bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of radiomics-based machine-learning classifiers for the pretreatment prediction of pathologic complete response to neoadjuvant therapy in breast cancer
Authors: Li Xue , Li Chunmei , Wang Hong , Jiang Lei , Chen Min 
Published: July 2024

Background
Machine learning classifiers are increasingly used to create predictive models for pathological complete response (pCR) in breast cancer after neoadjuvant therapy (NAT). Few studies have compared the effectiveness of different ML classifiers. This study evaluated radiomics models based on pre- and post-contrast first-phase T1 weighted images (T1WI) in predicting breast cancer pCR after NAT and compared the performance of ML classifiers.

Methods
This retrospective study enrolled 281 patients undergoing NAT from the Duke-Breast-Cancer-MRI dataset. Radiomic features were extracted from pre- and post-contrast first-phase T1WI images. The Synthetic Minority Oversampling Technique (SMOTE) was applied, then the dataset was randomly divided into training and validation groups (7:3). The radiomics model was built using selected optimal features. Support vector machine (SVM), random forest (RF), decision tree (DT), k-nearest neighbor (KNN), extreme gradient boosting (XGBoost), and light gradient boosting machine (LightGBM) were classifiers. Receiver operating characteristic curves were used to assess predictive performance.

Results
LightGBM performed best in predicting pCR [area under the curve (AUC): 0.823, 95% confidence interval (CI) [0.743–0.902], accuracy 74.0%, sensitivity 85.0%, specificity 67.2%]. During subgroup analysis, RF was most effective in pCR prediction in luminal breast cancers (AUC: 0.914, 95% CI [0.847–0.981], accuracy 87.0%, sensitivity 85.2%, specificity 88.1%). In triple-negative breast cancers, LightGBM performed best (AUC: 0.836, 95% CI [0.708–0.965], accuracy 78.6%, sensitivity 68.2%, specificity 90.0%).

Conclusion
The LightGBM-based radiomics model performed best in predicting pCR in patients with breast cancer. RF and LightGBM showed promising results for luminal and triple-negative breast cancers, respectively.
Wingbeat Frequency in Small and Large-sized Fruit Fly, Drosophila melanogaster, in Eastern Uttar Pradesh, India
Authors: Mathew Isaac L. , Singh Deepak 
Published: July 2024

Drosophila melanogaster was evaluated for wingbeat frequencies based on its general body size. Apart from the critical role of flight in foraging, competing for a mate and evading predators, its flight tone is crucial in intraspecific auditory communication. The average wing beat frequencies during free flight of local Drosophila melanogaster was found to range from 215.63 ±5.26 to 261.20 ±6.53 Hz, from the smallest to large-sized flies respectively. The significant difference in wingbeat frequency between the two groups is due to the distinct differences in wing size and body weight. Variations seen within the group is a function of several factors like insect body weight, wing dimensions, age, metabolic status, locomotory requirements and ambient climatic conditions.
Geographical Indications of Vegetable Crops in India- Role in Farmer’s Empowerment and Agro-biodiversity Management
Authors: Reddy Jakkireddy Rajashekar , Prasanna P. A. Lakshmi 
Published: July 2024

In this paper an attempt has been made to study role of Geographical Indications (GIs) in farmers’ empowerment and biodiversity management focusing on vegetable crops GIs. Data was collected from GI registry website. Till 2023-24, 200 agricultural GIs were registered constituting 31 percent of total GIs registered in India. Total number of registered GIs in vegetables was 32 constituting 16 percent of agricultural GIs. In case of 19 vegetable GIs, farmers’ organizations were the exclusive registered owners of GIs indicating farmers’ empowerment. But only with respect to 13 vegetable GIs, authorised users were registered till 2023-24, indicating gap and lag in effective use of GIs in farmers’ empowerment. Registered vegetables GIs were spread across 10 crops. Maximum number of GIs were registered in chilli crop (14) and it was followed by brinjal (6). 32 Vegetable GIs registered in India were spread across 16 states. Maharashtra state had highest number of vegetable GIs i.e., 5 followed by Goa (4) and Kerala (4). Registered GIs in chilli crop was spread across 13 states. 6 GIs in brinjal were spread across 6 states. Similarly, 3 GIs in garlic and onion were spread across 3 states. This pattern indicates potential role of GIs in agro-biodiversity conservation.
Morpho-Molecular and Management of Pomegranate (Punica granatum L.) Wilt Caused by Ceratocystis fimbriata Ellis and Halst
Authors: Lokure Suhas , Y, M Somasekhara, , GK Ravichandra 
Published: July 2024

Pomegranate wilt poses a significant threat to pomegranate production, holding considerable economic importance in the cultivated regions of pomegranates. The study investigated the wilt in pomegranate cultivation, revealing characteristic symptoms including yellowing and/or wilting of the leaves on a single branch usually in the upper crown and senescence. Brown discoloration was observed in the root, stem and branches of severely affected plants. The cross-sectioned root and stem portions of the wilted plants showed only the presence of brown discolorations in the vascular regions. The wilt incidence in Karnataka ranging from 1.14 to 62.06 Percent. PCR analysis and 18S rDNA region was sequenced, it has been confirmed C. fimbriata as the causal organism for pomegranate wilt and Phylogenetic analyses placed the pomegranate isolates among members of the LAC of the C. fimbriata complex; specifically, to populations that appear to be native to eastern and northern South America. Optimal growth of the pathogen was observed at 30 °C with pH 7.0 and best media for culturing C. fimbriata is Potato dextrose agar and Potato carrot agar, in vitro evaluation of fungicides showed propiconazole and mancozeb highest inhibiting mycelial growth. Trichoderma viride (Tv-3) and Bacillus subtilis emerged as the most effective bio-agent, while pongamia leaf extract exhibited maximum fungal growth inhibition. These can be used for the management of wilt disease.
Microduplication of 15q13.3 and Xq21.31 in a family with tourette syndrome and comorbidities
Authors: Melchior Linea , Bertelsen Birgitte , Debes Nanette Mol , Groth Camilla , Skov Liselotte , Mikkelsen Jens D , Brøndum‐Nielsen Karen , Tümer Zeynep 
Published: July 2013

ABSTRACTTourette syndrome (TS) is a childhood onset neurodevelopmental disorder. Although it is widely accepted that genetic factors play a significant role in TS pathogenesis the etiology of this disorder is largely unknown. Identification of rare copy number variations (CNVs) as susceptibility factors in several neuropsychiatric disorders such as attention deficit‐hyperactivity disorder (ADHD), autism and schizophrenia, suggests involvement of these rare structural changes also in TS etiology. In a male patient with TS, ADHD, and OCD (obsessive compulsive disorder) we identified two microduplications (at 15q13.3 and Xq21.31) inherited from a mother with subclinical ADHD. The 15q duplication included the CHRNA7 gene; while two genes, PABPC5 and PCDH11X, were within the Xq duplication. The Xq21.31 duplication was present in three brothers with TS including the proband, but not in an unaffected brother, whereas the 15q duplication was present only in the proband and his mother. The structural variations observed in this family may contribute to the observed symptoms, but further studies are necessary to investigate the possible involvement of the described variations in the TS etiology. © 2013 Wiley Periodicals, Inc.
The Impact of the Mukaiyama Aldol Reaction in Total Synthesis
Authors: Kan S. B. Jennifer , Ng Kenneth K.‐H. , Paterson Ian 
Published: July 2013

AbstractFour decades since Mukaiyama’s first reports on the successful application of silicon and boron enolates in directed aldol reactions, the ability of this highly controlled carbon–carbon bond‐forming method to simultaneously define stereochemistry, introduce complexity, and construct the carbon skeleton with a characteristic 1,3‐oxygenation pattern has made it a powerful tool for natural product synthesis. This Minireview highlights a number of representative total syntheses that demonstrate the impact of the Mukaiyama aldol reaction and discusses the underlying mechanistic rationale that determines the stereochemical outcomes.
The effect of pH and calcium ions on the stability of amphiphilic and anionic β‐sheet peptide hydrogels
Authors: Zarzhitsky Shlomo , Edri Hodaya , Azoulay Ziv , Cohen Ifat , Ventura Yvonne , Gitelman Anna , Rapaport Hanna 
Published: July 2013

ABSTRACTAmphiphilic peptides can form bottom‐up‐designed self‐assembled hydrogels composed of elongated fibril matrices that could find uses in various biologically‐related systems, acting as platforms for drug delivery or scaffolds that mimic extracellular matrices in tissue regeneration systems. We have previously reported that the amphiphilic and anionic β‐sheet forming peptide, Pro‐Asp‐(Phe‐Asp)5‐Pro, PFD‐5, generates hydrogels that template calcium‐phosphate mineral and as such, were able to enhance bone formation in vivo. Our earlier results prompted us to further exploit the effects of pH and calcium ion concentration on PFD‐5 peptide in solution, in hydrogels and in mineral‐loaded hydrogel compositions. Circular dichroism‐based characterization of solutions of the peptide demonstrated transitions between the unfolded state to a β‐sheet structure as function of peptide concentration, pH and calcium ion concentration. FTIR measurements were employed to monitor differences between the structure of the peptide in solution and in hydrogels. Rheology and dissolution studies demonstrated the improved stability of hydrogels prepared by a two‐step procedure, where the peptides are dissolved and self‐assemble in the first step, while in the second step, calcium ions are allowed to adsorb onto the system. These results, highlighting the effects of a few central factors on the structure, assembly and stability of amphiphilic and anionic β‐sheet peptide systems, will contribute to the further development of designed self‐assembled peptide systems from solutions to hydrogels and hydrogel‐loaded matrices, such as mineral putty compositions. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 760–772, 2013.
A serendipitous survey of prediction algorithms for amyloidogenicity
Authors: Roland Bartholomew P. , Kodali Ravindra , Mishra Rakesh , Wetzel Ronald 
Published: July 2013

ABSTRACTThe 17‐ amino acid N‐terminal segment of the Huntingtin protein, httNT, grows into stable α‐helix rich oligomeric aggregates when incubated under physiological conditions. We examined 15 scrambled sequence versions of an httNT peptide for their stabilities against aggregation in aqueous solution at low micromolar concentration and physiological conditions. Surprisingly, given their derivation from a sequence that readily assembles into highly stable α‐helical aggregates that fail to convert into β‐structure, we found that three of these scrambled peptides rapidly grow into amyloid‐like fibrils, while two others also develop amyloid somewhat more slowly. The other 10 scrambled peptides do not detectibly form any aggregates after 100 h incubation under these conditions. We then analyzed these sequences using four previously described algorithms for predicting the tendencies of peptides to grow into amyloid or other β‐aggregates. We found that these algorithms—Zyggregator, Tango, Waltz, and Zipper—varied greatly in the number of sequences predicted to be amyloidogenic and in their abilities to correctly identify the amyloid forming members of this scrambled peptide collection. The results are discussed in the context of a review of the sequence and structural factors currently thought to be important in determining amyloid formation kinetics and thermodynamics. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 780–789, 2013.
Chemical modulation of bioactive compounds via oligopeptide or amino acid conjugation
Authors: Kwak Seon‐Yeong , Yang Jin‐Kyoung , Kim Jong‐Ho , Lee Yoon‐Sik 
Published: July 2013

ABSTRACTConjugation of an oligopeptide or an amino acid to bioactive compounds is one of the simplest chemical modifications to modulate the biological functions of the compounds. Recently, numerous methods have been proposed for the modification of their properties, including the alteration of their chemical and physical properties, and of their original bioactivities. We review the current knowledge of the adaptability of oligopeptide or amino acid conjugation for modulating the biological activities of biomolecules. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 584–591, 2013.
Biomimetic synthesis of cyclic peptides using novel thioester surrogates
Authors: Hemu Xinya , Taichi Misako , Qiu Yibo , Liu Ding‐Xiang , Tam James P. 
Published: July 2013

ABSTRACTAcyl shifts involving N‐S and S‐S rearrangements are reactions central to the breaking of a peptide bond and forming of thioester intermediates in an intein‐catalyzed protein splicing that ultimately leads to the formation of a new peptide bond by an uncatalyzed S‐N acyl shift reaction. To mimic these three acyl shift reactions in forming thioesters and the subsequent peptide ligation, here we describe the development of two 9‐fluorenylmethoxycarbonyl (Fmoc)‐compatible thioester surrogates that can undergo uncatalyzed N‐S, S‐S, and S‐N acyl shifts for preparing thioesters and cyclic peptides. These surrogates were incorporated as a C‐terminal amido moiety of a target peptide using Fmoc chemistry by solid‐phase synthesis, and then transformed into a thioester or thiolactones via two acyl shift reactions with or without the presence of an external thiol under acidic conditions. The proposed intein‐mimetic thioester surrogates were prepared using readily available starting materials including N‐methyl cysteine or 2‐thioethylbutylamide. A key functional moiety shared in their design is the thioethylamido (TEA) moiety, which is essential to effect a proximity‐driven N‐S acyl shift under a favorable five‐member ring transition in the breaking of a peptide bond. Thus, the tandem series of acyl shifts effected by a TEA moiety in a thioester surrogate together with a thioethylamino moiety of an N‐terminal Cys residue in a linear peptide precursor are chemical mimics of an intein, as they mediate both excision and ligation reactions in forming cyclic peptides including cyclic conotoxin and sunflower trypsin inhibitor described herein. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 492–501, 2013.
Development of a novel nanoparticle by dual modification with the pluripotential cell‐penetrating peptide PepFect6 for cellular uptake, endosomal escape, and decondensation of an siRNA core complex
Authors: Mitsueda Asako , Shimatani Yuri , Ito Masahiro , Ohgita Takashi , Yamada Asako , Hama Susumu , Gräslund Astrid , Lindberg Staffan , Langel Ülo , Harashima Hideyoshi , Nakase Ikuhiko , Futaki Shiroh , Kogure Kentaro 
Published: July 2013

ABSTRACTDevelopment of novel devices for effective nucleotide release from nanoparticles is required to improve the functionality of nonviral delivery systems, because decondensation of nucleotide/polycation complexes is considered as a key step for cytoplasmic delivery of nucleotides. Previously, PepFect6 (PF6) comprised chloroquine analog moieties and a stearylated cell‐penetrating peptide to facilitate endosomal escape and cellular uptake, respectively, was developed as a device for efficient siRNA delivery. As PF6 contains bulky chloroquine analog moieties, the polyplexes are expected to be loose structure, which facilitates decondensation. In the present study, siRNA was electrostatically condensed by PF6, and the PF6/siRNA complexes were coated with lipid membranes. The surface of the nanoparticles encapsulating the PF6/siRNA core (PF6‐NP) was modified with PF6 for endosomal escape (PF6/PF6‐NP). The RNAi effect of PF6/PF6‐NP was compared with those of stearylated cell‐penetrating peptide octaarginine (R8)‐modified PF6‐NP, R8‐modified nanoparticles encapsulating the R8/siRNA core (R8‐NP) and PF6‐modified R8‐NP. Nanoparticles encapsulating the PF6 polyplex, especially PF/PF‐NP, showed a significant knockdown effect on luciferase activity of B16‐F1 cells stably expressing luciferase. siRNA was widely distributed within the cytoplasm after transfection of the nanoparticles encapsulating the PF6 polyplex, while siRNA encapsulated in the R8‐presenting nanoparticles was localized within the nuclei. Thus, the siRNA distribution was dependent on the manner of peptide‐modification. In conclusion, we have successfully developed PF6/PF6‐NP exhibiting a potent RNAi effect resulting from high cellular uptake, efficient endosomal escape and decondensation of the polyplexes based on the multifunctional cell penetrating peptide PF6. PF6 is therefore a useful pluripotential device for siRNA delivery. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 698–704, 2013.
One‐Pot Multifunctional Catalysis with NNN‐Pincer Zr‐MOF: Zr Base Catalyzed Condensation with Rh‐Catalyzed Hydrogenation
Authors: Rasero‐Almansa Antonia M. , Corma Avelino , Iglesias Marta , Sánchez Félix 
Published: July 2013

AbstractWe describe the postsynthetic modification of Zr‐based metal organic frameworks (MOFs) containing chiral NNN‐pincer ligands based on aminopyridineimines, as well as the subsequent formation of (NNN)‐M‐Zr‐MOF complexes (M=Rh, Ir). With these new multifunctional materials, we performed a cascade of condensation reactions followed by hydrogenation of the resulting double bond. If the condensation reaction occurs between an aldehyde and ethyl nitroacetate, (NNN)–M–Zr‐MOF complexes catalyze the one‐pot synthesis of nitroalkenes, in which ZrIV Lewis sites play a role similar to that of the generally used TiIV in homogeneous catalysis. These multifunctional hybrid catalysts retain their crystalline framework even after the reaction, and they were isolated easily from the reaction mixture through filtration and reused several times without a significant degradation in activity. Moreover, there was no contribution from leached active species and conversion was possible only in the presence of the solid catalyst.
Metal‐Free Polymerization of Phenylsilane: Tris(pentafluorophenyl)borane‐Catalyzed Synthesis of Branched Polysilanes at Elevated Temperatures
Authors: Feigl Andreas , Chiorescu Ion , Deller Katrin , Heidsieck Sven U. H. , Buchner Magnus R. , Karttunen Virve , Bockholt Andreas , Genest Alexander , Rösch Notker , Rieger Bernhard 
Published: July 2013

AbstractThe strong organoborane Lewis acid B(C6F5)3 catalyzes the polymerization of phenylsilane at elevated temperatures forming benzene and SiH4 as side‐products. The resulting polymer is a branched polysilane with an irregular substitution pattern, as revealed by 2D NMR spectroscopy. Having explored the mechanism of this novel metal‐free polymerization by computational chemistry methods at the DFT level, we have suggested that unusual cationic active species, namely monomer‐stabilized silyl cations, propagate the polymerization. Hydride abstraction of SiH3 moiety by the catalyst in the initiation step was found to be kinetically preferred by around 9 kcal mol−1 over activation by coordination of the monomer at the aromatic ring. The formation of linear SiSi bonds during propagation was calculated to be less favorable than branching and ligand scrambling, which accounts for the branched and highly substituted form of the polymer that was obtained. This novel type of polymerization bears the potential for further optimization with respect to degree of polymerization and structure control for both primary as well as secondary silanes, which can be polymerized by sterically less hindered boranes.
Polynitroethyl‐ and Fluorodinitroethyl Substituted Boron Esters
Authors: Klapötke Thomas M. , Krumm Burkhard , Moll Richard 
Published: July 2013

AbstractThe reaction of boron oxide with various nitro‐substituted ethanols (2‐nitroethanol, 2‐fluoro‐2,2‐dinitroethanol, 2,2,2‐trinitroethanol) furnished the corresponding nitroethyl borates B(OCH2CH2NO2)3 (1), B(OCH2CF(NO2)2)3 (2), and B(OCH2C(NO2)3)3 (3). Fluorination of the anion [(NO2)2CCH2OH]− (4) resulted in 2‐fluoro‐2,2‐dinitroethanol (5), a precursor for 2, and was thoroughly characterized. An interesting condensation was observed with the anion 4 to form the unusual dianion [(NO2)2CCH2C(NO2)2]2− (6). All compounds were fully characterized by multinuclear NMR spectroscopy, vibrational spectroscopy (IR, Raman), mass spectrometry and elemental analysis. The chemical, physical and energetic properties of 1–3 and 5 are reported, as well as quantum chemical calculations at the CBS‐4M level of theory to predict the enthalpies and energies of formation. X‐ray diffraction studies were performed, and the crystal structures for compounds 1–6 were determined and discussed thoroughly. The boron esters 1–3 are of interest as possible candidates for smoke‐free, green colorants in pyrotechnic applications, and in case of 2 and 3 also as promising high energy oxidizers.
Structure‐Activity Relationship, Cytotoxicity and Mode of Action of 2‐Ester‐substituted 1,5‐Benzothiazepines as Potent Antifungal Agents
Authors: Kang Wang , Du Xingqiong , Wang Lanzhi , Hu Lijuan , Dong Yuhuan , Bian Yanqing , Li Yuan 
Published: July 2013

AbstractOur studies examined the structural features responsible for the antifungal activity of 2‐ethoxycarbonyl‐1,5‐benzothiazepine (7a). Three series of 1,5‐benzothiazepine derivatives were synthesized and screened for their antifungal activity. The results suggested that the ethoxycarbonyl group at the 2 position and the imine moiety on the seven‐membered ring are essential for activity. The most potent of the synthesized analogues (7a, 7b) were further studied by evaluating their cytotoxicity and mode of action (for 7a). The results showed that compounds 7a and 7b were relatively safe for BV2 cells, but compound 7a interfered with Cryptococcus neoformans cell wall integrity by increasing the chitinase activity. Therefore, compound 7a was considered safe as an antifungal agent for animal cells.
Theoretical Study of Substituent Effects on the Gas‐Phase Acidities of Benzoic and Phenylacetic Acids
Authors: Nakata Kazuhide , Fujio Mizue , Nishimoto Kichisuke , Tsuno Yuho 
Published: July 2013

AbstractThe relative gas‐phase acidities of 25 ring‐substituted benzoic and phenylacetic acids were theoretically determined with proton‐transfer reactions. The energies and geometries of the acids and their corresponding anions, which were involved in the reactions, were calculated at the B3LYP/6‐311+G(2d,p) level of theory. The obtained substituent effects were compared with each other and those of phenols. The acidities of the benzoic and phenylacetic acids were governed by three kinds of electronic effects (inductive, resonance, and saturation effects), which confirmed that the acidities were reflected in the nature of the benzoate and phenylacetate anions, respectively. Substituent effect analyses with an extended Yukawa–Tsuno equation, ${ - {\rm{\Delta }}E_X = \rho \left( {\sigma ^0 + r^ - {\rm{\Delta }}\bar \sigma _{\rm{R}}^ - + s{\rm{\Delta }}\bar \sigma _{\rm{S}} } \right)}$, gave excellent linear correlations for both anionic systems. The degrees of through‐resonance and saturation effects in the phenylacetate anion, as reflected by the resultant r− and s values, were unexpectedly larger than those in the benzoate anion, which were mainly attributed to hyperconjugation and through‐space interactions between the anionic moiety and the benzene π‐electron system, respectively. The acidities of the benzoic acids (or stabilities of the benzoate anions) constituted a better system than the acidities of phenylacetic acids (or stabilities of the phenylacetate anions) for a standard of the normal substituent constants (σ0) for anions in the gas phase, in contrast to solution‐phase results.