and expression pattern were also characterised recently. Structure of all the four lupine genes is similar: they consist of nine exons and eight introns, analogously located, except Luplu;CycB1;3 lacking 7th intron. Analysis of 5'-regulatory sequences of two of them showed that both comprise M-specific activators (MSA), common to plant genes induced in late G2 and early M. Putative repressor binding sites CDE/CHR found in animal G2-specific promoters can also be detected in lupine genes. Controlling region of Luplu;CycB1;4 gene that is highly activated by IAA, contains up to 7 auxin response elements, while insensible to IAA Luplu;CycB1;4 gene have no such motifs. Further studies should be undertaken to determine precisely the functions of putative regulatory elements in the expression of lupine mitotic cyclins.
Characterization of DNA sequences localized 11 to 17.5 kb upstream of the chicken embryonic pi-globin gene.
Authors: Pietrowska M , Rusin M , Widłak P , Razin S V , Rzeszowska-Wolny J
Published: December 2019

We have analyzed the DNA fragment localized about 11 to 17.5 kb upstream of the chicken alpha-globin gene domain (the fragment was designed as alpha-0). The nucleotide sequence of its 3.3 kb-long 5' part was established and interactions with nuclear matrix proteins were studied. The DNA region localized about 16 kb upstream of the embryonic pi-globin gene showed high affinity to nuclear matrices in vitro. Two palindromes and a cluster of inverted repeats were co-localized in the same region. The whole 6.6 kb alpha-0 fragment decreased the activity of linked CAT reporter gene when transfected into chicken erythroblastoid cells.
Mutagenic specificity of imidazole ring-opened 7-methylpurines in M13mp18 phage DNA.
Authors: Tudek B , Graziewicz M , Kazanova O , Zastawny T H , Obtułowicz T , Laval J
Published: December 2019

The most abundant lesion formed in DNA upon modification with methylating agents 7-methylguanine, under alkaline conditions is converted into 2,6-diamino-4-hydroxy-5N-methyl-formamidopyrimidine (Fapy-7MeGua). We have previously shown that treatment of dimethylsulfate methylated DNA with NaOH creates mutagenic base derivatives leading to a 60-fold increase in the frequency of A-->G transitions and a 2-3-fold increase of G-->T and G-->C transversions. We have analyzed which lesions lead to these mutations. We compared mutagenic spectra in the lacZ gene of M13mp18 phage DNA modified with dimethylsulfate and NaOH after selective elimination of damaged bases from molecules used for transfection into SOS-induced E. coli. Partial elimination of Fapy-7MeGua from phage DNA performed by its digestion with formamidopyrimidine-DNA glycosylase resulted in a 2-3-fold decrease of G-->T and G-->C transversions. Selective depurination of methylated bases (9 h, 37 degrees C, pH 7.0) resulting in almost complete loss of 7MeAde as demonstrated by HPLC analysis of [3H]MNU alkylated phage DNA used as a probe, caused a dramatic, 9-fold decrease of A-->G transitions. Alkali-catalysed rearrangement of 7MeAde was followed by HPLC analysis of [3H]MNU alkylated poly(A) and poly(dA). After incubation of these oligonucleotides in NaOH, 7MeAde disappeared from both chromatograms, but only in polyA, 2 new peaks migrating with retention time different from that of 1MeAde, 3MeAde or 7MeAde were detected, suggesting formation of two rotameric forms of Fapy-7MeAde as observed for Fapy-7MeGua. Thus the miscoding lesion, giving rise to A-->G transitions derived from 7MeAde was Fapy-7MeAde. Fapy-7MeGua was at least an order of magnitude less mutagenic, but in SOS-induced cells it gave rise to G-->T and G-->C transversions.
Annexin VI: an intracellular target for ATP.
Authors: Bandorowicz-Pikuła J , Danieluk M , Wrzosek A , Buś R , Buchet R , Pikuła S
Published: December 2019

Annexin VI (AnxVI), an Ca2+- and phospholipid-binding protein, interacts in vitro with ATP in a calcium-dependent manner. Experimental evidence indicates that its nucleotide-binding domain which is localized in the C-terminal half of the protein differs structurally from ATP/GTP-binding motifs found in other nucleotide-binding proteins. The amino-acid residues of AnxVI directly involved in ATP binding have not been yet defined. Binding of ATP to AnxVI induces changes in the secondary and tertiary structures of protein, affecting the affinity of AnxVI for Ca2+ and, in consequence, influencing the Ca2+-dependent activities of AnxVI: binding to F-actin and to membranous phospholipids, and self-association of the annexin molecules. These observations suggest that ATP is a functional ligand for AnxVI in vivo, and ATP-sensitive AnxVI may play the role of a factor coupling vesicular transport and calcium homeostasis to cellular metabolism.
Tautomers of styrylquinoline derivatives containing a methoxy substituent: computation of their population in aqueous solution and their interaction with RSV integrase catalytic core.
Authors: Ouali M , Laboulais C , Leh H , Gill D , Xhuvani E , Zouhiri F , Desmaele D , D'Angelo J , Auclair C , Mouscadet J F , Le Bret M
Published: December 2019

8-Hydroxy-2-[2-(3-hydroxy-4-methoxyphenyl)ethenyl]-7-quinoline carboxylic acid and 8-hydroxy-2-[2-(3-methoxy-4-hydroxyphenyl)ethenyl]-7-quinoline carboxylic acid inhibit the processing and strand transfer reactions catalyzed by HIV-1 integrase with an IC50 of 2 microM. Some of their spectral properties are briefly reported. Their fluorescence is so weak that it is of no use in an experimental determination of the binding to the protein and we resorted to computer simulation. Both styrylquinoline derivatives, in their monoanionic form, have several dozens of tautomers and each of these forms has four planar rotamers. In this work computer simulations have been performed to determine which tautomer is the most abundant in aqueous solution and which binds to the Rous sarcoma virus (RSV) integrase catalytic core. As the substituents on the quinoline moiety are the same as on salicylic acid, the energies of hydroxy benzoic acid tautomers were also computed both in vacuo and embedded in a continuous medium which had the dielectric constant of bulk water, using the recent CPCM technique. The CPCM method was then applied to the two integrase inhibitors to estimate the tautomer population in water. The binding site of the compounds on the RSV integrase catalytic core was determined through a docking protocol, consisting of coupling a grid search method with full energy minimization. The designed method is a way leading to identification of potent integrase inhibitors using in silico experiments.
The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: molecular dynamics simulations.
Authors: Mazerski J , Antonini I , Martelli S
Published: December 2019

Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.
Kinetics of a nucleoside release from lactide-caprolactone and lactide-glycolide polymers in vitro.
Authors: Kryczka T , Grieb P , Bero M , Kasperczyk J , Dobrzynski P
Published: December 2019

We assessed the rate of release of a model nucleoside (adenosine, 5%, w/w) from nine different lactide-glycolide or lactide-caprolactone polymers. The polymer discs were eluted every second day with an artificial cerebrospinal fluid at the elution rate roughly approximating the brain extracellular fluid formation rate. Adenosine in eluate samples was assayed by HPLC. Three polymers exhibited a relatively constant release of adenosine for over four weeks, resulting in micromolar concentrations of nucleoside in the eluate. This points to the necessity of further development of polymers of this types as intracerebral nucleoside delivery systems for local treatment of brain tumors.
Biomimetic polyesters and their role in ion transport across cell membranes.
Authors: Jedliński Z , Kurcok P , Adamus G , Juzwa M
Published: December 2019

Syntheses of biomimetic low-molecular weight poly-(R)-3-hydroxybutanoate mediated by three types of supramolecular catalysts are presented. The utility of these synthetic polyesters for preparation of artificial channels in phospholipid bilayers capable of sodium and calcium ion transport across cell membranes, is discussed. Further studies on possible applications of these bio-polymers for manufacturing drugs of prolonged activity are under way.
N4-amino-acid derivatives of 6-azacytidine: structure-activity relationship.
Authors: Alexeeva I , Palchikovskaya L , Shalamay A , Nosach L , Zhovnovataya V , Povnitsa O , Dyachenko N
Published: December 2019

Several N4-derivatives of 6-azacytidine were synthesized using of Vorbrüggen's condensation method. Their antiviral activity with respect to the adenovirus serotypes 2 and 5 in Hep-2 cells culture was studied and primary specific activity was determined. Correlation between chemical structure of new 6-azacytidine derivatives and their biological properties is discussed.
N-Methyl-N-D-fructosyl amphotericin B methyl ester (MF-AME), a novel antifungal agent of low toxicity: monomer/micelle control over selective toxicity.
Authors: Cybulska B , Gadomska I , Mazerski J , Borowski J G E , Cheron M , Bolard J
Published: December 2019

Rational chemical modification of amphotericin B (AMB) led to the synthesis of sterically hindered AMB derivatives. The selected optimal compound, N-methyl-N-D-fructosyl amphotericin B methyl ester (MF-AME) retains the broad spectrum of antifungal activity of the parent antibiotic, and exhibits a two orders of magnitude lower toxicity in vivo and in vitro against mammalian cells. Comparative studies of MF-AME and AMB comprising the determination of the spectroscopic properties of monomeric and self-associated forms of the antibiotics, the investigation of the influence of self-association on toxicity to human red blood cells, and of the antibiotic-sterol interaction were performed. On the basis of the results obtained it can be assumed that the improvement of the selective toxicity of MF-AME could in part be a consequence of the diminished concentration of water soluble oligomers in aqueous medium, and the better ability to differentiate between cholesterol and ergosterol.
Comparative studies on cell stimulatory, permeabilizing and toxic effects induced in sensitive and multidrug resistant fungal strains by amphotericin B (AMB) and N-methyl-N-D-fructosyl amphotericin B methyl ester (MFAME).
Authors: Szlinder-Richert J , Cybulska B , Grzybowska J , Borowski E , Prasad R
Published: December 2019

N-Methyl-N-D-fructosyl-amphotericin B methyl ester (MFAME) is a new derivative of amphotericin B, which is characterised by low toxicity to mammalian cells and good solubility in water of its salts. The antifungal activity and effects of MFAME towards Candida albicans and Saccharomyces cerevisiae multidrug resistant MDR(+) and sensitive MDR(-) strains was compared with those of parent compound. The results obtained indicate that MDR(+) S. cerevisiae was sensitive to MFAME as well as to AMB. MFAME exhibited the same effects on fungal cells studied as parent antibiotic. The two antibiotics, depending on the dose applied induced cell stimulation, K+ efflux, and/or had a toxic effect.
Glutathione conjugation in male reproductive system: studies on glutathione-S-transferase of bull and boar epididymis.
Authors: Ciszewska-Piłczyńska A , Barańczyk-Kuźma A
Published: December 2019

Male reproductive organs are extremely sensitive to the negative influence of toxic environmental factors as well as drugs, and until now not many attempts have been made at studying the detoxication enzymes and the relationship between the activity of those enzymes and spermatozoa fertility. In the present work we studied cytosolic glutathione-S-transferases (GST, EC 2.5.1.18) from different parts (head, corpus and tail) of bull and boar epididymis. We isolated two molecular forms of GST from each part of epididymis, characterized their biochemical properties and examined the mechanism of the catalyzed reaction. On the basis of their substrate specificity and isoelectric point, the isoforms were found to belong to the near neutral GST class mi. All examined GST forms exhibited higher affinity towards GSH than towards 1-chloro-2,4-dinitrobenzene (CDNB) and bull epididymis GST forms showed biphasic Lineweaver-Burk double reciprocal curves in the presence of GSH as a variable substrate. Boar epididymis anionic GST had the -SH groups both in the GSH and the CDNB binding place, whereas the cationic GST form--arginine residues in the CDNB binding place. Bull epididymis GST forms contained neither thiol nor arginine residues essential for catalytic activity.
Inhibition and activation of enzymes. The effect of a modifier on the reaction rate and on kinetic parameters.
Authors: Fontes R , Ribeiro J M , Sillero A
Published: December 2019

A combined analysis of enzyme inhibition and activation is presented, based on a rapid equilibrium model assumption in which one molecule of enzyme binds one molecule of substrate (S) and/or one molecule of a modifier X. The modifier acts as activator (essential or non-essential), as inhibitor (total or partial), or has no effect on the reaction rate (v), depending on the values of the equilibrium constants, the rate constants of the limiting velocity steps, and the concentration of substrate ([S]). Different possibilities have been analyzed from an equation written to emphasize that v = f([X]) is, in general and at a fixed [S], a hyperbolic function. Formulas for Su (the value of [S], different from zero, at which v is unaffected by the modifier) and v(su) (v at that particular [S]) were deduced. In Lineweaver-Burk plots, the straight lines related to different [X] generally cross in a point (P) with coordinates (Su, v(su)). In certain cases, point P is located in the first quadrant which implies that X acts as activator, as inhibitor, or has no effect, depending on [S]. Furthermore, we discuss: (1) the apparent Vmax and Km displayed by the enzyme in different situations; (2) the degree of effect (inhibition or activation) observed at different concentrations of substrate and modifier; (3) the concept of Ke, a parameter that depends on the concentration of substrate and helps to evaluate the effect of the modifier: it equals the value of [X] at which the increase or decrease in the reaction rate is half of that achieved at saturating [X]. Equations were deduced for the general case and for particular situations, and used to obtain computer-drawn graphs that are presented and discussed. Formulas for apparent Vmax, Km and Ke have been written in a way making it evident that these parameters can be expressed as pondered means.
An easy procedure to transform the ratio of two polynomials of first degree into Michaelis-Menten-type equations. Application to the ordered Uni Bi enzyme mechanism.
Authors: Fontes R , Ribeiro J M , Sillero A
Published: December 2019

It is not always clear that some equations affected by complicated factors can, actually, be interpreted as a ratio of two polynomials of first degree and so that they can be, in general, represented by rectangular hyperbolas. In this paper we present an easy procedure to rearrange those equations into Michaelis-Menten-type equations and so to make the aspects of these rectangular hyperbolas more clear, particularly for researchers familiar with general biochemistry. As an example, the method is applied to transform the classical rate equation of the Cleland's Ordered Uni Bi enzyme mechanism.
FROM PRINT TO SCREEN: METHODOLOGY, MEDIA, AND TRANSITION OF QUR’ANIC LEARNING IN INDONESIA
Authors: Rohman Muhamad Zulfar
Published: December 2019

This article aims to discuss the shift in the methodology of Qur’anic learning in Indonesia that is influenced by media. There are four cases used to map the contestations in the traditional era: Baghdadi, Qiroati, Iqro ', and Yanbu'a. Those have the same characteristic, namely face-to-face learning which is then challenged by the new media that infiltrate the Islamic world. One of the new media described in this paper is the Qur’anCall that is initiated by the PPPA Daarul Qur’an led by the famous preacher Yusuf Mansur. This is a learning and teaching platform for the Qur'an based on a video call. The character possessed by the Qur’anCall is very different from the traditional methodology. Based on this issue, the author examines the changes in Qur’anic learning in the traditional and modern eras then elaborates the effects that have caused. The finding shows that there are degradations from various performative aspects which are inherent in the traditional methods of Qur’anic learning. Furthermore, the authority of the Qur’anic teacher who was once held by the Qur'anic experts can be in the hands of people with low qualifications.
Współczesne teorie grzeczności językowej i ich wpływ na badania w obszarze glottodydaktyki polonistycznej
Authors: Sztabnicka-Gradowska Emilia
Published: December 2019

Głównym celem artykułu jest przedstawienie ewolucji teorii grzeczności językowej na przestrzeni ostatnich pięćdziesięciu lat. W pierwszej części zestawiono ze sobą najważniejsze założenia trzech klasycznych teorii grzeczności językowej. W kolejnym kroku dokładnie opisano krytykę tych pierwszych podejść oraz zaprezentowano teorie, które powstały na gruncie tej dyskusji. Nazwano je postmodernistycznymi i dyskursywnymi. Cześć trzecia koncentruje się na przywołaniu nazwisk badaczy, którzy wychodzą poza paradygmat postmodernistyczny i dyskursywny. W czwartej części przywołano najnowsze podejścia do badań nad grzecznością językową i przedstawiono, jaki wpływ mają one na badania w obszarze glottodydaktyki polonistycznej.
Świadomość lingwistyczna (przyszłych) lektorów języka polskiego jako obcego – kilka uwag o znajomości fleksji imiennej
Authors: Karasek Magdalena , Gaze Mateusz
Published: December 2019

Artykuł porusza zagadnienie świadomości lingwistycznej studentów – słuchaczy specjalizacji glottodydaktycznej na Wydziale Filologicznym Uniwersytetu Łódzkiego. W tekście zostały przedstawione i omówione wyniki analizy badania ankietowego przeprowadzonego w grupie 52 studentów. W kwestionariuszu umieszczono pytania dotyczące podstawowych problemów z gramatyki funkcjonalnej języka polskiego z zakresu fleksji imiennej, które omawiane są przez nauczyciela języka polskiego jako obcego podczas zajęć z cudzoziemcami. Analiza materiału badawczego zaowocowała propozycją wprowadzenia pojęcia glottodadaktycznej świadomości lingwistycznej, związanej ze specyfiką pracy nauczyciela języka obcego, będącej dopełnieniem świadomości lingwistycznej.
Jaką rolę odgrywają zasoby elektroniczne w nauce języka polskiego jako obcego/odziedziczonego? Wyniki badań ankietowych
Authors: Kosch Natalie
Published: December 2019

Artykuł powstał na podstawie wyników anonimowej ankiety internetowej przeprowadzonej w międzynarodowej grupie uczących się języka polskiego jako obcego/odziedziczonego. Pokazuje, czy i jakich zasobów elektronicznych uczący się używają do nauki gramatyki, słownictwa, ortografii i wymowy. Definiuje rolę, jaką pełni lektor języka polskiego przy strategii uczenia się przez Internet.