bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 genotypic resistance: automated sequence analysis and interpretation.
Authors: Goujon C P , Schneider V M , Jacomet C , Nicolas J C 
Published: July 2002

Abstract
SUMMARY: We present here GRANT ( G enotypic R esistance An alysis T ool), a program that automatically detects resistance-related mutations in HIV-1 protein sequences, and comments on the degree of resistance conferred when possible. This program is easily user-customizable, allowing immediate updates as new resistance mutations are discovered, or use with an organism other than HIV. AVAILABILITY: The package is available free of charge over the internet, either directly from the authors, or by anonymous ftp (ftp. infobiogen.fr/pub/logiciels/mac/biology or windows as appropriate). Versions exist for PPC and 68K Apple Macintosh running MacOS 7.5 or higher. Microsoft Excel 5.0 is required for quality output. A PC version is in progress. CONTACT: goujon@infobiogen.fr
Post-processing long pairwise alignments
Authors: Zhang Zheng , Berman Piotr , Wiehe Thomas , Miller Webb 
Published: July 2002

Abstract
Motivation: The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. For alignments computed by dynamic programming, current approaches for selecting similar regions may have potential flaws. For instance, the criterion of Smith and Waterman can lead to inclusion of an arbitrarily poor internal segment. Other approaches can generate an alignment scoring less than some of its internal segments.
Results: We develop an algorithm that decomposes a long alignment into sub-alignments that avoid these potential imperfections. Our algorithm runs in time proportional to the original alignment’s length. Practical applications to alignments of genomic DNA sequences are described.
Availability: Software is available at http://globin.cse.psu.edu/
Contact: webb@cse.psu.edu
Monotremes and the evolution of rapid eye movement sleep
Authors: Siegel J. M. , Manger P. R. , Nienhuis R. , Fahringer H. M. , Pettigrew J. D. 
Published: July 2002

Early studies of the echidna led to the conclusion that this monotreme did not have rapid eye movement (REM) sleep. Because the monotremes had diverged from the placental and marsupial lines very early in mammalian evolution, this finding was used to support the hypothesis that REM sleep evolved after the start of the mammalian line. The current paper summarizes our recent work on sleep in the echidna and platypus and leads to a very different interpretation. By using neuronal recording from mesopontine regions in the echidna, we found that despite the presence of a high–voltage cortical electroencephalogram (EEG), brainstem units fire in irregular bursts intermediate in intensity between the regular non–REM sleep pattern and the highly irregular REM sleep pattern seen in placentals. Thus the echidna displays brainstem activation during sleep with high–voltage cortical EEG. This work encouraged us to do the first study of sleep, to our knowledge, in the platypus. In the platypus we saw sleep with vigorous rapid eye, bill and head twitching, identical in behaviour to that which defines REM sleep in placental mammals. Recording of the EEG in the platypus during natural sleep and waking states revealed that it had moderate and high–voltage cortical EEGs during this REM sleep state. The platypus not only has REM sleep, but it had more of it than any other animal. The lack of EEG voltage reduction during REM sleep in the platypus, and during the REM sleep–like state of the echidna, has some similarity to the sleep seen in neonatal sleep in placentals. The very high amounts of REM sleep seen in the platypus also fit with the increased REM sleep duration seen in altricial mammals.Our findings suggest that REM sleep originated earlier in mammalian evolution than had previously been thought and is consistent with the hypothesis that REM sleep, or a precursor state with aspects of REM sleep, may have had its origin in reptilian species.
Development and Testing of an Electronic Health Record‐Integrated Patient‐Reported Outcome Application and Intervention to Improve Efficiency of Rheumatoid Arthritis Care
Authors: Solomon Daniel H. , Dalal Anuj K. , Landman Adam B. , Santacroce Leah , Altwies Hallie , Stratton Jackie , Rudin Robert S. 
Published: September 2022

ObjectiveMany patients with rheumatoid arthritis (RA) have difficulty finding clinicians to treat them because of workforce shortages. We developed an app to address this problem by improving care efficiency. The app collects patient‐reported outcomes (PROs) and can be used to inform visit timing, potentially reducing the volume of low‐value visits. We describe the development process, intervention design, and planned study for testing the app.MethodsWe employed user‐centered design, interviewing patients and clinicians, to develop the app. To improve visit efficiency, symptom tracking logic alerts clinicians to PRO trends: worsening PROs generate alerts suggesting an earlier visit, and stable or improving PROs generate notifications that scheduled visits could be delayed. An interrupted time‐series analysis with a nonrandomized control population will allow assessment of the impact of the app on visit frequency.ResultsPatient interviews identified several of the following needs for effective app and intervention design: the importance of a simple user interface facilitating rapid answering of PROs, the availability of condensed summary information with links to more in‐depth answers to common questions regarding RA, and the need for clinicians to discuss the PRO data during visits with patients. Clinician interviews identified the following user needs: PRO data must be easy to view and use during the clinical workflow, and there should be reduced interval visits when PROs are trending worse. Some clinicians believed visits could be delayed for patients with stable PROs, whereas others raised concerns.ConclusionPRO apps may improve care efficiency in rheumatology. Formal evaluation of an integrated PRO RA app is forthcoming.
Vibration‐Assisted Charge Transport through Positively Charged Dimer Junctions
Authors: Zhu Xin , Wang Boyu , Xiong Wan , Zhou Shuyao , Qu Kai , Lü Jing‐Tao , Chen Hongliang , Jia Chuancheng , Guo Xuefeng 
Published: September 2022

AbstractIntermolecular charge transport plays a vital role in the fields of electronics, as well as biochemical systems. Here, we design supramolecular dimer junctions and investigate the effects of charge state and energy level alignment on charge transport under nanoconfinement. Incoherent tunneling caused by thermally‐induced vibrations is enhanced in positively charged systems. The transition between coherent and incoherent tunneling is associated with specific molecular vibration modes. Positively charged systems with smaller torsional barriers and vibrational frequencies result in lower transition temperatures. Multiple thermal effects have a great impact on the conductance in the off‐resonant tunneling, while thermally‐induced vibron‐assisted tunneling contributes more to the transport in the resonant tunneling. These investigations offer a deep mechanism understanding of intermolecular charge transport and facilitate the development of practical functional molecular devices.
Unique Double Intramolecular and Intermolecular Exciton Coupling in Ethene‐Bridged aza‐BODIPY Dimers for High‐Efficiency Near‐Infrared Photothermal Conversion and Therapy
Authors: Guo Xing , Yang Jinming , Li Mao , Zhang Fan , Bu Weibin , Li Heng , Wu Qinghua , Yin Dengke , Jiao Lijuan , Hao Erhong 
Published: September 2022

AbstractSpatial electronic communications of chromophores are both theoretically and practically fascinating. Despite intramolecular or intermolecular exciton coupling was observed in multichromophoric oligomers and J‐aggregates, respectively, it is unusual that they both occur in the same molecule. Herein, ethene‐bridged aza‐BODIPY dimers with intramolecular exciton splitting have been developed. By encapsulating the dimer into F‐127 polymer, J‐type aggregated nanoparticles were produced, which showed obvious intermolecular exciton coupling and dramatically redshifted absorption and emission peaks at 936 and 1003 nm, respectively. The fabricated nanoagents have high photothermal conversion ability (η=60.3 %) and are ultra‐photostable, leading to complete tumor ablation with 915 nm laser irradiation. This phototherapeutic nanoplatform through modulating both intra‐ and intermolecular exciton couplings is a valuable paradigm for developing photothermal agents for tumor treatment.
Quantifying the Influence of Covalent Metal‐Ligand Bonding on Differing Reactivity of Trivalent Uranium and Lanthanide Complexes
Authors: Fetrow Taylor V. , Zgrabik Joshua , Bhowmick Rina , Eckstrom Francesca D. , Crull George , Vlaisavljevich Bess , Daly Scott R. 
Published: September 2022

AbstractQualitative differences in the reactivity of trivalent lanthanide and actinide complexes have long been attributed to differences in covalent metal‐ligand bonding, but there are few examples where thermodynamic aspects of this relationship have been quantified, especially with U3+ and in the absence of competing variables. Here we report a series of dimeric phosphinodiboranate complexes with trivalent f‐metals that show how shorter‐than‐expected U−B distances indicative of increased covalency give rise to measurable differences in solution deoligomerization reactivity when compared to isostructural complexes with similarly sized lanthanides. These results, which are in excellent agreement with supporting DFT and QTAIM calculations, afford rare experimental evidence concerning the measured effect of variations in metal‐ligand covalency on the reactivity of trivalent uranium and lanthanide complexes.
From Inert to Catalytically Active Milling Media: Galvanostatic Coating for Direct Mechanocatalysis
Authors: Wohlgemuth Maximilian , Mayer Maike , Rappen Marisol , Schmidt Fabian , Saure Roman , Grätz Sven , Borchardt Lars 
Published: September 2022

AbstractThe inert milling balls, commonly utilized in mechanochemical reactions, were coated with a layer of Pd and utilized as catalyst in the direct mechanocatalytic Suzuki reaction. With high yields (>80 %), the milling balls can be recycled multiple times in the absence of any solvents, ligands, catalyst‐molecules and ‐powders, while utilizing as little as 0.8 mg of Pd per coated milling ball. The coating sequence, the support material, and the layer thickness were examined towards archiving high catalyst retention, low abrasion and high conversion. The approach was transferred to the coating of milling vessels revealing the interplay between catalytically available surface area and the mechanical energy impact in direct mechanocatalysis.
On the regularity and stability of the Mayer‐type convex optimal control problems
Authors: Djendel Khelifa , Zhang Haisen , Zhou Zhongcheng 
Published: September 2022

AbstractThis paper is devoted to sufficient condition for Strong Metric sub‐Regularity (SMsR for short) of the set‐valued mapping corresponding to the local description of Pontryagin maximum principle for the Mayer‐type optimal control problems with convexity condition of the Hamiltonian and functional. In particular, stability property of optimal control for the Mayer‐type problem has been established for the occasion of a polyhedral control set and entirely bang‐bang solution structure. Moreover, based on the sufficiency of SMsR and stability property of optimal control, we give the approximate errors of Euler discretization methods utilized to such problems.
Current Status of Formulations and Scalable Processes for Producing Sulfidic Solid‐State Batteries
Authors: Batzer Mattis , Heck Carina , Michalowski Peter , Kwade Arno 
Published: September 2022

AbstractSolid‐state batteries possess the potential to combine increased energy densities, high voltages, as well as safe operation and therefore are considered the future technology for electrical energy storage. In particular, sulfides as solid electrolyte are promising candidates due to their high ionic conductivities and the possibility of a scalable production. This review aims to demonstrate ways to manufacture suspension‐based sulfidic solid‐state batteries both on a laboratory scale and on an industrial level, focusing on the assessment of current knowledge and its discussion from a process engineering point of view. In addition to the influence of process parameters during mechanochemical synthesis of the solid electrolyte, formulation strategies for electrodes and separators are presented. The process chain from dispersion to cell assembly is evaluated. Scale‐up technologies are considered in comparison to established techniques in the field of conventional lithium‐ion batteries with liquid electrolyte summarizing the current status of sulfidic solid‐state battery production.
Is One of the Least Coordinating Anions Suitable to Serve as Electrolyte Salt for Magnesium‐Ion Batteries?
Authors: Schmidt Alexei , Koger Hendrik , Barthélemy Antoine , Studer Gauthier , Esser Birgit , Krossing Ingo 
Published: September 2022

AbstractWeakly coordinating anions (WCAs) are considered promising candidates for application as electrolytes in multivalent post‐lithium batteries. One strong candidate as electrolyte salt for Mg battery application is [Mg(L)x][Al(ORF)4]2 (L=MeCN (acetonitrile), DME (1,2‐dimethoxyethane); x=3, 6; RF=C(CF3)3) that contains [Al(ORF)4]− as one of the least coordinating WCAs known. Here we present a novel synthetic route, for which vibrational, NMR and XRD analyses show the formation of a clean, pristine electrolyte salt without the common contaminants found in published synthetic routes. The electrochemistry of this pristine and pure [Mg(DME)3][Al(ORF)4]2 electrolyte (0.2 m in DME) was investigated via cyclic voltammetry (CV). In contrast to previous publications using impure materials, the CV showed no sign for Mg deposition from the pristine electrolyte for all conditions tested. This also holds when including the additives LiCl, NaCl, MgCl2, Li[BH4] or a mixture of MgCl2/Mg[HMDS]2 (HMDS=hexamethyldisilazide) in THF. Quantum chemical calculations suggested the possibility of anion decomposition at the negative electrode, leading to an electronically insulating MgF2 layer (rutile structure) on all the electrode materials tested. This hypothesis was confirmed by an XPS investigation of electrodes exposed to the electrolytes containing the WCAs [Al(ORF)4]− and [Al(OC(H)(CF3)2)4]− at negative potentials, which only showed the presence of MgF2 for the [Al(ORF)4]− electrolyte, but not for the related [Al(OC(H)(CF3)2)4]− electrolyte (which allowed to deposit magnesium reversibly on the electrode).
Two‐Electron Tetrathiafulvalene Catholytes for Nonaqueous Redox Flow Batteries
Authors: Daub Nicolas , Hendriks Koen H. , Janssen René A. J. 
Published: September 2022

AbstractTetrathiafulvalene (TTF) exhibits two reversible oxidation steps and is used as a novel multi‐electron catholyte for nonaqueous organic redox flow batteries. To increase solubility in polar organic solvents, TTF derivatives with polar side chains are synthesized. 4‐Methoxymethyltetrathiafulvalene emerges as a promising two‐electron catholyte because it is a liquid at room temperature and miscible with acetonitrile. Bulk‐electrolysis experiments and UV‐vis‐NIR absorption spectroscopy reveal excellent cycling stability for the first and second electrochemical oxidations. In the doubly oxidized state, the TTF derivatives show a reversible about 1 % loss of the state of charge per day, due to extrinsic effects. In a symmetric redox flow battery, 4‐methoxymethyltetrathiafulvalene shows a volumetric capacity loss of only 0.2 % per cycle with a Coulombic efficiency (CE) of 99.6 %. In an asymmetric redox flow battery with a pyromellitic diimide as two‐electron anolyte, the capacity loss is 0.8 % per cycle, with CE>99 % in each cycle.
Applications of surface‐enhanced Raman spectroscopy based on portable Raman spectrometers: A review of recent developments
Authors: Wang Wei , Ma Pinyi , Song Daqian 
Published: September 2022

AbstractRecently, the surface‐enhanced Raman spectroscopy (SERS) technique emerges as a potential promising analytical tool for rapid, sensitive, and selective detection which can provide unique information about the substances in the presence of plasmonic nanostructures via finger‐printing SERS spectra. The progress in nanostructure SERS substrates and portable Raman spectrometers will promote this novel detection technique to play an important role in the future rapid on‐site assay. In this review, we summarized the latest research on SERS detection technique combined based on nanostructure SERS‐active substrates with portable Raman spectrometers and their potential on‐site detection applications in environment pollutants, agricultural pollutants, biomedical analysis, and other newly emerging fields (focusing particularly on the last 5 years of research). The future perspective of SERS for on‐site analysis is also discussed.
Chitosan‐based nanoscale systems for doxorubicin delivery: Exploring biomedical application in cancer therapy
Authors: Ashrafizadeh Milad , Hushmandi Kiavash , Mirzaei Sepideh , Bokaie Saied , Bigham Ashkan , Makvandi Pooyan , Rabiee Navid , Thakur Vijay Kumar , Kumar Alan Prem , Sharifi Esmaeel , Varma Rajender S. , Aref Amir Reza , Wojnilowicz Marcin , Zarrabi Ali , Karimi‐Maleh Hassan , Voelcker Nicolas H. , Mostafavi Ebrahim , Orive Gorka 
Published: September 2022

AbstractGreen chemistry has been a growing multidisciplinary field in recent years showing great promise in biomedical applications, especially for cancer therapy. Chitosan (CS) is an abundant biopolymer derived from chitin and is present in insects and fungi. This polysaccharide has favorable characteristics, including biocompatibility, biodegradability, and ease of modification by enzymes and chemicals. CS‐based nanoparticles (CS‐NPs) have shown potential in the treatment of cancer and other diseases, affording targeted delivery and overcoming drug resistance. The current review emphasizes on the application of CS‐NPs for the delivery of a chemotherapeutic agent, doxorubicin (DOX), in cancer therapy as they promote internalization of DOX in cancer cells and prevent the activity of P‐glycoprotein (P‐gp) to reverse drug resistance. These nanoarchitectures can provide co‐delivery of DOX with antitumor agents such as curcumin and cisplatin to induce synergistic cancer therapy. Furthermore, co‐loading of DOX with siRNA, shRNA, and miRNA can suppress tumor progression and provide chemosensitivity. Various nanostructures, including lipid‐, carbon‐, polymeric‐ and metal‐based nanoparticles, are modifiable with CS for DOX delivery, while functionalization of CS‐NPs with ligands such as hyaluronic acid promotes selectivity toward tumor cells and prevents DOX resistance. The CS‐NPs demonstrate high encapsulation efficiency and due to protonation of amine groups of CS, pH‐sensitive release of DOX can occur. Furthermore, redox‐ and light‐responsive CS‐NPs have been prepared for DOX delivery in cancer treatment. Leveraging these characteristics and in view of the biocompatibility of CS‐NPs, we expect to soon see significant progress towards clinical translation.
Comprehensive association analysis of speech recognition thresholds after cisplatin‐based chemotherapy in survivors of adult‐onset cancer
Authors: Shahbazi Mohammad , Zhang Xindi , Dinh Paul C. , Sanchez Victoria A. , Trendowski Matthew R. , Shuey Megan M. , Nguyen Tessa ,   Regeneron Genetics Center, Feldman Darren R. , Vaughn David J. , Fung Chunkit , Kollmannsberger Christian , Martin Neil E. , Einhorn Lawrence H. , Cox Nancy J. , Frisina Robert D. , Travis Lois B. , Dolan Mary Eileen 
Published: September 2022

AbstractPurposeDeficits in speech understanding constitute one of the most severe consequences of hearing loss. Here we investigate the clinical and genetic risk factors for symmetric deterioration of speech recognition thresholds (SRT) among cancer survivors treated with cisplatin.MethodsSRT was measured using spondaic words and calculating the mean of measurements for both ears with symmetric SRT values. For clinical associations, SRT‐based hearing disability (SHD) was defined as SRT≥15 dB hearing loss and clinical variables were derived from the study dataset. Genotyped blood samples were used for GWAS with rank‐based inverse normal transformed SRT values as the response variable. Age was used as a covariate in association analyses.ResultsSHD was inversely associated with self‐reported health (p = 0.004). Current smoking (p = 0.002), years of smoking (p = 0.02), BMI (p < 0.001), and peripheral motor neuropathy (p = 0.003) were positively associated with SHD, while physical activity was inversely associated with SHD (p = 0.005). In contrast, cumulative cisplatin dose, peripheral sensory neuropathy, hypertension, and hypercholesterolemia were not associated with SHD. Although no genetic variants had an association p value < 5 × 10−8, 22 genetic variants were suggestively associated (p < 10−5) with SRT deterioration. Three of the top variants in 10 respective linkage disequilibrium regions were either positioned within the coding sequence or were eQTLs for genes involved in neuronal development (ATE1, ENAH, and ZFHX3).ConclusionCurrent results improve our understanding of risk factors for SRT deterioration in cancer survivors. Higher BMI, lower physical activity, and smoking are associated with SHD. Larger samples would allow for expansion of the current findings on the genetic architecture of SRT.
Genomics‐Guided Efficient Identification of 2,5‐Diketopiperazine Derivatives from Actinobacteria
Authors: Liu Jing , Li Shu‐Ming 
Published: September 2022

AbstractSecondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics‐guided approach by performing genome mining and heterologous expression to uncover novel CDPS‐derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase‐related and dimeric DKPs are also presented.