Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

‘Proteochemometric modeling’ is a bioactivity modeling technique founded on the description of both small molecules (the ligands), and proteins (the targets). By combining those two elements of a ligand – target interaction proteochemometrics techniques model the interaction complex or the full ligand – target interaction space, and they are able to quantify the similarity between both ligands and targets simultaneously. Consequently, proteochemometric models or complex based models, can be considered an extension of QSAR models, which are ligand based. As proteochemometric models are able to incorporate target information they outperform conventional QSAR models when extrapolating from the activities of known ligands on known targets to novel targets. Vice versa, proteochemometrics can be used to virtually screen for selective compounds that are solely active on a single member of a subfamily of targets, as well as to select compounds with a desired bioactivity profile – a topic particularly relevant with concepts such as ‘ligand polypharmacology’ in mind. Here we illustrate the concept of proteochemometrics and provide a review of relevant methodological publications in the field. We give an overview of the target families proteochemometrics modeling has previously been applied to, and introduce some novel application areas of the modeling technique. We conclude that proteochemometrics is a promising technique in preclinical drug research that allows merging data sets that were previously considered separately, with the potential to extrapolate more reliably both in ligand as well as target space.
Functionalization of Imidazo[1,2‐a]pyridines by Means of Metal‐Catalyzed Cross‐Coupling Reactions

This review surveys recent developments (reported in the last fifteen years) in organometallic-chemistry-based methods for the functionalization of imidazo[1,2-a]pyridines, in particular the decoration of the pyridine and imidazole rings by means of reactions such as Sonogashira, Heck, Negishi, Suzuki–Miyaura, and Stille cross-coupling, as well as by C–H activation, C-arylation, C-alkenylation, and carbonylation. Results relating to one-pot double functionalization of two different positions on the imidazo[1,2-a]pyridine system are also reviewed. Procedures in which metal-based catalysis is not involved in the functionalization of imidazo[1,2-a]pyridines are not included.
Determination of phosphorus and other elements in atmospheric aerosols using synchrotron total‐reflection X‐ray fluorescence

In this study, P and other low Z elements were determined in aerosol particulates from ambient air using synchrotron radiation-induced total-reflection X-ray fluorescence analysis. Atmospheric transport of nutrients such as P or Si to the oceans is a key factor to marine plankton growth. Concentration of these elements in marine air masses is generally low (P < 10 ng/m3). Therefore, analytical procedures enabling for low detection limits are of interest. Because particle size is strongly correlated to its origin and sedimentation, the aerosols were collected with the aid of a low-pressure Berner impactor, which separates the aerosol particulates in nine size fractions with the smallest fraction from 15 to 30 nm. To be able to determine low Z elements, measurements were performed under vacuum conditions at the FLUO beamline at the ANKA synchrotron. An excitation energy of 3.5 keV near the P K-edge but below the Ca K absorption edge was chosen to avoid interferences of the P K-line with the detector escape artifact of the Ca-Kα line. The result showed P was present in concentration from 2 to 180 ng/m3. Detection limits were found to be generally 0.2–0.3 ng/m3 for a collecting time of 1 h for the aerosols, which is an improvement to detection limits reported in other studies. Other elements such as S, Cl, and Si were determined as well. Si like P is a nutrient for marine plankton (diatoms). S and Cl play an important role in cloud formation, e.g. polar stratospheric clouds. Copyright © 2013 John Wiley & Sons, Ltd.
Effect of soil moisture regime, nitrogen and modified urea materials on yield and quality of geranium (Pelargonium graveolens) grown on alfisols

Two field experiments were conducted during 1996–98 at Bangalore, India to study the effect of soil moisture regimes (0·3, 0·6 and 0·9 IW:CPE ratios) irrigation water:cumulative pan evaporation (IW:CPE) ratios and three rates of nitrogen application (0, 100 and 200 kg/ha) and in another experiment, three soil moisture regimes (0·3, 0·6 and 0·9 IW: CPE ratios), two rates of nitrogen application (100 and 200 kg/ha) and modified urea materials [prilled urea (PU) and dicyandiamide coated urea (DCDCU)] on oil content, herbage, oil yield and quality of geranium grown on altisols. Soil moisture maintained at 0·6 IW:CPE ratio significantly increased the herbage and oil yields of geranium. Application of 200 kg N/ha gave the maximum herbage and oil yield compared with those obtained from 0 and 100 kg N/ha. DCDCU produced higher yield than PU. The concentration and quality of essential oil were not influenced either by soil-moisture regime, rates or carriers of N.
Effect of alkali and ultraviolet (UV) radiation pretreatment on physical and mechanical properties of 1,6‐hexanediol diacrylate–grafted jute yarn by UV radiation

To improve the physicomechanical properties of jute yarn, grafting with 1,6-hexanediol diacrylate (HDDA) monomer was performed by a UV radiation technique. A series of HDDA solutions of various concentrations in methanol were prepared. A small quantity of photoinitiator (Darocur-1664) was also added to HDDA solutions. To optimize the conditions for grafting, the effects of monomer concentration, soaking time, and radiation doses were studied by varying the number of soaking times along with variation of monomer concentrations and UV radiation intensities. The extent of polymer loading and the mechanical properties like tensile strength (TS), elongation at break (Eb), and tensile modulus of both treated and untreated jute were investigated. The highest tensile strength, polymer loading, and modulus were achieved with 5% HDDA concentration, 5 min soaking time, and the 4th pass of UV radiation. This set of conditions was selected as optimum and produced enhanced tensile strength (67%), modulus (108%), and polymer loading (11%) over those of virgin fiber. To further improve the mechanical properties the jute yarns were pretreated with alkali (5% NaOH) solution and after that the alkali-treated yarn were treated under UV radiation of various intensities. The pretreated samples were grafted with optimized monomer concentration (5% HDDA). Increased properties of alkali + UV-pretreated and grafted samples such as polymer loading (12%), tensile strength (103%), elongation at break (46%), and modulus (114%) were achieved over those of virgin jute yarn. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 18–24, 2004
Comparison of Size-Dependent Structural and Electronic Properties of Anatase and Rutile Nanoparticles

Size-dependent variations in the electronic and structural properties of anatase and rutile nanoparticles have been compared. The anatase nanoparticles of the present study were prepared by hydrothermal ripening of an anatase sol and had diameters in the range 2−130 nm whereas the rutile nanoparticles were prepared by calcination of sol−gel derived rutile and had diameters in the range 3.6−60 nm. The hydrothermally ripened anatase nanoparticles had similar surface structures as deduced from the XANES as previously reported sol−gel anatase materials prepared through calcination (Luca et al., J. Phys. Chem. B 1998, 102, 10650). The optical band gap (Eg) of the anatase nanoparticles as deduced from their electronic absorption spectra showed some variation with size but Eg was not a smooth function of crystallite size, as would be dictated by the effective mass model for both types of anatase nanoparticles. In distinct contrast to the anatase nanoparticles, rutile nanoparticles showed a smooth size dependent .
Variation of Ionic Strength Reveals the Interfacial Water Structure at a Charged Mineral Surface

We have used visible-infrared sum-frequency generation spectroscopy to study the structure of water molecules that form the interface with fused silica. Spectra throughout the OH-stretching region were collected in two different polarization schemes so that the orientation of interfacial water molecules could be studied. A depth profiling experiment was performed by varying the ionic strength, thereby peeling away the outskirts of this interfacial region, leaving water molecules progressively closer to the charged interface. As the ionic strength increases, the spectral intensity drops since the interfacial region is becoming thinner. However, we notice a change in the relative contribution of tetrahedrally coordinated molecules compared to those that make less hydrogen bonds. We have the opportunity to study these two water species individually; we conclude that the higher coordination species exists some distance away from the interface and is oriented close to the plane of the surface with a mean tilt .
Influence of Temperature and the BZ Substrate on Aggregation-Disaggregation Self-Oscillation of a Polymer Chain

We synthesized a self-oscillating polymer chain with a negatively charged moiety. The polymer chain caused the aggregation-disaggregation self-oscillation under the constant temperature induced by the Belousov-Zhabotinsky (BZ) reaction. In this study, we investigated the influence of temperature and the concentration of sodium bromate on the aggregation-disaggregation self-oscillation of the polymer solution (1.0 wt%) in a strongly acidic condition. As a consequence, we clarified that the life-time of the self-oscillation increased with decrease in the concentration of sodium bromate. On the other hand, the lifetime of the self-oscillation decreased with increase in temperature. In high temperature condition (48 and 60 °C), the amplitude of the self-oscillation was significantly inhomogeneous. Moreover, the frequency of the self-oscillation increased with increasing temperature. On the other hand, the frequency decreased with increase in the concentration of sodium bromate. This tendency was opposite to that in the acid-free condition and the 2.0 wt% AMPS-containing polymer solution.
Rapid Multiresidue Determination Method for 100 Pesticides in Vegetables by One Injection Using Gas Chromatography/Mass Spectrometry with Selective Ion Storage Technology

Abstract A rapid multiresidue determination method for 100 pesticides (including organophosphorus, organochlorine, carbamate, and pyrethrines) in vegetables was described. The study focused on the fast separation and determination of target analytes. By optimizing the chromatographic condition and selecting specific ions of analytes, all analytes were determined by gas chromatography/ion‐trap mass spectrometry in selective ion storage mode (GC‐MS/SIS) within 35min. The sample was extracted by dichloromethane and acetone, cleaned up by graphitized carbon black (GCB) solid‐phase tubes. The limit of quantitation (LOQ) for most analytes was 0.01mg/kg.
Hallucination, imagery, dreaming: reassembling stimulus-independent perceptions based on Edmund Parish's classic misperception framework

Within the broad field of human perception lies the category of stimulus-independent perceptions, which draws together experiences such as hallucinations, mental imagery and dreams. Traditional divisions between medical and psychological sciences have contributed to these experiences being investigated separately. This review aims to examine their similarities and differences at the levels of phenomenology and underlying brain function and thus reassemble them within a common framework. Using Edmund Parish's historical work as a guiding tool and the latest research findings in the cognitive, clinical and computational sciences, we consider how different perspectives may be reconciled and help generate novel hypotheses for future research. This article is part of the theme issue ‘Offline perception: voluntary and spontaneous perceptual experiences without matching external stimulation’.
Following the Morphology Formation In Situ in Printed Active Layers for Organic Solar Cells

The device performance of organic polymer:fullerene bulk heterojunction solar cells strongly depends on the interpenetrating network of the involved donor and acceptor materials in the active layer. Since morphology formation depends on the conditions of film preparation, the final morphology varies for different deposition methods. In order to understand and optimize industrial coating processes and, therefore, the performance of the solar cells produced, a deeper understanding of structure formation is important. In situ measurements of slot‐die printed polymer:fullerene active layers are presented that reveal insights into the evolution of the structure. Polymer crystallization and ordering is monitored by in situ grazing incidence wide angle X‐ray scattering (GIWAXS), and in situ grazing incidence small‐angle X‐ray scattering (GISAXS). The development of the morphology exhibits five stages independent of the drying conditions. Two growth rates are observed, an initial slow formation of poly(3‐hexylthiophene‐2,5‐diyl) crystallites in well‐aligned edge‐on orientation followed by a rapid crystal growth. By combining the GIWAXS and GISAXS measurements, a five‐stage growth and assembly process is found and described in detail along with a proposed model of the structural evolution. The findings are an important step in tailoring the assembly process.
Zmiany pozornej powierzchni właściwej korzeni życicy wielokwiatowej (Lolium multiflorum L.) determinowane toksycznością kadmu

S t r e s z c z e n i e . Badania przeprowadzono na korzeniach Lolium multiflorum L. Rośliny pochodziły ze stacji badawczej w Dublanach, Uniwersytetu Rolniczego we Lwowie. Przed siewem nasion, do gleby (czarnoziem leśno-stepowy, wyługowany, wytworzony z lessu o pH = 6,8) dodano roztwór CdCl2w ilościach kadmu 0 (obiekt kontrolny), 3, 15, 30 mg·kg gleby. Rośliny zebrano w fazie kwitnienia i w fazie pełnej dojrzałości nasion. Pozorną powierzchnię właściwą korzeni tych roślin wyznaczano z izoterm adsorpcji pary wodnej, których pomiar przeprowadzono zgodnie z Polską Normą PN-Z-190101. Do opisu danych doświadczalnych adsorpcji-desorpcji pary wodnej zastosowano model równania BET. Korzenie roślin pochodzące z obiektów z Cd charakteryzowały się mniejszą wielkością pozornej powierzchni właściwej niż korzenie z obiektów kontrolnych. Stwierdzono że, ilości kadmu 15 i 30 mg·kg gleby wpłynęły istotnie na spadek wielkości pozornej powierzchni właściwej korzeni Lolium multiflorum L. w fazie kwitnienia. Dla korzeni zebranych w fazie pełnej dojrzałości nasion, istotny spadek tego parametru wykazano dla dawki kadmu 30 mg·kg gleby. Kadm dodany do gleby w ilości 3 mg·kg tylko nieznacznie wpłynął na wielkość pozornej powierzchni właściwej korzeni Lolium multiflorum L. Dawki kadmu dodane w ilości 30 mg·kg, spowodowały, że względne zmiany wielkości pozornej powierzchni właściwej korzeni starszych (faza pełnej dojrzałości nasion) były większe niż dla korzeni zebranych w fazie kwitnienia roślin. Intensywność zmian pozornej powierzchni właściwej korzeni zależała nie tylko od odporności roślin i stężenia czynnika stresowego, ale również od czasu ekspozycji rośliny na stres. Obserwowane zmiany pozornej powierzchni właściwej badanych korzeni, związane były prawdopodobnie ze zmianami w procesach fizjologicznych, które zachodziły w roślinie pod wpływem przedłużającego się stresu. S ł o wa k l u c z o w e : kadm, korzenie rajgrasu, pozorna powierzchnia właściwa
Current Researches, Rationale, Plausibility, and Evidence Gaps on Metformin for the Management of Hypertensive Disorders of Pregnancy

Hypertensive disorders of pregnancy (HDP) are a group of morbid pregnancy complications, with preeclampsia (PE) being the most common subclassification among them. PE affects 2%–8% of pregnancies globally and threatens maternal and fetal health seriously. However, the only effective treatment of PE to date is the timely termination of pregnancy, albeit with increased perinatal risks. Hence, more emerging therapies for PE management are in urgent need. Originally introduced as the first-line therapy for type 2 diabetes mellitus, metformin (MET) has now been found in clinical trials to significantly reduce the incidence of gestational hypertension and PE in pregnant women with PE-related risks, including but not limited to pregestational diabetes mellitus, gestational diabetes mellitus, polycystic ovary syndrome, or obesity. Additionally, existing clinical data have preliminarily ensured the safety of taking MET during human pregnancies. Relevant lab studies have indicated that the underlying mechanism includes angiogenesis promotion, endothelial protection, anti-inflammatory effects, and particularly protective effects on trophoblast cells against the risk factors, which are beneficial to placental development. Together with its global availability, easy administration, and low cost, MET is expected to be a promising option for the prevention and treatment of PE. Nevertheless, there are still some limitations in current studies, and the design of the relevant research scheme is supposed to be further improved in the future. Herein, we summarize the relevant clinical and experimental researches to discuss the rationale, safety, and feasibility of MET for the management of HDP. At the end of the article, gaps in current researches are proposed. Concretely, experimental MET concentration and PE models should be chosen cautiously. Besides, the clinical trial protocol should be further optimized to evaluate the reduction in the prevalence of PE as a primary endpoint. All of those evidence gaps may be of guiding significance to improve the design of relevant experiments and clinical trials in the future.
Comparisons of the Sexual Cycles for the Coccidian Parasites Eimeria and Toxoplasma

Toxoplasma gondii and Eimeria spp. are widely prevalent Coccidian parasites that undergo sexual reproduction during their life cycle. T. gondii can infect any warm-blooded animal in its asexual cycle; however, its sexual cycle is restricted to felines. Eimeria spp. are usually restricted to one host species, and their whole life cycle is completed within this same host. The literature reviewed in this article comprises the recent findings regarding the unique biology of the sexual development of T. gondii and Eimeria spp. The molecular basis of sex in these pathogens has been significantly unraveled by new findings in parasite differentiation along with transcriptional analysis of T. gondii and Eimeria spp. pre-sexual and sexual stages. Focusing on the metabolic networks, analysis of these transcriptome datasets shows enrichment for several different metabolic pathways. Transcripts for glycolysis enzymes are consistently more abundant in T. gondii cat infection stages than the asexual tachyzoite stage and Eimeria spp. merozoite and gamete stages compared to sporozoites. Recent breakthroughs in host-pathogen interaction and host restriction have significantly expanded the understating of the unique biology of these pathogens. This review aims to critically explore advances in the sexual cycle of Coccidia parasites with the ultimate goal of comparing and analyzing the sexual cycle of Eimeria spp. and T. gondii.
Toward Regulatory Effects of Curcumin on Transforming Growth Factor-Beta Across Different Diseases: A Review

Immune response, proliferation, migration and angiogenesis are juts a few of cellular events that are regulated by transforming growth factor-β (TGF-β) in cells. A number of studies have documented that TGF-β undergoes abnormal expression in different diseases, e.g., diabetes, cancer, fibrosis, asthma, arthritis, among others. This has led to great fascination into this signaling pathway and developing agents with modulatory impact on TGF-β. Curcumin, a natural-based compound, is obtained from rhizome and roots of turmeric plant. It has a number of pharmacological activities including antioxidant, anti-inflammatory, anti-tumor, anti-diabetes and so on. Noteworthy, it has been demonstrated that curcumin affects different molecular signaling pathways such as Wnt/β-catenin, Nrf2, AMPK, mitogen-activated protein kinase and so on. In the present review, we evaluate the potential of curcumin in regulation of TGF-β signaling pathway to corelate it with therapeutic impacts of curcumin. By modulation of TGF-β (both upregulation and down-regulation), curcumin ameliorates fibrosis, neurological disorders, liver disease, diabetes and asthma. Besides, curcumin targets TGF-β signaling pathway which is capable of suppressing proliferation of tumor cells and invading cancer cells.
Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.