bluuebunny/crossref_metadata_2025_split huggingface dataset:
PatternHunter: faster and more sensitive homology search
Authors: Ma Bin , Tromp John , Li Ming 
Published: July 2002

Abstract
Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation.
Results: We present a new homology search algorithm ‘PatternHunter’ that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop.
Availability: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.
Contact: mli@cs.ucsb.edu
Sequence complexity profiles of prokaryotic genomic
sequences: A fast algorithm for calculating linguistic
complexity
Authors: Troyanskaya Olga G. , Arbell Ora , Koren Yair , Landau Gad M. , Bolshoy Alexander 
Published: July 2002

Abstract
Motivation: One of the major features of genomic DNA sequences, distinguishing them from texts in most spoken or artificial languages, is their high repetitiveness. Variation in the repetitiveness of genomic texts reflects the presence and density of different biologically important messages. Thus, deviation from an expected number of repeats in both directions indicates a possible presence of a biological signal. Linguistic complexity corresponds to repetitiveness of a genomic text, and potential regulatory sites may be discovered through construction of typical patterns of complexity distribution.
Results: We developed software for fast calculation of linguistic sequence complexity of DNA sequences. Our program utilizes suffix trees to compute the number of subwords present in genomic sequences, thereby allowing calculation of linguistic complexity in time linear in genome size. The measure of linguistic complexity was applied to the complete genome of Haemophilus influenzae. Maps of complexity along the entire genome were obtained using sliding windows of 40, 100, and 2000 nucleotides. This approach provided an efficient way to detect simple sequence repeats in this genome. In addition, local profiles of complexity distribution around the starts of translation were constructed for 21 complete prokaryotic genomes. We hypothesize that complexity profiles correspond to evolutionary relationships between organisms. We found principal differences in profiles of the GC-rich and other (non-GC-rich) genomes. We also found characteristic differences in profiles of AT genomes, which probably reflect individual species variations in translational regulation.
Availability: The program is available upon request from Alexander Bolshoy or at http://csweb.haifa.ac.il/library/#complex
Contact: bolshoy@research.haifa.ac.il
* To whom correspondence should be addressed.
4 O.T. was a summer student at Haifa University. Her present address is Stanford Medical Informatics, Stanford University, CA 94305, USA.
Sequence‐structure analysis of FAD‐containing proteins
Authors: Dym Orly , Eisenberg David 
Published: July 2002

AbstractWe have analyzed structure‐sequence relationships in 32 families of flavin adenine dinucleotide (FAD)‐binding proteins, to prepare for genomic‐scale analyses of this family. Four different FAD‐family folds were identified, each containing at least two or more protein families. Three of these families, exemplified by glutathione reductase (GR), ferredoxin reductase (FR), and p‐cresol methylhydroxylase (PCMH) were previously defined, and a family represented by pyruvate oxidase (PO) is newly defined. For each of the families, several conserved sequence motifs have been characterized. Several newly recognized sequence motifs are reported here for the PO, GR, and PCMH families. Each FAD fold can be uniquely identified by the presence of distinctive conserved sequence motifs. We also analyzed cofactor properties, some of which are conserved within a family fold while others display variability. Among the conserved properties is cofactor directionality: in some FAD‐structural families, the adenine ring of the FAD points toward the FAD‐binding domain, whereas in others the isoalloxazine ring points toward this domain. In contrast, the FAD conformation and orientation are conserved in some families while in others it displays some variability. Nevertheless, there are clear correlations among the FAD‐family fold, the shape of the pocket, and the FAD conformation. Our general findings are as follows: (a) no single protein ‘pharmacophore’ exists for binding FAD; (b) in every FAD‐binding family, the pyrophosphate moiety binds to the most strongly conserved sequence motif, suggesting that pyrophosphate binding is a significant component of molecular recognition; and (c) sequence motifs can identify proteins that bind phosphate‐containing ligands.
Improved affinity of engineered streptavidin for the Strep‐tag II peptide is due to a fixed open conformation of the lid‐like loop at the binding site
Authors: Korndörfer Ingo P. , Skerra Arne 
Published: July 2002

AbstractThe Strep‐tag II is a nine‐amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants '1' and '2,' which had been engineered for 10‐fold higher affinity towards the Strep‐tag II. Both streptavidin mutants carry mutations at positions 44, 45, and 47, that is, in a flexible loop region close to the binding site. The crystal structures of the two apo‐proteins and their complexes with the Strep‐tag II peptide were refined at resolutions below 2 Å. Both in the presence and absence of the peptide, the lid‐like loop next to the ligand pocket—comprising residues 45 through 52—adopts an 'open' conformation in all four subunits within the asymmetric unit. The same loop was previously described to be disordered in the wild‐type apo‐streptavidin and to close over the pocket upon complexation of the natural ligand biotin. Our findings suggest that stabilization of the 'open' loop conformation in the absence of a ligand abolishes the need for conformational rearrangement prior to the docking of the voluminous peptide. Because no direct contacts between the flexible part of the loop and the peptide ligand were detected, it seems likely that the higher affinity of the two streptavidin mutants for the Strep‐tag II is caused by a predominantly entropic mechanism.
AeiA is a novel autophagy‐related protein that promotes peroxisome degradation by pexophagy in Aspergillus oryzae
Authors: Nishio Joichiro , Takahashi Yoshiaki , Kasahara Masahiro , Takeda Yoichi , Kikuma Takashi 
Published: January 2023

Autophagy is classified into nonselective and selective autophagy, depending on the specificity of substrate degradation. In the filamentous fungus Aspergillus oryzae, selective autophagy, which includes pexophagy and mitophagy, has been observed. However, the molecular mechanism underlying selective autophagy in filamentous fungi remains unclear. Here, we identified a novel protein that interacts with the autophagy‐related protein Atg8 in A. oryzae, named AoAtg8‐interacting protein A (AeiA). AeiA was localized to AoAtg8‐positive autophagic membrane structures and peroxisomes. Moreover, peroxisomal trafficking into the vacuole was reduced in AeiA disruptants. Taken together, AeiA is a novel selective autophagy‐related protein that contributes to pexophagy in A. oryzae.
Gamma passing rates of daily EPID transit images correlate to PTV coverage for breast cancer IMRT treatment plans
Authors: Sánchez‐Artuñedo David , Reyes López Victoria , Granado Carrasco Raquel , Beltran‐Vilagrasa Mercè , Duch‐Guillen Maria Amor , Hermida‐López Marcelino 
Published: January 2023

AbstractPurposeThe use of the transit image obtained with the electronic portal‐imaging device (EPID) is becoming an extended method to perform in‐vivo dosimetry. The transit images acquired during each fraction can be compared with a predicted image, if available, or with a baseline image, usually the obtained in the first fraction. This work aims to study the dosimetric impact of the failing fractions and to evaluate the appropriateness of using a baseline image in breast plans.Material and methodsTwenty breast patients treated in a Halcyon were retrospectively selected. For each patient and fraction, the treatment plan was calculated over the daily CBCT image. For each fraction, the differences respect to the treatment plan values of OARs and PTV dosimetric parameters were analyzed: ΔDmean, ΔD95%, ΔD98%, ΔD2%, ΔV36Gy, ΔV38.5Gy, and ΔV43.5Gy.Daily fractions were ranked according to the differences found in the dosimetric parameters between the treatment plan and the daily CBCT to establish the best fraction. The daily transit images acquired in every fraction were compared to the first fraction using the global gamma index with the Portal Dosimetry tool. The comparison was repeated using the best fraction image as a baseline.We assessed the correlation of the dosimetric differences obtained from the CBCT images‐based treatment plans with the gamma index passing rates obtained using first fraction and best fraction as baseline.ResultsAverage values of ‐11.6% [‐21.4%, ‐3.3%] and ‐3.2% [‐1.0%, ‐10.3%] for the ∆PTVD98% and ∆PTVD95% per every 10% decrease in the passing rate were found, respectively.When using the best fraction as baseline patients were detected with failing fractions that were not detected with the first fraction as baseline.ConclusionThe gamma passing rates of daily transit images correlate with the coverage loss parameters in breast IMRT plans. Using first fraction image as baseline can lead to the non‐detectability of failing fractions.
Computation of maximal output admissible sets for linear systems with polynomial constraints
Authors: Cotorruelo Andres , Garone Emanuele , Kolmanovsky Ilya V. , Ramirez Daniel R. , Limon Daniel 
Published: January 2023

AbstractIn this technical note we study the computation of the Maximal Output Admissible Set for linear systems subject to polynomial constraints. The computation of an inner approximation of the Maximal Output Admissible Sets requires the determination of constraint redundancy. We use a procedure to determine polynomial constraint redundancy based on a consequence of Putinar's Positivstellensatz. Further, we present a modification of the algorithm to compute the Maximal Output Admissible Set with improved performance. Lastly, demonstrate the potential for practical applications in two case studies of spacecraft rendezvous and control of an electromagnetic actuator.
Spring‐Like Ammonium Salt Assisting Stress Release for Low‐Temperature Deposited FAPbI3 Films Toward Flexible Photovoltaic Application
Authors: Chen Chun‐Hao , Hu Fan , Su Zhen‐Huang , Yu Yan‐Jun , Wang Kai‐Li , Shi Yi‐Ran , Chen Jing , Xia Yu , Gao Xing‐Yu , Wang Zhao‐Kui , Liao Liang‐Sheng 
Published: January 2023

AbstractThe substrates of conventional flexible perovskite solar cells (FPSCs) are thermoplastic polymer material polyethylene naphthalate (PEN), which will deform during high temperature annealing process. In addition, lead iodide (PbI2) permanently formed and the substrate undergoes reversible deformation from 20 °C to 200 °C and back to 20 °C. Therefore, to balance the substrate supporting capacity and the crystalline quality of narrow band gap α‐phase formamidinium lead iodide (α‐FAPbI3), an annealing process of 120 °C for 30 minutes is determined. Additionally, there will also be a large number of gaps and lattice strain at the perovskite grain boundaries during the annealing process as the FAPbI3 phase transition is accompanied by much lattice shrinkage. As a result, 1,6‐hexanediammonium diiodide (HADI) is chosen to passivate the defects and release the stress of perovskite film. Therefore, a recorded 1.4% extended stretch rate of the flexible film is attained. Finally, the champion PCE of 21.14% under AM 1.5G and 31.52% under 1062 lux is achieved after HADI treatment, accompanied by a better long‐term and mechanical stability. This study provides annealing process optimization and stress relief strategies for the further development of narrow band gap FPSCs.
Molecular Engineering of Cyclic Azobenzene‐Peptide Hybrid Ligands for the Purification of Human Blood Factor VIII via Photo‐Affinity Chromatography
Authors: Prodromou Raphael , Moore Brandyn David , Chu Wenning , Deal Halston , San Miguel Adriana , Brown Ashley Carson , Daniele Michael Angelo‐Anthony , Pozdin Vladimir Aleksandrovich , Menegatti Stefano 
Published: January 2023

AbstractThe use of benign stimuli to control the binding and release of labile biologics for their isolation from complex feedstocks is a key goal of modern biopharmaceutical technology. This study introduces cyclic azobenzene‐peptide (CAP) ligands for the rapid and discrete photo‐responsive capture and release of blood coagulation factor VIII (FVIII). A predictive method—based on amino acid sequence and molecular architecture of CAPs—is developed to correlate the conformation of cis/trans‐CAP photo‐isomers to FVIII binding and release. Combined in silico ‐ in vitro analysis of FVIII:peptide interactions guide the design of a rational approach to optimize isomerization kinetics and biorecognition of CAPs. A photoaffinity adsorbent, prepared by conjugating selected CAP G‐cycloAZOB[Lys‐YYKHLYN‐Lys]‐G on translucent chromatographic beads, features high binding capacity (>6 mg of FVIII per mL of resin) and rapid photo‐isomerization kinetics (τ < 30 s) when exposed to 420–450 nm light at the intensity of 0.1 W cm−2. The adsorbent purifies FVIII from a recombinant harvest using a single mobile phase, affording high product yield (>90%), purity (>95%), and blood clotting activity. The CAPs introduced in this report demonstrate a novel route integrating gentle operational conditions in a rapid and efficient bioprocess for the purification of life‐saving biotherapeutics.
Mapping the Three‐Dimensional Nanostructure of the Ionic Liquid–Solid Interface Using Atomic Force Microscopy and Molecular Dynamics Simulations
Authors: Elbourne Aaron , Dupont Madeleine , Kariuki Rashad , Meftahi Nastaran , Daeneke Torben , Greaves Tamar L. , McConville Christopher F. , Bryant Gary , Bryant Saffron J. , Besford Quinn A. , Christofferson Andrew J. 
Published: January 2023

AbstractIonic liquids (ILs) are a widely investigated class of solvents for scientific and industrial applications due to their desirable and “tunable” properties. The IL–solid interface is a complex entity, and despite intensive investigation, its true nature remains elusive. The understanding of the IL–solid interface has evolved over the last decade from a simple 1D double layer, to a 2D ordered interface, and finally a liquid‐specific, complex 3D ordered liquid interface. However, most studies depend solely on one technique, which often only examine one aspect of the interfacial nanostructure. Here, a holistic study of the protic IL–solid interface is presented, which provides a more detailed picture of IL interfacial solvation. The 3D nanostructure of the ethylammonium nitrate (EAN)–mica interface is investigated using a combination of 1D, 2D, and 3D amplitude modulated‐atomic force microscopy and molecular dynamics simulations. Importantly, it is found that the EAN–mica interface is more complex than previously reported, possessing surface‐adsorbed, near‐surface, surface‐normal, and lateral heterogeneity, which propagates at relatively large distances from the solid substrate. The work presented in this study meaningfully enhances the understanding of the IL–solid interface.
Independent Manipulation of Aperture and Radiation Fields in a Transmission‐Reflection Integrated Complex‐Amplitude Metasurface
Authors: Li Zhenfei , Zhang Jin , Liu Ji , Liu Longhai , Wang Xiong , Premaratne Malin , Yao Jianquan , Zhu Weiren 
Published: January 2023

AbstractMetasurfaces have superior performance in flexible wave manipulation used for various multifunctional devices. However, they remain challenging for the completely spatial manipulation of electromagnetic waves including wave propagation direction and distance degrees of freedom. Here, a novel strategy of multiplexing metasurface with a non‐interleaved meta‐atoms array is introduced. The design fully explores wave propagation direction and distance degrees of freedom by combining irregular complex‐amplitude encoding method and transmission‐reflection selective meta‐atom. Therein, by limiting effective meta‐atoms to a specific geometry and encoding highly selective phase sequences for wavefront shaping to these meta‐atoms, the distance multiplexing properties of aperture and radiation fields can be designed to suit application needs. Also, the transmission‐reflection integrated meta‐atoms is further engineered to increase the propagation direction degrees of freedom in electromagnetic manipulation. As proof of concept, a six‐channel metasurface operating in one transmitted mode and two reflected modes are experimentally generated, enabling us to reconstruct an aperture‐field printing image and a radiation‐field holographic image for each mode simultaneously. This strategy may have an alternative route for potential applications such as data storage, image encryption, and information communication systems.
Breathable Encapsulated Liquid Metal Foam‐Based Soft Stress Sensor
Authors: Xu Jin , Wang Zhimin , Wang Xinxin , Wu Yali , Xing Ruizhe , Yu Tingting , Li Yang , Ao Jinping , Tao Yebo , Bai Bowen , Dickey Michael D. , Zhang Dongguang , Yang Jiayi 
Published: January 2023

AbstractLiquid metal (LM)‐based soft and wearable sensors have great potential for applications in human motion monitoring and human‐machine interfaces. To avoid smearing of exposed LM, it is necessary to encapsulate LM with elastomers, which decreases the breathability and results in discomfort and even skin irritation. To solve this problem, this work proposes a breathable encapsulated LM foam (BELMF)‐based soft stress sensor. By using two polydimethylsiloxane foam layers, the BELMF‐based sensor achieves non‐smearing and breathability. Meanwhile, a three‐dimensional electrode is designed to implement the electric connection without decreasing breathability. Appling stress to the BELMF‐based sensor makes the LM foam collapse and forms new conductive paths, which reduces the resistance of the sensor. The sensitivity of the BELMF‐based sensor can reach 1.4 Pa−1. The mechanisms of the breathable encapsulation and the sensor are investigated through experiments and simulations. In addition, the potential applications of the BELMF‐based sensor for monitoring human motion are demonstrated.
Soft Ball‐Based Triboelectric–Electromagnetic Hybrid Nanogenerators for Wave Energy Harvesting
Authors: Pang Yaokun , Fang Yuhui , Su Jiaji , Wang Huigang , Tan Yeqiang , Cao Changyong (Chase) 
Published: January 2023

AbstractTriboelectric nanogenerator (TENG) provides a new cost‐effective strategy to harvest water wave energy due to the broad options of triboelectric materials and the high efficiency in low‐frequency energy harvesting. Here, a new triboelectric–electromagnetic hybrid nanogenerator (TEHG) consisting of a soft ball‐based triboelectric nanogenerator (SB‐TENG) and an electromagnetic generator (EMG) is reported for harvesting wave energy. The soft balls are utilized as one triboelectric layer to increase the contact area with the copper electrodes. The critical parameters that may affect the energy harvesting performance of the SB‐TENG are investigated, including the type of the filled liquids, the thickness of the silicone shell, the number of layers, and the added soft balls. Under an operating frequency of 1 Hz, the SB‐TENG and the EMG can reach a maximum output peak power of 0.5 and 8.5 mW, respectively. The TEHG has been demonstrated to power dozens of light‐emitting diodes and drives a digital temperature sensor to monitor the water temperature for an extended period. This study provides a new design and approach to improve the output performance of TENGs and presents an excellent prospect for building a self‐powered water‐sensing system driven by low‐frequency water waves.
Highly Reliable Physical Bending Sensors using Heterostructured Floating Gate Organic Transistor
Authors: Seo Jungyoon , Choi Giheon , Hwang Taehoon , Han Songyeon , Kim Youngjin , Choi Hyun Ho , Lee Hwa Sung 
Published: January 2023

AbstractHerein, a piezovoltage‐modulated field‐effect transistor (PVMFET) is proposed that provides physical sensing capabilities while maintaining excellent FET performance through the combination of a piezovoltage (PV) capacitor sensing medium and an FET structure that can amplify signal responses to external stimuli. The PV generated in the piezoelectric poly(vinylidene fluoride)‐co‐trifluoroethylene‐based PV capacitor through bending deformation modulates the effective gate voltage induced in the PV‐modulated gate. In particular, in the device, it is found that the piezo‐responsive modulation of the effective gate electric field is enhanced by the applied gate voltage, corresponding to the higher modulation of channel current at the higher gate voltage under bending. Accordingly, a PVMFET‐based physical sensor that can accurately estimate the bending angle is implemented. The sensor exhibits a high sensitivity, repeatability, and a sensing linearity of 0.98 while the bending angle is varied from 0° to 93°. The sensing performance remains constant even when the bending frequency changed from 0.25 to 1.0 Hz at the largest bending angle (93°) measured, confirming the effectiveness of the sensor platform. The proposed PVMFET‐based physical sensor platform is suitable for applications that require stable driving performance and the simultaneous detection of external physical stimuli in real time.
Recent Development and Applications of Sensors for the Detection of Matrix Metalloproteinases
Authors: Zhang Huayue , Wu Miaomiao , Ta Hang Thu , Xu Zhi Ping , Zhang Run 
Published: January 2023

AbstractMatrix metalloproteinases (MMPs) are a class of zinc‐dependent endopeptidases that play important roles in disease progression. High expression of MMPs is associated with various diseases, including cancer, cardiovascular diseases, neurological diseases, and inflammatory diseases. For better understanding the roles of MMPs in these diseases’ development and the potential in early diagnosis and treatment monitoring, a number of sensors have recently been developed for MMPs detection in vitro and in vivo. These sensors are designed mainly based on the exploration of MMPs’ molecular structure and enzymatic activity. This review seeks to provide a summary for the development and application of the sensors for the detection of MMPs in the past three years. The research hotspots, current challenges, and further research directions in this field are also discussed.