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"Deniz, Fatma"
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The practice of reproducible research : case studies and lessons from the data-intensive sciences
\"The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. Each of the thirty-one case studies in this volume describes the workflow that an author used to complete a real-world research project, highlighting how particular tools, ideas, and practices have been combined to support reproducibility. Authors emphasize the very practical how, rather than the why or what, of conducting reproducible research. Part 1 contains an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible.\"--Provided by publisher.
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Visual and linguistic semantic representations are aligned at the border of human visual cortex
Semantic information in the human brain is organized into multiple networks, but the fine-grain relationships between them are poorly understood. In this study, we compared semantic maps obtained from two functional magnetic resonance imaging experiments in the same participants: one that used silent movies as stimuli and another that used narrative stories. Movies evoked activity from a network of modality-specific, semantically selective areas in visual cortex. Stories evoked activity from another network of semantically selective areas immediately anterior to visual cortex. Remarkably, the pattern of semantic selectivity in these two distinct networks corresponded along the boundary of visual cortex: for visual categories represented posterior to the boundary, the same categories were represented linguistically on the anterior side. These results suggest that these two networks are smoothly joined to form one contiguous map.
This study shows that visual areas pass information to the amodal semantic system through semantically selective channels aligned at the border of visual cortex. This architecture might support the integration of visual perception and semantic memory.
Journal Article
Investigating COX-2 and 5-LOX Enzyme-Related Anti-Inflammatory and Antioxidant Activities and Phytochemical Features of Scutellaria salviifolia Benth
Scutellaria species are widely utilized and have demonstrated diverse biological effects for various diseases, both globally and in traditional Chinese medicine, due to the presence of bioactive compounds with unique structures. This study was conducted to reveal the in vitro effects and phytochemical properties of Scutellaria salviifolia Benth., an endemic species of Türkiye. The inhibitory effects of methanol extracts prepared separately from the aerial and root parts of S. salviifolia on the COX-2 and 5-LOX enzymes and their DPPH and ABTS radical scavenging activities were evaluated using in vitro methods. Additionally, the phenolic compounds of the extracts were compared based on Q-TOF LC/MS analysis. The extracts of S. salviifolia exhibited a high inhibitory effect on COX-2 enzyme activity, comparable to that of celecoxib. Still, they showed no significant effects in the 5-LOX enzyme inhibition assay. In the antioxidant activity assays, the percentage of inhibitory effects of both extracts against DPPH and ABTS were similar. A total of 29 and 27 compounds were detected in the aerial part and root extracts, respectively. Among the identified compounds, 18 were common to both the aerial part and root extracts. S. salviifolia may serve as a valuable alternative to the most well-known Scutellaria species, including S. baicalensis and S. barbata.
Journal Article
Phonemic segmentation of narrative speech in human cerebral cortex
Speech processing requires extracting meaning from acoustic patterns using a set of intermediate representations based on a dynamic segmentation of the speech stream. Using whole brain mapping obtained in fMRI, we investigate the locus of cortical phonemic processing not only for single phonemes but also for short combinations made of diphones and triphones. We find that phonemic processing areas are much larger than previously described: they include not only the classical areas in the dorsal superior temporal gyrus but also a larger region in the lateral temporal cortex where diphone features are best represented. These identified phonemic regions overlap with the lexical retrieval region, but we show that short word retrieval is not sufficient to explain the observed responses to diphones. Behavioral studies have shown that phonemic processing and lexical retrieval are intertwined. Here, we also have identified candidate regions within the speech cortical network where this joint processing occurs.
The neural dynamics underlying speech comprehension are not well understood. Here, the authors show that phonemic-to-lexical processing is localized to a large region of the temporal cortex, and that segmentation of the speech stream occurs mostly at the level of diphones.
Journal Article
X-ray crystalographic data, absolute configuration, and anticholinesterase effect of dihydromyricitrin 3-O-rhamnoside
Based on our continuous effort to investigate chemistry and biology of the plant secondary metabolites, we were able to isolate a glycosidal flavonoid
1
from the Wild Egyptian Artichoke. The activity of dihydromyricetin 3-
O
-rhamnoside (sin. dihydromyricitrin, ampelopsin 3-
O
-rhamnoside) (
1
) against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE); its absolute configuration using X-ray crystallography were determined for the first time. Inhibitory activity of
1
against AChE and BChE enzymes were determined using a slightly modified version of Ellman’s method. Compound
1
was revealed to have a potent inhibition against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with IC
50
values of 0.070 ± 0.008 and 0.071 ± 0.004 mM, respectively, where IC
50
values of the reference drug (galanthamine) were 0.023 ± 0.15 and 0.047 ± 0.91 mM. Compound
1
could be a promising molecule against Alzheimer’s disease.
Journal Article
Gallic Acid, 3-Hydroxytyrosol, and Quercetin Modulate Cholinesterase Activity in Drosophila melanogaster
The current study investigates the modulatory effects of gallic acid (GA), 3-hydroxytyrosol (3-HT), and quercetin (QUE) on key cholinesterase enzymes using Drosophila melanogaster (fruit fly) head homogenates as a source of central cholinesterases following in vivo larval exposure. The choice of these plant phenolics was predicated on their cholinesterase (ChE) inhibitory effect reported recently by our group. The study utilized D. melanogaster larvae subjected to varying doses of GA, 3-HT, and QUE, subsequently evaluating enzymatic activity of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Galanthamine HBr was used as a positive control. All three phenolic compounds exhibited elevated ΔOD/min values for BChE inhibition compared to the negative control (ethanol). GA and QUE inhibited AChE, though with lower potency than galanthamine; at 1 mM, GA and QUE achieved 79.23% and 80.98% inhibition, respectively, compared to 98.34% for galanthamine. Interestingly, the effect of 3-HT on AChE was inversely related to the dose. The results indicate that GA and QUE modulate cholinesterase activity in vivo, consistent with our prior in vitro reports. This study also provides the first in vivo evidence of 3-HT’s ChE-modulating activity in Drosophila within a whole-organism model.
Journal Article
Correction: Arkyurek et al. Gallic Acid, 3-Hydroxytyrosol, and Quercetin Modulate Cholinesterase Activity in Drosophila melanogaster. Int. J. Mol. Sci. 2026, 27, 859
In the original publication [...]
Journal Article
Multicenter prospective surveillance study of viral agents causing meningoencephalitis
The frequency of bacterial factors causing central nervous system infections has decreased as a result of the development of our national immunization program. In this study, it is aimed to obtain the data of our local surveillance by defining the viral etiology in cases diagnosed with meningoencephalitis for 1 year. Previously healhty 186 children, who applied with findings suggesting viral meningoencephalitis to 8 different tertiary health centers between August 2018 and August 2019, in Istanbul, were included. The cerebrospinal fluid (CSF) sample was evaluated by polymerase chain reaction. The M:F ratio was 1.24 in the patient group, whose age ranged from 1 to 216 months (mean 40.2 ± 48.7). Viral factor was detected in 26.8%. Enterovirus was the most common agent (24%) and followed by Adenovirus (22%) and HHV type 6 (22%). In the rest of the samples revealed HHV type 7 (10%), EBV (6%), CMV (6%), HSV type 1 (6%), Parvovirus (4%) and VZV (2%). The most common symptoms were fever (79%) and convulsions (45.7%). Antibiotherapy and antiviral therapy was started 48.6% and 4% respectively. Mortality and sequela rate resulted 0.53% and 3.7%, respectively. This highlights the importance of monitoring trends in encephalitis in Turkey with aview to improving pathogen diagnosis for encephalitis and rapidly identifying novel emerging encephalitis-causing pathogens that demand public health action especially in national immunisation programme.
Journal Article
Chromatographic Analysis and Enzyme Inhibition Potential of Reynoutria japonica Houtt.: Computational Docking, ADME, Pharmacokinetic, and Toxicokinetic Analyses of the Major Compounds
Background: Reynoutria japonica Houtt. has been used for inflammatory diseases, skin burns, and high cholesterol in traditional Chinese medicine, and the roots and rhizomes of the plant were registered in the Chinese Pharmacopoeia. This study evaluated the enzyme inhibitory activities of R. japonica extracts from Türkiye. Its major phytochemical content was elucidated, molecular interaction studies of the main compounds were conducted, and toxicokinetic predictions and absorption, distribution, metabolism, and elimination studies were performed with in silico methods. Methods: R. japonica extracts were tested for their enzyme inhibitory activities using an ELISA microplate reader. The phytochemical profile was elucidated by LC-MS QTOF. Docking and other in silico studies evaluated interactions of its main components with cholinesterase, collagenase, and elastase. Results: R. japonica exhibited significant cholinesterase inhibitory effectiveness, while the stem and root extracts showed moderate tyrosinase inhibition. R. japonica leaf (IC50 = 117.20 ± 4.84 g/mL) and flower extracts (IC50 = 111.40 ± 1.45 µg/mL) exhibited considerable elastase activity. R. japonica leaf (IC50 = 171.00 ± 6.76 g/mL) and root (IC50 = 160.00 ± 6.81 g/mL) extracts displayed similar and potent collagenase inhibition. In the LC-MS QTOF analysis, procyanidin dimer, catechin, piceid, torachrysone, and its glucoside isomers were identified as the major components and resveratrol as the minor component. Galloylglucose showed the strongest binding at cholinesterase via key hydrogen bonds, while emodin-6-glucoside and emodin formed stable interactions with elastase. Piceid displayed significant polar and water-mediated contacts with collagenase. These findings underscore the potential of these ligands as protein inhibitors. In silico predictions reveal that emodin possessed the most favorable drug-like properties but posed potential interaction risks. Conclusions: This research represents the first investigation of the bioactivity and phytochemistry of R. japonica grown and documented in 2020 in Türkiye. Our findings point out that R. japonica could be used for cosmetic purposes, and further studies on neurological disorders could be performed.
Journal Article