bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.
Authors: Briffeuil P , Baudoux G , Lambert C , De Bolle X , Vinals C , Feytmans E , Depiereux E 
Published: July 2002

Abstract
MOTIVATION: The prediction reliability of seven multiple alignment servers currently available on the Internet (ClustalW, MAP, PIMA, Block Maker, MSA, MEME and Match-Box) has been evaluated in terms of power (sensitivity) and confidence (selectivity). Therefore, the alignments obtained have been respectively compared to refined structural alignments for 20 families of related proteins with low levels of identity. RESULTS: Results clearly show that any powerful method remains reliable when the rate of identity falls. For some methods, power and confidence decrease linearly with the rate of identity, while other methods emphasize reliability at the cost of a lower power. Increasing the number of related sequences included in the alignment may either improve or decrease the quality of the predictions substantially. For some methods, the gain in power or in confidence is quite systematic; for others, the effect of the addition of homologous sequences is highly unpredictable. Extracting the consensus between two different methods may increase the overall confidence of the predictions tremendously. Our conclusions induce users of sequence alignment methods on the Internet to select the most suitable technique according to their requirements in terms of selectivity and sensitivity. AVAILABILITY: The aligned sequences of the 20 alignments of structure can be obtained automatically by sending the message 'send: cabios_tests.txt' by e-mail to 'matchbox@biq.fundp.ac.be'. CONTACT: eric.depiereux@fundp.ac.be
An integrated system for high throughput

TaqMan™ based SNP genotyping
Authors: Hampe Jochen , Wollstein Andreas , Lu Timothy , Frevel Hans-Jürgen , Will Marcus , Manaster Carl , Schreiber Stefan 
Published: July 2002

Abstract
Summary: We have developed an integrated laboratory information system that allows the flexible handling of pedigree, phenotype and genotype information. Specifically, it includes client applications for an integrated data import from TaqMan typing files, Mendel checking, data export, handling of pedigree and phenotype information and analysis features.
Availability: The SQL source code, sources and binaries of the client applications (NT and Windows95/98 platforms) and additional documentation are available at http://www.mucosa.de/.
Contact: J.Hampe@mucosa.de
* To whom correspondence should be addressed.
The ABC transporter family efflux pump PvdRT‐OpmQ of Pseudomonas putida KT2440: purification and initial characterization
Authors: Stein Nicola Victoria , Eder Michelle , Brameyer Sophie , Schwenkert Serena , Jung Heinrich 
Published: February 2023

Tripartite efflux systems of the ABC‐type family transport a variety of substrates and contribute to the antimicrobial resistance of Gram‐negative bacteria. PvdRT‐OpmQ, a member of this family, is thought to be involved in the secretion of the newly synthesized and recycled siderophore pyoverdine in Pseudomonas species. Here, we purified and characterized the inner membrane component PvdT and the periplasmic adapter protein PvdR of the plant growth‐promoting soil bacterium Pseudomonas putida KT2440. We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR. In addition, we provide the first biochemical evidence for direct interactions between pyoverdine and PvdRT.
Elevated CO2 levels did not induce species- or tissue-specific damage in young-of-year salmonids
Authors: Traynor Emma M. , Hasler Caleb T. 
Published: February 2023

Abstract

Objective
The broad objective of our study was to use a histological approach to examine possible tissue-level effects of exposure to elevated CO2 in freshwater young-of-year salmonids.

Methods
To study these effects, young-of-year Arctic Char Salvelinus alpinus, Rainbow Trout Oncorhynchus mykiss, and Brook Trout S. fontinalis were exposed to either control levels of CO2 (1400 μatm) or elevated levels of CO2 (5236 μatm) for 15 days. Fish were then sampled for gill, liver, and heart tissues and histologically analyzed.

Result
A species effect was observed for the length of secondary lamellae, as Arctic Char had significantly shorter secondary lamellae than the other species. No notable changes within the gills and livers of Arctic Char, Brook Trout, or Rainbow Trout exposed to elevated CO2 were observed.

Conclusion
Generally, our results indicated that elevated CO2 levels over 15 days do not induce catastrophic tissue damage and it is unlikely that fish health would be seriously impacted. Ongoing research dedicated to examining how elevated CO2 long-term may affect internal tissues of fish will allow for a more comprehensive understanding of how fish may fair with ongoing climate change and in aquaculture facilities.
Nucleotide‐Driven Molecular Sensing of Monkeypox Virus Through Hierarchical Self‐Assembly of 2D Hafnium Disulfide Nanoplatelets and Gold Nanospheres
Authors: Moitra Parikshit , Iftesum Maria , Skrodzki David , Paul Priyanka , Sheikh Elnaz , Gray Jennifer Lynn , Dighe Ketan , Sheffield Zach , Gartia Manas Ranjan , Pan Dipanjan 
Published: February 2023

AbstractLiquid interfaces facilitate the organization of nanometer‐scale biomaterials with plasmonic properties suitable for molecular diagnostics. Using hierarchical assemblage of 2D hafnium disulfide nanoplatelets and zero‐dimensional spherical gold nanoparticles, the design of a multifunctional material is reported. When the target analyte is present, the nanocomposites’ self‐assembling pattern changes, altering their plasmonic response. Using monkeypox virus (MPXV) as an example, the findings reveal that adding genomic DNA to the nanocomposite surface increases the agglomeration between gold nanoparticles and decreases the π‐stacking distance between hafnium disulfide nanoplatelets. Further, this self‐assembled nanomaterial is found to have minimal cross‐reactivity toward other pathogens and a limit of detection of 7.6 pg µL−1 (i.e., 3.57 × 104 copies µL−1) toward MPXV. Overall, this study helped to gain a better understanding of the genomic organization of MPXV to chemically design and develop targeted nucleotides. The study has been validated by UV–vis spectroscopy, X‐ray diffraction, scanning transmission electron microscopy, surface‐enhanced Raman microscopy and electromagnetic simulation studies. To the best knowledge, this is the first study in literature reporting selective molecular detection of MPXV within a few minutes and without the use of any high‐end instrumental techniques like polymerase chain reactions.
Telecom‐Wavelength Organic Single‐Crystal Lasers Triggered by the Molecular Conformation‐Dependent Cascaded Proton Transfer Processes
Authors: Wu Jun‐Jie , Yu Shuwen , Liu Yanping , Yan Chang‐Cun , Yang Wan‐Ying , Xie Wanfeng , Wang Xue‐Dong , Sun Chaofan , Liao Liang‐Sheng 
Published: February 2023

AbstractOrganic semiconductor molecules possess chemical tunability and large stimulated emission cross section, representing a promising candidate for laser gain medium. However, for the pursuit of telecom‐wavelength organic lasers, one of the major obstacles is the lack of effective energy‐level systems with high optical gain to compensate the exciton deactivation losses. Herein, the effects of molecular conformation‐dependent distinct cascaded proton‐transfer six‐level energy gain systems on lasing emission properties are systematically investigated based on organic polymorphs, proving that an energy‐level gain system without reversible transition channels is more conducive to the formation of efficient population inversion and high optical gain. Notably, the one‐way irreversible six‐level energy system of β‐phase polymorph supports more favorable population inversions than the two‐way reversible six‐level system of α‐phase polymorph due to the irreversible excited‐state second proton transfer and the irreversible ground‐state recovery, achieving the amplified spontaneous emission at telecom‐wavelength of ≈850 nm. This study provides useful guidelines for constructing efficient energy‐level gain systems, promoting the exploration of high‐gain organic semiconductor laser materials from visible to near‐infrared region.
Bidirectional Targeted Therapy Enables Efficient, Stable, and Eco‐Friendly Perovskite Solar Cells
Authors: Qi Xingnan , Song Chongping , Zhang Weihai , Shi Yueqing , Gao Yueyue , Liu Heng , Chen Rui , Shang Luwen , Tan Hairen , Tan Furui , Wang Hsing‐Lin 
Published: February 2023

AbstractPerovskite solar cells (PSCs) have witnessed rapid development toward commercialization based on their superior efficiency except for some remained misgivings about their poor stability primarily originating from interfacial problems. Robust back interface for neutralization of crystal defects, depression of dopant lithium ions (Li+) diffusion, and even inhibition of toxic lead (Pb) leakage is highly desirable; however, it remains a great challenge. Herein, a cost‐effective interfacial therapy approach is developed to simultaneously alleviate the obstacles aforementioned. A small molecule, 1,4‐dithiane with unique chair structure, is adapted to interact with under‐coordinated Pb2+ on perovskite surface and Li+ from hole transport layer, neutralizing interfacial defects and suppressing Li+ diffusion. Besides, the presence of 1,4‐dithiane can efficiently modulate interfacial energetics, enhance hydrophobicity of PSCs, and anchor Pb atoms via SPb bond. Consequently, the target devices perform better than control devices when exposed to light‐soaking, moisture, and thermal stress owing to the synergistic suppression of trap‐state density, ions migration, and moisture permeation. The optimized target device delivers a champion efficiency of 23.27% with mitigated Pb leakage. This study demonstrates a promising functionalized modification strategy for constructing efficient, stable, and eco‐friendly PSCs.
White Light and Color‐Tuning Long Persistent Luminescence from Metal Halide Based Metal‐Organic Frameworks
Authors: Wang Zheng , Mo Jun‐Ting , Pan Jun‐Jie , Pan Mei 
Published: February 2023

AbstractRoom temperature phosphorescence (RTP) materials with long persistent luminescence (LPL) have raised particular attention among researchers for their potential uses in chemical sensing, optical recording devices, biological imaging, and security systems applications, due to the long‐lived triplet states. In this study, one‐pot method of reaction of appropriate ratio of crown ether ligand (15‐Crown‐5) and metallic salts (CdX2) is utilized to yield three metal halide‐based complexes (namely 15‐5‐CdCl2, 15‐5‐CdBr2, and 15‐5‐CdI2). In solid state, three complexes exhibit nearly standard white light emission with CIE coordinates of (0.28, 0.32), (0.31, 0.39), (0.30, 0.34) at room temperature under UV radiation of 340 nm. Meanwhile, they display the excitation‐dependent room temperature phosphorescence from blue/cyan to green/yellow, especially, 15‐5‐CdCl2 and 15‐5‐CdBr2 exhibit color‐tunable and visible LPL with time‐resolved luminescence lifetime as high as 1–2 s. Single‐crystal X‐ray diffraction analysis and theoretical calculations reveal that the bright LPL of 15‐5‐CdCl2 and 15‐5‐CdBr2 arise from the crown ether ligand and aggregation state induced by halogen‐bond. The thus obtained LPL provides potentials in lighting and displaying devices, optical recording devices, security systems and so on.
A Self‐Powered, Rechargeable, and Wearable Hydrogel Patch for Wireless Gas Detection with Extraordinary Performance
Authors: Wu Zixuan , Wang Hao , Ding Qiongling , Tao Kai , Shi Wenxiong , Liu Chuan , Chen Jun , Wu Jin 
Published: February 2023

AbstractFlexible gas sensors play an indispensable role in diverse applications spanning from environmental monitoring to portable medical electronics. Full wearable gas monitoring system requires the collaborative support of high‐performance sensors and miniaturized circuit module, whereas the realization of low power consumption and sustainable measurement is challenging. Here, a self‐powered and reusable all‐in‐one NO2 sensor is proposed by structurally and functionally coupling the sensor to the battery, with ultrahigh sensitivity (1.92%/ppb), linearity (R2 = 0.999), ultralow theoretical detection limit (0.1 ppb), and humidity immunity. This can be attributed to the regulation of the gas reaction route at the molecular level. The addition of amphiphilic zinc trifluoromethanesulfonate (Zn(OTf)2) enables the H2O‐poor inner Helmholtz layer to be constructed at the electrode–gel interface, thereby facilitating the direct charge transfer process of NO2 here. The device is then combined with a well‐designed miniaturized low‐power circuit module with signal conditioning, processing and wireless transmission functions, which can be used as wearable electronics to realize early and remote warning of gas leakage. This study demonstrates a promising way to design a self‐powered, sustainable, and flexible gas sensor with high performance and its corresponding wireless sensing system, providing new insight into the all‐in‐one system of gas detection.
AIEgens/Mitochondria Nanohybrids as Bioactive Microwave Sensitizers for Non‐Thermal Microwave Cancer Therapy
Authors: Yu Xinghua , Lyu Ming , Ou Xupei , Liu Wenquan , Yang Xing , Ma Xiaoxi , Zhang Tianfu , Wang Longnan , Zhang Ying‐Chuan , Chen Sijie , Kwok Ryan T. K. , Zheng Zheng , Cui Hong‐Liang , Cai Lintao , Zhang Pengfei , Tang Ben Zhong 
Published: February 2023

AbstractAggregation‐induced emission luminogens (AIEgens) are widely used as photosensitizers for image‐guided photodynamic therapy (PDT). Due to the limited penetration depth of light in biological tissues, the treatments of deep‐seated tumors by visible‐light‐sensitized aggregation‐induced emission (AIE) photosensitizers are severely hampered. Microwave dynamic therapy attracts much attention because microwave irradiation can penetrate very deep tissues and sensitize the photosensitizers to generate reactive oxygen species (ROS). In this work, a mitochondrial‐targeting AIEgen (DCPy) is integrated with living mitochondria to form a bioactive AIE nanohybrid. This nanohybrid can not only generate ROS under microwave irradiation to induce apoptosis of deep‐seated cancer cells but also reprogram the metabolism pathway of cancer cells through retrieving oxidative phosphorylation (OXPHOS) instead of glycolysis to enhance the efficiency of microwave dynamic therapy. This work demonstrates an effective strategy to integrate synthetic AIEgens and natural living organelles, which would inspire more researchers to develop advanced bioactive nanohybrids for cancer synergistic therapy.
Biomimetic Bilayered Scaffolds for Tissue Engineering: From Current Design Strategies to Medical Applications
Authors: Bertsch Christelle , Maréchal Hélène , Gribova Varvara , Lévy Benjamin , Debry Christian , Lavalle Philippe , Fath Léa 
Published: February 2023

AbstractTissue damage due to cancer, congenital anomalies, and injuries needs new efficient treatments that allow tissue regeneration. In this context, tissue engineering shows a great potential to restore the native architecture and function of damaged tissues, by combining cells with specific scaffolds. Scaffolds made of natural and/or synthetic polymers and sometimes ceramics play a key role in guiding cell growth and formation of the new tissues. Monolayered scaffolds, which consist of uniform material structure, are reported as not being sufficient to mimic complex biological environment of the tissues. Osteochondral, cutaneous, vascular, and many other tissues all have multilayered structures, therefore multilayered scaffolds seem more advantageous to regenerate these tissues. In this review, recent advances in bilayered scaffolds design applied to regeneration of vascular, bone, cartilage, skin, periodontal, urinary bladder, and tracheal tissues are focused on. After a short introduction on tissue anatomy, composition and fabrication techniques of bilayered scaffolds are explained. Then, experimental results obtained in vitro and in vivo are described, and their limitations are given. Finally, difficulties in scaling up production of bilayer scaffolds and reaching the stage of clinical studies are discussed when multiple scaffold components are used.
Spin‐Controlled Helical Quantum Sieve Chiral Spectrometer
Authors: Maity Arnab , Hershkovitz‐Pollak Yael , Gupta Ritu , Wu Weiwei , Haick Hossam 
Published: February 2023

AbstractThis article reports on a molecular‐spin‐sensitive‐antenna (MSSA) that is based on stacked layers of organically functionalized graphene on a fibrous helical cellulose network for carrying out spatiotemporal identification of chiral enantiomers. The MSSA structures combine three complementary features: (i) chiral separation via a helical quantum sieve for chiral trapping, (ii) chiral recognition by a synthetically implanted spin‐sensitive center in a graphitic lattice; and (iii) chiral selectivity by a chirality‐induced‐spin mechanism that polarizes the local electronic band‐structure in graphene through chiral‐activated Rashba spin–orbit interaction field. Combining the MSSA structures with decision‐making principles based on neuromorphic artificial intelligence shows fast, portable, and wearable spectrometry for the detection and classification of pure and a mixture of chiral molecules, such as butanol (S and R), limonene (S and R), and xylene isomers, with 95–98% accuracy. These results can have a broad impact where the MSSA approach is central as a precautionary risk assessment against potential hazards impacting human health and the environment due to chiral molecules; furthermore, it acts as a dynamic monitoring tool of all parts of the chiral molecule life cycles.
The Emerging Layered Hydroxide Plates with Record Thickness for Enhanced High‐Mass‐Loading Energy Storage
Authors: Guo Wei , Dun Chaochao , Marcus Matthew A. , Venturi Victor , Gainsforth Zack , Yang Feipeng , Feng Xuefei , Viswanathan Venkatasubramanian , Urban Jeffrey J. , Yu Chang , Zhang Qiuyu , Guo Jinghua , Qiu Jieshan 
Published: February 2023

AbstractThe past decade has witnessed the development of layered‐hydroxide‐based self‐supporting electrodes, but the low active mass ratio impedes its all‐around energy‐storage applications. Herein, the intrinsic limit of layered hydroxides is broken by engineering F‐substituted β‐Ni(OH)2 (Ni–F–OH) plates with a sub‐micrometer thickness (over 700 nm), producing a superhigh mass loading of 29.8 mg cm−2 on the carbon substrate. Theoretical calculation and X‐ray absorption spectroscopy analysis demonstrate that Ni–F–OH shares the β‐Ni(OH)2‐like structure with slightly tuned lattice parameters. More interestingly, the synergy modulation of NH4+ and F− is found to serve as the key enabler to tailor these sub‐micrometer‐thickness 2D plates thanks to the modification effects on the (001) plane surface energy and local OH− concentration. Guided by this mechanism, the superstructures of bimetallic hydroxides and their derivatives are further developed, revealing they are a versatile family with great promise. The tailored ultrathick phosphide superstructure achieves a superhigh specific capacity of 7144 mC cm−2 and a superior rate capability (79% at 50 mA cm−2). This work highlights a multiscale understanding of how exceptional structure modulation happens in low‐dimensional layered materials. The as‐built unique methodology and mechanisms will boost the development of advanced materials to better meet future energy demands.
Interlayer‐Spacing Engineering of Lead‐Free Perovskite Single Crystal for High‐Performance X‐Ray Imaging
Authors: Chen Ming , Dong Xiaofeng , Chu Depeng , Jia Binxia , Zhang Xiaojie , Zhao Zeqin , Hao Jinglu , Zhang Yunxia , Feng Jiangshan , Ren Xiaodong , Liang Yuqian , Shi Ruixin , Najar Adel , Liu Yucheng , Liu Shengzhong (Frank) 
Published: February 2023

AbstractLead‐free A3Bi2I9‐type perovskites are demonstrated as a class of promising semiconductors for high‐performance X‐ray detection due to their high bulk resistivity and strong X‐ray absorption, as well as reduced ion migration. However, due to their long interlamellar distance along their c‐axis, their limited carrier transport along the vertical direction is a bottleneck for their detection sensitivity. Herein, a new A‐site cation of aminoguanidinium (AG) with all‐NH2 terminals is designed to shorten the interlayer spacing by forming more and stronger NH···I hydrogen bonds. The prepared large AG3Bi2I9 single crystals (SCs) render shorter interlamellar distance for a larger mobility‐lifetime product of 7.94 × 10−3 cm2 V−1, which is three times higher than the value measured on the best MA3Bi2I9 SC (2.87 × 10−3 cm2 V−1). Therefore, the X‐ray detectors fabricated on the AG3Bi2I9 SC exhibit high sensitivity of 5791 uC Gy−1 cm−2, a low detection limit of 2.6 nGy s−1, and a short response time of 690 µs, all of which are far better than those of the state‐of‐the‐art MA3Bi2I9 SC detectors. The combination of high sensitivity and high stability enables astonishingly high spatial resolution (8.7 lp mm−1) X‐ray imaging. This work will facilitate the development of low‐cost and high‐performance lead‐free X‐ray detectors.
Multiexciton Generation from a 2D Organic–Inorganic Hybrid Perovskite with Nearly 200% Quantum Yield of Red Phosphorescence
Authors: Wang Shuaiqi , Feng Shangwei , Li Renfu , Jin Jiance , Wu Junyan , Zheng Wei , Xia Zhiguo , Chen Xueyuan , Ling Qidan , Lin Zhenghuan 
Published: February 2023

Abstract2D organic–inorganic hybrid perovskites (OIHPs) show obvious advantages in the field of optoelectronics due to their high luminescent stability and good solution processability. However, the thermal quenching and self‐absorption of excitons caused by the strong interaction between the inorganic metal ions lead to a low luminescence efficiency of 2D perovskites. Herein, a 2D Cd‐based OIHP phenylammonium cadmium chloride (PACC) with a weak red phosphorescence (ΦP < 6%) at 620 nm and a blue afterglow is reported. Interestingly, the Mn‐doped PACC exhibits very strong red emission with nearly 200% quantum yield and 15 ms lifetime, thus resulting in a red afterglow. The experimental data prove that the doping of Mn2+ not only induces the multiexciton generation (MEG) process of the perovskite, avoiding the energy loss of inorganic excitons, but also promotes the Dexter energy transfer from organic triplet excitons to inorganic excitons, thus realizing the superefficient red‐light emission of Cd2+. This work suggests that guest metal ions can induce host metal ions to realize MEG in 2D bulk OIHPs, which provides a new idea for the development of optoelectronic materials and devices with ultrahigh energy utilization.
Energy‐Trapping Management in X‐Ray Storage Phosphors for Flexible 3D Imaging
Authors: Zhou Xinquan , Han Kai , Wang Yexin , Jin Jiance , Jiang Shangda , Zhang Qinyuan , Xia Zhiguo 
Published: February 2023

AbstractX‐ray imaging has received sustained attention for healthcare diagnostics and nondestructive inspection. To develop photonic materials with tunable photophysical properties in principle accelerates radiation detection technologies. Here the rational design and synthesis of doped halide perovskite CsCdCl3:Mn2+, R4+ (R = Ti, Zr, Hf, and Sn) are reported as next generation X‐ray storage phosphors, and the capability is greatly improved by trap management via Mn2+ site occupation manipulation and heterovalent substitution. Specially, CsCdCl3:Mn2+, Zr4+ displays zero‐thermal‐quenching (TQ) radioluminescence and anti‐TQ X‐ray‐activated persistent luminescence even up to 448 K, further revealing the charge‐carrier compensation and redeployment mechanisms. X‐ray imaging with the resolution of 12.5 lp mm−1 is demonstrated, and convenient 3D X‐ray imaging for the curved objects is realized in a time‐lapse manner. This work demonstrates efficient modulation of energy traps to achieve high storage capacities and promote future research into flexible X‐ray detectors.