bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIR predictor and optimizer: Web‐tools for accurate prediction of translation initiation rate and precision gene design in Saccharomyces cerevisiae
Authors: Chakarborty Sulagno , Irshad Inayat Ullah , Mahima  , Sharma Ajeet K. 
Published: May 2024

AbstractTranslation initiation is the primary determinant of the rate of protein production. The variation in the rate with which this step occurs can cause up to three orders of magnitude differences in cellular protein levels. Several mRNA features, including mRNA stability in proximity to the start codon, coding sequence length, and presence of specific motifs in the mRNA molecule, have been shown to influence the translation initiation rate. These molecular factors acting at different strengths allow precise control of in vivo translation initiation rate and thus the rate of protein synthesis. However, despite the paramount importance of translation initiation rate in protein synthesis, accurate prediction of the absolute values of initiation rate remains a challenge. In fact, as of now, there is no available model for predicting the initiation rate in Saccharomyces cerevisiae. To address this, we train a machine learning model for predicting the in vivo initiation rate in S. cerevisiae transcripts. The model is trained using a diverse set of mRNA transcripts, enabling the comparison of initiation rates across different transcripts. Our model exhibited excellent accuracy in predicting the translation initiation rate and demonstrated its effectiveness with both endogenous and exogenous transcripts. Then, by combining the machine learning model with the Monte‐Carlo search algorithm, we have also devised a method to optimize the nucleotide sequence of any gene to achieve a specific target initiation rate. The machine learning model we've developed for predicting translation initiation rates, along with the gene optimization method, are deployed as a web server. Both web servers are accessible for free at the following link: ajeetsharmalab.com/TIRPredictor. Thus, this research advances our fundamental understanding of translation initiation processes, with direct applications in biotechnology.
EDUPERES and GAMERES: A smart interactive education platform and digital gamification for basic circuit analysis
Authors: Uluskan Seçkin 
Published: May 2024

AbstractThis paper introduces Education Platform for Equivalent Resistance (EDUPERES) and Gamification of Equivalent Resistance (GAMERES), two different parts of a new computer aided education platform with interactive and imaginative design and game elements, which have been created during 4 years. In Vocational School of Transportation of Eskişehir Technical University, electrical circuit analysis is a compact course which exhaustively yet quickly covers all the DC and AC circuit concepts. During the course, it is observed that some students have difficulties in some basic capabilities such as calculation of equivalent resistance of either a standard or a compact circuit, dividing currents, and so on. More sadly, this inability spreads to the rest of the semester. This study aims to overcome this issue through a smart interactive education platform and gamification. The first part, that is, EDUPERES visualizes and animates the solutions of electrical circuits. To make the students exercise circuit questions, it provides an interface which simulates the comfort of using paper and pencil. This platform is powered by a smart algorithm to watch almost all of the actions of the students and to give prompt warnings. It allows students to transform the shapes of compact circuits during circuit reduction. The second part, that is, GAMERES imaginatively converts the circuit questions into action, competition, shooter, puzzle, and maze games. Via box plots and Mann–Whitney–Wilcoxon nonparametric tests, it is shown that EDUPERES and GAMERES can significantly increase students' learning. The success of EDUPERES and GAMERES is discussed with regard to previous studies and gamers' motivations.
Anticancer Potential of the S‐Heterocyclic Ring Containing Drugs and its Bioactivation to Reactive Metabolites
Authors: Maji Sumit , Debnath Biplab , Panda Shambo , Manna Tanusree , Maity Arindam , Dayaramani Richa , Nath Rajarshi , Khan Shah Alam , Akhtar Md Jawaid 
Published: May 2024

AbstractSulfur‐containing heterocyclic derivatives have been disclosed for binding with a wide range of cancer‐specific protein targets. Various interesting derivatives of sulfur‐containing heterocyclics such as benzothiazole, thiazole, thiophene, thiazolidinedione, benzothiophene, and phenothiazine, etc have been shown to inhibit diverse signaling pathways implicated in cancer. Significant progress has also been made in molecular targeted therapy against specific enzymes such as kinase receptors due to potential binding interactions inside the ATP pocket. Sulfur‐containing heterocyclic ring metal complexes i. e., benzothiazole, thiazole, thiophene, benzothiophene and phenothiazines are among the most promising active anticancer compounds. However, sulfur heteroaromatic rings, particularly thiophene, are of high structural alert due to their metabolism to reactive metabolites. The mere presence of a structural alert itself does not determine compound toxicity therefore, this review focuses on some specific findings that shed light on factors influencing the toxicity. In the current review, synthetic strategies of introducing the sulfur core ring in the synthesized derivatives are discussed with their structure‐activity relationships to enhance our understanding of toxicity mechanisms and develop safer therapeutic options. The sulfur‐containing marketed anticancer drugs included in this review direct the synthesis of novel compounds and will help in the development of potent, safer sulfur‐based anticancer drugs in near future.
Irciniaplysins A−D: New Psammaplysin Derivatives from Philippine Marine Sponge Ircinia sp.
Authors: Ang Aileen May G. , Uy Mylene M. , Ohta Emi , Ômura Hisashi , Ohta Shinji 
Published: May 2024

AbstractFour new psammaplysin derivatives (1–4) with fatty acyl substituents, designated irciniaplysins A−D, and three known psammaplysins (5–7) were isolated from a marine sponge Ircinia sp. Their structures were elucidated using extensive spectroscopic analyses. The positions of the double bonds and the branch points of the fatty acyl side chains were determined by GC‐MS analysis of their fatty acid methyl ester (FAME) derivatives. Irciniaplysins A (1) and B (2) contained an unusual long‐chain fatty acyl substituent with a 5,9‐diene unit. The isolated compounds were evaluated for their cytotoxic activity against the human colorectal carcinoma (HCT 116) cells, however, none of these compounds showed significant activity.
Dentigerous cyst in the medial wall of maxillary sinus
Authors: Mohebiniya Maryam , Jadidi Soheila 
Published: May 2024

Key Clinical MessageThis is the image of dentigerous cyst detected in the medial wall of maxillary sinus, a rare location for the mentioned cyst, which emphasizes the superiority of radiographic features from the site of the lesion. Moreover, the present case showed no facial asymmetry despite the extension of the lesion.
Vulvovaginitis due to Enterobius vermicularis in a girl and epidemic enterobiasis in her family
Authors: Davoodi Lotfollah , Soleymani Eissa , Oladi Ziaeddin , Azar Shadi Shayesteh , Parandin Fatemeh , Mizani Azadeh , Mirbadie Seyed Reza , Hajizadeh Fatemeh , Fakhar Mahdi 
Published: May 2024

Key Clinical MessageHere we present a case of a 4‐year‐old girl who suffered from vulvovaginitis caused by Enterobius vermicularis. All members of her family were also infected by this helminth. Treatment with mebendazole was administered to all family members and it was found that the entire family had been cured.AbstractVulvovaginitis, an inflammation of the vulvovaginal mucous membranes, is a common reason for pediatric gynecology consultations. One of the causes of this condition is a parasitic worm known as Enterobius vermicularis (E. vermicularis). In girls, adult worms can infiltrate the vagina and release eggs, leading to the development of vulvovaginitis. Furthermore, these worms have the ability to invade the endometrial cavity too. Here we present a case of a 4‐year‐old girl who suffered from vulvovaginitis caused by E. vermicularis. All members of her family were also infected by this parasitic helminth. In the vaginal sample, apart from the eggs, the female adult worm was observed under the microscope. Treatment with mebendazole was administered to all family members, and their progress was followed for a period of 3 weeks, during which it was found that the entire family had been cured. This patient experienced significant improvement in symptoms related to severe anxiety, nervousness, vaginal inflammation, itching, and vulvovaginitis caused by E. vermicularis. To prevent infection by E. vermicularis, it is crucial to disinfect underwear and bed sheets. In kindergartens, the spread of this parasite should not be underestimated, and asymptomatic individuals who have been exposed to infected persons should receive treatment to prevent an epidemic. Maintaining cleanliness and hygiene, especially after using the toilet, is of the most importance, particularly for girls who are more susceptible to E. vermicularis infection. Additionally, it is essential for all family members to be aware of the transmission routes of this parasite.
Insight into the Stability of Pentazolyl Derivatives based on Covalent Bond
Authors: Jiang Tianyu , Xia Honglei , Zhang Wenquan , Liu Tianlin 
Published: May 2024

AbstractPentazole is regarded as a unique inorganic molecule that possess organic heterocyclic structure. Therefore, the research on pentazolyl derivatives represents a cutting‐edge direction in both contemporary inorganic chemistry and heterocyclic chemistry. Moreover, their synthesis is regarded as the most significant research topic in the field of energetic materials due to the great potential of pentazolyl derivatives to breakthrough the energy bottleneck of CHNO‐based energetic materials. However, synthesizing pentazolyl derivatives is challenging. To provide a theoretical support for the synthesis, we conducted theoretical studies on six single‐ring pentazolyl derivatives with different functional groups. The results suggest that derivatization reduces the bond strength and weakens the aromaticity of the pentazolate ring. Further analysis showed that derivatization mainly affects the π aromaticity of the pentazolate ring, and ultimately causing poor stability of the pentazolyl derivatives. Among the six derivatives investigated in this study, fluoro pentazole (cyclo‐N5‐F) and hydroxyl pentazole (cyclo‐N5‐OH) possess good aromaticity, which is similar to the reported cyclo‐N5‐NCHN(CH3)2. Further calculations show that the kinetic stability of cyclo‐N5‐OH is higher than that of cyclo‐N5‐F. These results collectively indicate that cyclo‐N5‐OH is a promising candidate for synthesizing single‐ring pentazolyl derivatives.
Theoretical Prediction and Comprehensive Characterization of an All‐Nitrogenatomic Ring, Cyclo[18]Nitrogen (N18)
Authors: Lu Tian 
Published: May 2024

AbstractThe cyclic molecule cyclo[18]carbon composed of 18 carbon atoms has been observed in condensed phase experiment in recent years and has attracted great attention. Through state‐of‐art quantum chemistry calculation, this study found that 18 nitrogen atoms can also form a macrocyclic system, cyclo[18]nitrogen (N18), though its lifetime is very short at room temperature and can only exist for a relatively long time at very low temperatures. We comprehensively theoretically studied properties of N18, including geometric configurations, thermal decomposition mechanism and rate, molecular dynamics behavior, energetic properties, vibrational and electronic spectra. We also discussed in depth the electronic structure of N18, including nature of the N−N bonds, lone‐pairs, charge distribution characteristics, electronic delocalization, and aromaticity. This work is not only the first exploration of the macrocyclic N18 molecule, but also the first time to systematically examine a very long‐chain substance fully composed of nitrogen atoms in isolated state.
Harnessing the 3D‐Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data
Authors: Magaña Paulyna , Nair Sreenath , Varadi Mihaly , Velankar Sameer 
Published: May 2024

AbstractRecent advancements in protein structure determination and especially in protein structure prediction techniques have led to the availability of vast amounts of macromolecular structures. However, the accessibility and integration of these structures into scientific workflows are hindered by the lack of standardization among publicly available data resources. To address this issue, we introduced the 3D‐Beacons Network, a unified platform that aims to establish a standardized framework for accessing and displaying protein structure data. In this article, we highlight the importance of standardized approaches for accessing protein structure data and showcase the capabilities of 3D‐Beacons. We describe four protocols for finding and accessing macromolecular structures from various specialist data resources via 3D‐Beacons. First, we describe three scenarios for programmatically accessing and retrieving data using the 3D‐Beacons API. Next, we show how to perform sequence‐based searches to find structures from model providers. Then, we demonstrate how to search for structures and fetch them directly into a workflow using JalView. Finally, we outline the process of facilitating access to data from providers interested in contributing their structures to the 3D‐Beacons Network. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Programmatic access to the 3D‐Beacons APIBasic Protocol 2: Sequence‐based search using the 3D‐Beacons APIBasic Protocol 3: Accessing macromolecules from 3D‐Beacons with JalViewBasic Protocol 4: Enhancing data accessibility through 3D‐Beacons
Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems
Authors: Wang Sai , Wu Dong‐Hai , Song Yong‐Duo , Wang Tuan‐Tuan , Fan Shi‐Di , Wu En‐Ni , Chen Nan‐Lin , Xia Wen‐Tong , Xu Min N. , Chen Zhong‐Bing , Wen Jing , Zhang Yang , Mo Ling , Xiang Lei 
Published: May 2024

AbstractFish are vital in river ecosystems; however, traditional investigations of fish usually cause ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offer an alternative, noninvasive approach for detecting fish species. In this study, the effects of environmental DNA (eDNA), coupled with PCR and next‐generation sequencing, and electrofishing for identifying fish community composition and diversity were compared. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected along the longitudinal (upstream–downstream) gradient of the rivers. Both fish population parameters, including species abundance and biomass, and eDNA OTU richness grouped 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with order‐/family‐level grouping, genus‐/species‐level grouping could more accurately reveal the differences between upstream zones I−III, midstream zones IV−V, and downstream zones VI–VIII. From the headwaters to the estuary, two environmental gradients significantly influenced the longitudinal distribution of the fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate identification of dominant, alien, and biomarker species in each spatial zone indicated that eDNA could characterize fish community attributes at a level similar to that of traditional approaches. Overall, our results demonstrated that eDNA metabarcoding can be used as an effective tool for revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.
Why are graminoid species more dominant? Trait‐mediated plant–soil feedbacks shape community composition
Authors: Huang Kailing , De Long Jonathan R. , Yan Xuebin , Wang Xiaoyi , Wang Chunlong , Zhang Yiwei , Zhang Yuanyuan , Wang Peng , Du Guozhen , van Kleunen Mark , Guo Hui 
Published: May 2024

AbstractSpecies traits may determine plant interactions along with soil microbiome, further shaping plant–soil feedbacks (PSFs). However, how plant traits modulate PSFs and, consequently, the dominance of plant functional groups remains unclear. We used a combination of field surveys and a two‐phase PSF experiment to investigate whether forbs and graminoids differed in PSFs and in their trait–PSF associations. When grown in forb‐conditioned soils, forbs experienced stronger negative feedbacks, while graminoids experienced positive feedbacks. Graminoid‐conditioned soil resulted in neutral PSFs for both functional types. Forbs with thin roots and small seeds showed more‐negative PSFs than those with thick roots and large seeds. Conversely, graminoids with acquisitive root and leaf traits (i.e., thin roots and thin leaves) demonstrated greater positive PSFs than graminoids with thick roots and tough leaves. By distinguishing overall and soil biota‐mediated PSFs, we found that the associations between plant traits and PSFs within both functional groups were mainly mediated by soil biota. A simulation model demonstrated that such differences in PSFs could lead to a dominance of graminoids over forbs in natural plant communities, which might explain why graminoids dominate in grasslands. Our study provides new insights into the differentiation and adaptation of plant life‐history strategies under selection pressures imposed by soil biota.
Reduced congestion and improved response to a fluid/sodium challenge in chronic heart failure patients after initiation of sacubitril/valsartan: The NATRIUM‐HF study
Authors: Mebazaa Alexandre , Davison Beth A. , Biegus Jan , Edwards Christopher , Murtagh Gillian , Varounis Christos , Hayrapetyan Hamlet , Sisakian Hamayak , Ter‐Grigoryan Victor R. , Takagi Koji , Novosadova Maria , Ponikowski Piotr , Cotter Gad 
Published: May 2024

AbstractAimsThe effects of initiating sacubitril/valsartan in patients with stable heart failure with reduced ejection fraction (HFrEF) on response to fluid and sodium expansion are unknown.Methods and resultsWe have explored changes in natriuresis, diuresis, and congestion in response to the administration of intravenous fluid/sodium load in patients with HFrEF before as compared to after the initiation of sacubitril/valsartan. At baseline (before sacubitril/valsartan initiation) and 2 and 3 months after the initiation, patients underwent an evaluation that consisted of three phases of 3 h: the rest phase (0–3 h), the load phase (3–6 h) in which 1 L of intravenous Ringer solution was administered, and the diuretic phase (6–9 h) at the beginning of which furosemide was administered. Overall, 216 patients completed the study. In comparison to baseline values, at 2 and 3 months after sacubitril/valsartan initiation, patients' diuresis and natriuresis in response to Ringer administration significantly increased (mean difference: 38.8 [17.38] ml, p = 0.0040, and 9.6 [2.02] mmol, p < 0.0001, respectively). Symptoms and signs of congestion after the fluid/sodium challenge were significantly decreased at months 2 and 3 compared to baseline. Compared to baseline, there was also an increment of natriuresis after furosemide administration on sacubitril/valsartan (9.8 [5.13] mmol, p = 0.0167). There was a significant decrease in body weight in subsequent visits when compared to baseline values (−0.50 [−12.7, 7.4] kg at 2 months, and −0.75 [−15.9, 7.5] kg at 3 months; both p < 0.0001).ConclusionsThe initiation of sacubitril/valsartan in HFrEF patients was associated with improvements in natriuresis, diuresis, and weight loss and better clinical adaptation to potentially decongestive stressors.
Improving performance of defect detection by setting skewed tolerance and joint tolerances in crimp force monitor
Authors: Zeng Liancheng , Qin Dali 
Published: May 2024

AbstractA Crimp Force Monitor (CFM) detects defects by whether the crimp force curve of the force sensor exceeds the set tolerance, with the goal of low defect miss rate and false alarm rate. In this study, typical defects made by hand are crimped with an automatic crimping machine together with good products to obtain continuous data of the crimping force curves and to process the data. For the peak and area deviations of the crimp force curve, the good products show skew‐normal distribution, and the defective samples show outliers and different deviation intensities in the positive and negative directions. Furthermore, by manually intervening in the batch production of multiple groups of defects and comparing the defect miss rate and false alarm rate of CFM with different tolerance settings, the peak skewed tolerance, joint loose tolerance and joint skewed tolerance tree settings can meet a low defect miss rate and low false alarm rate at the same time. The group test results verify the skew‐normal distribution of crimping force curve deviation rate and the characteristics of deviation intensities, providing reference for the tolerance setting of CFM in automated terminal crimping production.
Thermo‐economic analysis of gas‐to‐wire: A case for utilizing gas flaring in the Niger Delta region of Nigeria
Authors: Otuagoma Smith Orode , Eyenubo Ogheneakpobo Jonathan , Owebor Kesiena , Ebisine Ebimene Ezekiel , Okieke Ufuoma Jeffery , Ubara Stella Igho 
Published: May 2024

AbstractThis work investigated the thermo‐economics of gas‐to‐wire as a gas flaring mitigation option in a selected gas production facility, in the Niger Delta region of Nigeria, which flares 294 thousand standard cubic feet of natural gas, daily. The thermodynamics and economics aspects of the gas‐to‐wire plant were modeled, and implemented in the Engineering Equation Solver software. The thermodynamics was carried out to ascertain the technical feasibility of the proposed plant, while the economics analysis was done to ensure its cost competitiveness. The findings suggested that 19.2 MW of electricity could be generated from the flare gases. This could be achieved at a life cycle cost of 19.24 billion naira, and a unit cost of energy of 13.47 naira per kWh. Parametric simulation of interest rate, excess combustion air, exit temperature of flue gases, and expansion ratio of gas turbine were also done. Furthermore, the proposed power plant could meet the electricity needs of not less than 60,000 households in Delta State where the gas production facility is located at 550 kWh electricity per capita. The study has shown that gas‐to‐wire is one of the viable approaches to tackle gas flaring activities in Nigeria, to meet both the energy demand of its people and to preserve the environment. Thus, it is recommended that the Federal Government of Nigeria should give gas‐to‐wire a priority in its gas flaring utilization agenda.