bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pi-envelopes of Lie superalgebras
Authors: Bahturin Yuri , Montgomery Susan 
Published: July 2002

In this paper we find necessary and sufficient conditions on a finite-dimensional Lie superalgebra under which any associative PI-envelope of

L
L

is finite-dimensional. We also extend M. Scheunert’s result which enables one to pass from color Lie superalgebras to the ordinary ones, to the case of gradings by an arbitrary abelian group.
On the Well-Posedness of the Kirchhoff String
Authors: Arosio Alberto , Panizzi Stefano 
Published: July 2002

Let us consider the Cauchy problem for the quasilinear hyperbolic integro-differential equation

u

t
t

−
m

(

∫

∂

Ω

|

∇

x

u

|

2

d
x
)

δ

x

u
=
f
(
x
,
t
)

a
m
p
;

a
m
p
;

a
m
p
;
(
x
∈

Ω
,
t
>
0
)
,

u
(
⋅
,
t

)

|

∂
Ω

=
0

a
m
p
;

a
m
p
;

a
m
p
;
(
t
≥
0
)
,

\begin{align*} u_{tt} - m \left (\int _{_{\partial {\Omega }}} |\nabla _{x}u|^{2} \, dx \right ) \delta _{x}u= f(x,t) &&& (x\in \, \Omega , t > 0),\\ u(\cdot ,t)_{|\partial \Omega } =0 &&& (t\geq 0), \end{align*}

where

Ω
\Omega

is an open subset of

R

n

\mathbb {R}^{n}

and

m
m

is a positive function of one real variable which is continuously differentiable. We prove the well-posedness in the Hadamard sense (existence, uniqueness and continuous dependence of the local solution upon the initial data) in Sobolev spaces of low order.
SplitsTree: analyzing and visualizing evolutionary data.
Authors: Huson D H 
Published: July 2002

Abstract
MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.
MView: a web-compatible database search or multiple alignment viewer.
Authors: Brown N P , Leroy C , Sander C 
Published: July 2002

Abstract
SUMMARY: MView is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. AVAILABILITY: Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions. CONTACT: brown@ebi.ac.uk
MODELTEST: testing the model of DNA substitution.
Authors: Posada D , Crandall K A 
Published: July 2002

Abstract
SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
ESPript: analysis of multiple sequence alignments in PostScript.
Authors: Gouet P , Courcelle E , Stuart D I , M√©toz F 
Published: July 2002

Abstract
MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information. RESULTS: ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program. AVAILABILITY: ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.
Artemis: sequence visualization and annotation
Authors: Rutherford Kim , Parkhill Julian , Crook James , Horsnell Terry , Rice Peter , Rajandream Marie-Adèle , Barrell Bart 
Published: July 2002

Abstract
Summary: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format.
Availability: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis
Contact: kmr@sanger.ac.uk
CONSEL: for assessing the confidence of phylogenetic tree
selection
Authors: Shimodaira Hidetoshi , Hasegawa Masami 
Published: July 2002

Abstract
Summary: CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees. The main thrust of the program is to calculate the p-value of the Approximately Unbiased (AU) test using the multi-scale bootstrap technique. This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino–Hasegawa (KH) test, the Shimodaira–Hasegawa (SH) test, and the Weighted Shimodaira–Hasegawa (WSH) test. CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available.
Availability: The programs are written in C language. The source code for Unix and the executable binary for DOS are found at http://www.ism.ac.jp/~shimo/
Contact: shimo@ism.ac.jp
Analysis of genomic sequences by Chaos Game Representation
Authors: Almeida Jonas S. , Carriço João
   A. , Maretzek António , Noble Peter A. , Fletcher Madilyn 
Published: July 2002

Abstract
Motivation: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool.
Results: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA , thrB and thrC of the threonine operon.
Availability: A web page interface has been created where analyses of arbitrary sequences by CGR can be performed on-line (http://www.itqb.unl.pt:1111/biomat/resources/resources.htm). The test data-set used in this report is also included.
Contact: almeidaj@musc.edu; mfletcher@biol.sc.edu
Evaluation of methods for the prediction of membrane spanning
regions
Authors: Möller Steffen , Croning Michael D. R. , Apweiler Rolf 
Published: July 2002

Abstract
Motivation: A variety of tools are available to predict the topology of transmembrane proteins. To date no independent evaluation of the performance of these tools has been published. A better understanding of the strengths and weaknesses of the different tools would guide both the biologist and the bioinformatician to make better predictions of membrane protein topology.
Results: Here we present an evaluation of the performance of the currently best known and most widely used methods for the prediction of transmembrane regions in proteins. Our results show that TMHMM is currently the best performing transmembrane prediction program.
Contact: moeller@ebi.ac.uk; croning@ebi.ac.uk; apweiler@ebi.ac.uk
Support vector machine approach for protein subcellular
localization prediction
Authors: Hua Sujun , Sun Zhirong 
Published: July 2002

Abstract
Motivation: Subcellular localization is a key functional characteristic of proteins. A fully automatic and reliable prediction system for protein subcellular localization is needed, especially for the analysis of large-scale genome sequences.
Results: In this paper, Support Vector Machine has been introduced to predict the subcellular localization of proteins from their amino acid compositions. The total prediction accuracies reach 91.4% for three subcellular locations in prokaryotic organisms and 79.4% for four locations in eukaryotic organisms. Predictions by our approach are robust to errors in the protein N-terminal sequences. This new approach provides superior prediction performance compared with existing algorithms based on amino acid composition and can be a complementary method to other existing methods based on sorting signals.
Availability: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.
Contact: sunzhr@mail.tsinghua.edu.cn; huasj00@mails.tsinghua.edu.cn
Supplementary information: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.
* To whom correspondence should be addressed.
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster
Authors: Grant J. D. , Dunbrack R. L. , Manion F. J. , Ochs M. F. 
Published: July 2002

Abstract
Summary: BeoBLAST is an integrated software package that handles user requests and distributes BLAST and PSI-BLAST searches to nodes of a Beowulf cluster, thus providing a simple way to implement a scalable BLAST system on top of relatively inexpensive computer clusters. Additionally, BeoBLAST offers a number of novel search features through it's web interface, including the ability to perform simultaneous searches of multiple databases with multiple queries, and the ability to start a search using the PSSM generated from a previous PSI-BLAST search on a different database. The underlying system can also handle automated querying for high throughput work.
Availability: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/
Contact: jd_grant@fccc.edurl_dunbrack@fccc.edufj_manion@fccc.edum_ochs@fccc.edu
* To whom correspondence should be addressed.
Prosaposin treatment induces PC12 entry in the S phase of the cell cycle and prevents apoptosis: activation of ERKs and sphingosine kinase
Authors: MISASI ROBERTA , SORICE MAURIZIO , MARZIO LUISA DI , CAMPANA W. MARIE , MOLINARI SABRINA , CIFONE MARIA GRAZIA , PAVAN ANTONIO , PONTIERI GIUSEPPE M. , O’BRIEN JOHN S. 
Published: July 2002

ABSTRACTWe report that prosaposin treatment induced extracellular signal‐regulated kinases (ERKs) and sphingosine kinase activity, increased DNA synthesis, and prevented cell apoptosis. Prosaposin treatment induced pheochromocytoma cells (PC12) to enter the S phase of the cell cycle;this effect was inhibited by the MEK inhibitor PD98059, indicating that prosaposin‐induced ERK phosphorylation is required for stimulation of DNA synthesis. The prosaposin effect was also inhibited by pertussis toxin, indicating that the prosaposin receptor is a G‐protein‐coupled receptor. Prosaposin rescued PC12 cells from apoptosis induced by staurosporine or ceramide. Sphingosine kinase activity was increased by prosaposin treatment. We propose that this effect is a mechanism underlying the proliferative and anti‐apoptotic functions of prosaposin. Prosaposin appears to be a key regulatory factor in the ceramide‐S‐1‐P rheostat, which regulates cell fate.—Misasi, R., Sorice, M., Di Marzio, L., Campana, W. M., Molinari, S., Cifone, M. G., Pavan, A., Pontieri, G. M., O'Brien, J. S. Prosaposin treatment induces PC12 entry in the S phase of the cell cycle and prevents apoptosis: activation of ERKs and sphingosine kinase. FASEB J. 15, 467‐474 (2001)
The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience
Authors: Novére Nicolas Le , Changeux Jean-Pierre 
Published: July 2002

Multiple comparisons of receptor sequences, or receptor subunit sequences, has proved to be an invaluable tool in modern pharmacological investigations. Although of outstanding importance, general sequence databases suffer from several imperfections due to their size and their non–specificity. Room therefore exists for expert–maintained databases of restricted focus, where knowledge of the research field helps to filter the huge amount of data generated. Accordingly, neuroscientists have designed databases covering several types of proteins, in particular receptors for neurotransmitters.
Ligand–gated ion channels are oligomeric transmembrane proteins involved in the fast response to neurotransmitters. All these receptors are formed by the assembly of homologous subunits, and an unexpected wealth of genes coding for these subunits has been revealed during the last two decades. The Ligand Gated Ion Channel database (LGICdb) has been developed to handle this growing body of information. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences.
Shake‐up and shake‐off excitations with associated electron losses in X‐ray studies of proteins
Authors: Persson Petter , Lunell Sten , Szöke Abraham , Ziaja Beata , Hajdu Janos 
Published: July 2002

AbstractPhotoionization of an atom by X‐rays usually removes an inner shell electron from the atom, leaving behind a perturbed “hollow ion” whose relaxation may take different routes. In light elements, emission of an Auger electron is common. However, the energy and the total number of electrons released from the atom may be modulated by shake‐up and shake‐off effects. When the inner shell electron leaves, the outer shell electrons may find themselves in a state that is not an eigen‐state of the atom in its surroundings. The resulting collective excitation is called shake‐up. If this process also involves the release of low energy electrons from the outer shell, then the process is called shake‐off. It is not clear how significant shake‐up and shake‐off contributions are to the overall ionization of biological materials like proteins. In particular, the interaction between the outgoing electron and the remaining system depends on the chemical environment of the atom, which can be studied by quantum chemical methods. Here we present calculations on model compounds to represent the most common chemical environments in proteins. The results show that the shake‐up and shake‐off processes affect ∼20% of all emissions from nitrogen, 30% from carbon, 40% from oxygen, and 23% from sulfur. Triple and higher ionizations are rare for carbon, nitrogen, and oxygen, but are frequent for sulfur. The findings are relevant to the design of biological experiments at emerging X‐ray free‐electron lasers.
Lightweight Liquid Metal‐Elastomer Foam with Smart Multi‐Function
Authors: Yang Peng‐kun , Li Xin‐yang , Yang Xiao‐ying , Li Guan‐wu , Hu Zi‐juan , Huang Lu , Wu Ying‐peng 
Published: September 2022

AbstractLightweight metal‐polymer composited foam has drawn considerable attention in fields of wearable electronics, acoustic and electromagnetic shielding, automotive and aerospace manufacturing, owing to its unique advantages like electrical conductivity and mechanical properties. Herein, a facile strategy is studied for one‐step fabrication of multifunctional liquid metal (LM) permeated expancel microspheres foam (EMLM foam) with controllable shape and size. Specifically, the formation process and mechanism of bicontinuous structure with polymer and liquid metal are explored by real‐time monitoring and finite element simulation. Both experimental and simulating results confirmed a stable 3D metal interconnected network that can be constructed with lower limit of LM (3 vol.%). In addition, based on the unique features of reversible rigidity control, lightweight, electrical conductivity, and mechanical stability, the EMLM foam can exhibit intelligent performance in tunable acoustic, energy absorption, and thermal driving repair. Combined with EMLM foam's facile preparation process and versatility, it can provide the remarkable opportunity to develop the lightweight intelligent devices.
Wet‐Adhesive On‐Skin Sensors Based on Metal–Organic Frameworks for Wireless Monitoring of Metabolites in Sweat
Authors: Yang Xue , Yi Junqi , Wang Ting , Feng Yanan , Wang Jianwu , Yu Jing , Zhang Feilong , Jiang Zhi , Lv Zhisheng , Li Haicheng , Huang Tao , Si Duanhui , Wang Xiaoshi , Cao Rong , Chen Xiaodong 
Published: September 2022

AbstractMetal–organic frameworks (MOFs) with well‐defined porous structures and tailored functionalities have been widely used in chemical sensing. However, the integration of MOFs with flexible electronic devices for wearable sensing is challenging because of their low electrical conductivity and fragile mechanical properties. Herein, a wearable sweat sensor for metabolite detection is presented by integrating an electrically conductive Ni‐MOF with a flexible nanocellulose substrate. The MOF‐based layered film sensor with inherent conductivity, highly porous structure, and active catalytic properties enables the selective and accurate detection of vitamin C and uric acid. More importantly, the lightweight sensor can conformably self‐adhere to sweaty skin and exhibits high water‐vapor permeability. Furthermore, a wireless epidermal nutrition tracking system for the in situ monitoring of the dynamics of sweat vitamin C is demonstrated, the results of which are comparable to those tested by high‐performance liquid chromatography. This study opens a new avenue for integrating MOFs as the active layer in wearable electronic devices and holds promise for the future development of high‐performance electronics with enhanced sensing, energy production, and catalytic capabilities through the implementation of multifunctional MOFs.
Spatial Band Separation in a Surface Doped Heterolayered Structure for Realizing Efficient Singlet Oxygen Generation
Authors: Jin Sen , Shao Wei , Luo Xiao , Wang Hui , Sun Xianshun , He Xin , Zhang Xiaodong , Xie Yi 
Published: September 2022

AbstractSinglet oxygen (1O2) with electrical neutrality and long lifetime holds great promise in producing high‐added‐value chemicals via a selective oxidation reaction. However, photocatalytic 1O2 generation via the charge‐transfer mechanism still suffers from low efficiency due to the mismatched redox capacities and low concentration of photogenerated carriers in confined systems. Herein, by taking bismuth oxysilicate (Bi2O2SiO3) with alternating heterogeneous layered structure as a model, it is shown that iodine doping can facilitate the spatial redistributions of bands on alternated [Bi2O2] and [SiO3] layers, which can promote the separation and transfer of photogenerated charge carriers. Meanwhile, the band positions of Bi2O2SiO3 are optimized to match the redox potential of 1O2 generation. Benefiting from these features, iodine‐doped Bi2O2SiO3 exhibits efficient 1O2 generation with respect to its pristine counterpart, leading to promoted performance in the selective sulfide oxidation reaction. A new strategy is offered here for optimizing charge‐transfer‐mediated 1O2 generation.
Transition Metal Assisting Pre‐Lithiation Reduces the P/N Ratio to Balance the Energy Density and Cycle Life of Aqueous Batteries
Authors: Lv Tianshi , Zhu Xiangzhen , Lin Zejing , Suo Liumin 
Published: September 2022

AbstractAqueous Li‐ion batteries (ALIBs) are safe, environmentally friendly, and cost‐effective, promising for electric energy storage (EES). The high voltage ALIBs (HV‐ALIBs) supported by water‐in‐salt electrolytes are ideal for lowering the energy cost ($/Wh) of EES. However, HV‐ALIBs have been built with a high positive/negative capacity ratio (P/N ratio) to ensure their long‐term cycle life due to the irreversible Li consumption in the initial cycle induced by the solid electrolyte interface (SEI) formation and the parasitic reaction. Thus, the benefits of HV‐ALIBs in cost and energy density are mitigated inevitably. Generally, the feasible approach is adding per‐lithiation additives (PAs) to compensate for the capacity loss in the initial cycle. However, using PAs in ALIBs is challenging due to the high chemical activity of water. Here, a new strategy to achieve the pre‐lithiation by introducing manganese metal as a sacrificial PA for HV‐ALIBs that can provide over 900 mAh g−1 specific capacity without any adverse impact is proposed. The P/N ratio reduces to 1.02 by the LiMn2O4||TiO2 pouch cell using the sacrificial manganese PA. This results in a high initial energy density above 120 Wh kg−1 and outstanding cycle stability with a capacity retention of 80% after 400 cycles.
One‐Step Construction of a Polyporous and Zincophilic Interface for Stable Zinc Metal Anodes
Authors: Bie Zhe , Yang Qi , Cai Xinxin , Chen Ze , Jiao Zhaoyang , Zhu Junbo , Li Zhongfeng , Liu Jinzhang , Song Weixing , Zhi Chunyi 
Published: September 2022

AbstractThe development and application of rechargeable aqueous zinc‐ion batteries are seriously hindered by the problems of corrosion and dendrite growth on Zn metal anodes. Herein, a polyporous 3D zinc framework coupled with a zincophilic ZnSe overlayer (3D‐Zn@ZnSe) is synchronously obtained by one‐step electrochemical scanning, which precisely repairs intrinsic defects of the Zn foil surface and remodels the electrolyte/anode interface. The 3D‐Zn host formed by the pioneering electro‐oxidation significantly reduces the local current densities and facilitates adapting to the volume change during the plating/stripping. Meanwhile, the ZnSe overlayer obtained by electro‐deposition restrains the side reactions and promotes efficient desolvation, resulting in the acceleration of the deposition kinetics of Zn2+ on the zinc anode. As a result, the anodes present an enhanced cycling stability of zinc plating/stripping for over 2000 h with low overpotential, and the assembled 3D‐Zn@ZnSe||V2O5 cell retains 90.63% of its original capacity after 8500 cycles. The one‐step fabrication of polyporous interfaces with a zincophilic overlayer presents a promising strategy on improving the stability and reversibility of zinc anode for zinc‐based batteries.