bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMPALA: matching a protein sequence against a collection of
PSI-BLAST-constructed position-specific score matrices
Authors: A.Schäffer Alejandro , I.Wolf Yuri , P.Ponting Chris , V.Koonin Eugene , Aravind L. , F.Altschul Stephen 
Published: July 2002

Abstract
Motivation: Many studies have shown that database searches using position-specific score matrices (PSSMs) or profiles as queries are more effective at identifying distant protein relationships than are searches that use simple sequences as queries. One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST).
Results: This paper describes a new software package, IMPALA, designed for the complementary procedure of comparing a single query sequence with a database of PSI-BLAST-generated PSSMs. We illustrate the use of IMPALA to search a database of PSSMs for protein folds, and one for protein domains involved in signal transduction. IMPALA’s sensitivity to distant biological relationships is very similar to that of PSI-BLAST. However, IMPALA employs a more refined analysis of statistical significance and, unlike PSI-BLAST, guarantees the output of the optimal local alignment by using the rigorous Smith–Waterman algorithm. Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database.
Availability: The IMPALA source code, the wolf1187 database, and the aravind105 database are freely available from the NCBI ftp site ncbi.nlm.nih.gov. The databases may be found in the subdirectory ftp://ncbi.nlm.nih.gov/pub/impala. The source code is in ftp://ncbi.nlm.nih.gov/toolbox/ncbi˙tools. Some IMPALA executables for different implementations of UNIX are in ftp://ncbi.nlm.nih.gov/blast/executables. IMPALA has been added as a search option on the Blocks Database Server (http://blocks.fhcrc.org/blocks/impala.html)using a library of PSSMs derived from the BLOCKS database.
Contact: schaffer@helix.nih.gov
The hydrophobic cores of proteins predicted by wavelet analysis.
Authors: Hirakawa H , Muta S , Kuhara S 
Published: July 2002

Abstract
MOTIVATION: In the process of protein construction, buried hydrophobic residues tend to assemble in a core of a protein. Methods used to predict these cores involve use or no use of sequential alignment. In the case of a close homology, prediction was more accurate if sequential alignment was used. If the homology was weak, predictions would be unreliable. A hydrophobicity plot involving the hydropathy index is useful for purposes of prediction, and smoothing is essential. However, the proposed methods are insufficient. We attempted to predict hydrophobic cores with a low frequency extracted from the hydrophobicity plot, using wavelet analysis. RESULTS: The cores were predicted at a rate of 68.7%, by cross-validation. Using wavelet analysis, the cores of non-homologous proteins can be predicted with close to 70% accuracy, without sequential alignment. AVAILABILITY: The program used in this study is available from Intergalactic Reality (http://www.intergalact.com). CONTACT: hirakawa@grt.kyushu-u.ac.jp, kuhara@grt.kyushu-u.ac.jp
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Authors: Morgenstern B 
Published: July 2002

Abstract
MOTIVATION: The performance and time complexity of an improved version of the segment-to-segment approach to multiple sequence alignment is discussed. In this approach, alignments are composed from gap-free segment pairs, and the score of an alignment is defined as the sum of so-called weights of these segment pairs. RESULTS: A modification of the weight function used in the original version of the alignment program DIALIGN has two important advantages: it can be applied to both globally and locally related sequence sets, and the running time of the program is considerably improved. The time complexity of the algorithm is discussed theoretically, and the program running time is reported for various test examples. AVAILABILITY: The program is available on-line at the Bielefeld University Bioinformatics Server (BiBiServ) http://bibiserv.TechFak.Uni-Bielefeld.DE/dial ign/
Conformational and physicochemical DNA features specific for transcription factor binding sites.
Authors: Ponomarenko J V , Ponomarenko M P , Frolov A S , Vorobyev D G , Overton G C , Kolchanov N A 
Published: July 2002

Abstract
MOTIVATION: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental data make evident an important role of DNA conformational features for site functioning. However, Internet-available tools for revealing conformational and physicochemical DNA features significant for the site functioning and subsequent use of these features for site recognition have not been developed up to now. RESULTS: We suggest an approach for revealing significant conformational and physicochemical properties of functional sites implemented in the database B-DNA-VIDEO. This database is designed to study the sets of various transcription factor binding sites, providing evidence that transcription factor binding sites are characterized by specific sets of significant conformational and physicochemical DNA properties. For a fixed site, by using the B-DNA features selected for this site recognition, the C-program recognizing this site may be generated, control tested and stored in the database B-DNA-VIDEO. Each B-DNA-VIDEO entry links to the Web-applet recognizing the site, whose significant B-DNA features are stored in this entry as the 'site recognition programs'. The pairwise linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and the program tools package applicable immediately for recognizing the sites stored in the database. Indeed, this is the novelty. Hence, B-DNA-VIDEO is the Web resource of both 'searching for static data' and 'active computation' type, that is why it was called an 'activated database'. AVAILABILITY: B-DNA-VIDEO is available at http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/ and the mirror site at http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.
Domain size distributions can predict domain boundaries
Authors: Wheelan S. J. , Marchler-Bauer A. , Bryant S. H. 
Published: July 2002

Abstract
Motivation: The sizes of protein domains observed in the 3D-structure database follow a surprisingly narrow distribution. Structural domains are furthermore formed from a single-chain continuous segment in over 80% of instances. These observations imply that some choices of domain boundaries on an otherwise uncharacterized sequence are more likely than others, based solely on the size and segment number of predicted domains. This property might be used to guess the locations of protein domain boundaries.
Results: To test this possibility we enumerate putative domain boundaries and calculate their relative likelihood under a probability model that considers only the size and segment number of predicted domains. We ask, in a cross-validated test using sequences with known 3D structure, whether the most likely guesses agree with the observed domain structure. We find that domain boundary predictions are surprisingly successful for sequences up to 400 residues long and that guessing domain boundaries in this way can improve the sensitivity of threading analysis.
Availability: The DGS algorithm, for ‘Domain Guess by Size’, is available as a web service at http://www.ncbi.nlm.nih.gov/dgs. This site also provides the DGS source code.
Contact: bryant@ncbi.nlm.nih.gov
* To whom correspondence should be addressed.
Use of keyword hierarchies to interpret gene expression

patterns
Authors: Masys Daniel R. , Welsh John B. , Lynn Fink J. , Gribskov Michael , Klacansky Igor , Corbeil Jacques 
Published: July 2002

Abstract
Motivation: High-density microarray technology permits the quantitative and simultaneous monitoring of thousands of genes. The interpretation challenge is to extract relevant information from this large amount of data. A growing variety of statistical analysis approaches are available to identify clusters of genes that share common expression characteristics, but provide no information regarding the biological similarities of genes within clusters. The published literature provides a potential source of information to assist in interpretation of clustering results.
Results: We describe a data mining method that uses indexing terms (‘keywords’) from the published literature linked to specific genes to present a view of the conceptual similarity of genes within a cluster or group of interest. The method takes advantage of the hierarchical nature of Medical Subject Headings used to index citations in the MEDLINE database, and the registry numbers applied to enzymes.
Availability: We have created a publicly accessible website that provides this form of gene expression interpretation at http://www.array.ucsd.edu.
Contact: dmasys@ucsd.edu
8 To whom correspondence should be addressed at: University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0602, USA.
7 Present address: Genomics Institute of the Novartis Research Foundation, 3115 Merryfield Row, San Diego, CA 92121, USA.
Antibiotic dosing issues in lower respiratory tract infection: population-derived area under inhibitory curve is predictive of efficacy
Authors: Highet Vicki Sue , Forrest Alan , Ballow Charles H. , Schentag Jerome J. 
Published: July 2002

Abstract
Several lower respiratory tract infection (LRTI) trials have documented a correlation between clinical response and area under the inhibitory curve (24 h AUC/MIC; AUIC). The AUIC values in these studies were based on measured MICs and measured serum concentrations. This study evaluates AUIC estimates made using population pharmacokinetic parameters, and MICs from an automated microbiological susceptibility testing system. A computer database review over 2 years yielded 81 patients at Millard Fillmore Hospital with a culture-documented Gram-negative LRTI who had been treated with piperacillin and an aminoglycoside, ceftazidime, ciprofloxacin or imipenem. Their AUIC values were estimated using renal function, drug dosages and MIC values. Outcome groups (clinical and microbiological cures and failures) were related to the AUIC values using Kruskal–Wallis ANOVA, linear regression and classification and regression tree (CART) analysis. A significant breakpoint for clinical cures was an AUIC value at least 72 SIT −1⋅24 h (inverse serum inhibitory titre integrated over time). All antibiotics performed significantly better above this value than below it. Clinical cure was well described by a Hill-type equation. Within the piperacillin/aminoglycoside regimen, most of the activity came from the piperacillin, which had a higher overall AUIC value than the aminoglycoside. AUIC estimations based upon MIC values derived from the automated susceptibility testing method differed from NCCLS breakpoint data and from tube dilution derived values in this hospital by as much as three tube dilutions. These automated methods probably overestimated the MIC values of extremely susceptible organisms. The lack of precise MIC estimates in automated clinical microbiology methods impairs the use of AUIC to prospectively optimize microbiological outcome. Even ignoring this limitation and using the values as they are reported, the results of this analysis suggest that AUIC targets between 72 and 275 SIT −1⋅24 h are useful in predicting clinical outcome.
Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study
Authors: Amara Patricia , Andreoletti Pierre , Jouve HéLène Marie , Field Martin J. 
Published: July 2002

AbstractThe role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 →1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X‐ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H2O and O2 are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol−1 for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface.
Real-time Analysis of Skin Biopsy Specimens With 2-Photon Fluorescence Microscopy
Authors: Ching-Roa Vincent D. , Huang Chi Z. , Ibrahim Sherrif F. , Smoller Bruce R. , Giacomelli Michael G. 
Published: September 2022

ImportanceNonmelanoma skin cancers (NMSCs) are primarily diagnosed through paraffin section histologic analysis of skin biopsy specimens that requires days to weeks before a formal diagnosis is reported. Two-photon fluorescence microscopy (TPFM) has the potential for point-of-care diagnosis of NMSC and other dermatologic conditions, which could enable same-visit diagnosis and treatment.ObjectiveTo demonstrate that TPFM imaging of NMSC can occur within minutes of obtaining biopsies and provide similar histological features to those of conventional histology and evaluate TPFM diagnostic performance with respect to conventional histology.Design, Setting, and ParticipantsThis comparative effectiveness pilot study examined 29 freshly excised biopsies from confirmed NMSC lesions in patients presenting for treatment. Biopsies underwent imaging immediately with TPFM on site at Rochester Dermatologic Surgery (Victor, New York) between October 2019 and August 2021. The imaged biopsies were subsequently submitted for paraffin histology to produce coregistered images. Twelve of these coregistered image pairs (41.4%) were used as a training set. Fifteen (51.7%) were used in a masked evaluation by a board-certified dermatopathologist. Two (6.9%) were excluded from the study before evaluation because they could not be coregistered.Main Outcomes and MeasuresSensitivity, specificity, and accuracy of TPFM for NMSC biopsies were evaluated compared with conventional histology.ResultsFourteen of the 15 biopsy specimens (93.3%) in the evaluation set were identically diagnosed with TPFM and paraffin histology. The TPFM had 100% sensitivity (95% CI, 48%-100%), 100% specificity (95% CI, 69%-100%), and 100% accuracy (95% CI, 78%-100%) for basal cell carcinoma diagnosis. For squamous cell carcinoma diagnosis, TPFM had 89% sensitivity (95% CI, 52%-100), 100% specificity (95% CI, 54%-100%), and 93% accuracy (95% CI, 68%-100%). For overall NMSC diagnosis, TPFM had a 93% sensitivity (95% CI, 66%-100%), 100% specificity (95% CI, 3%-100%), and 93% accuracy (95% CI, 68%-100%). Examination of the 1 discordant pair revealed mismatched imaging planes as the source of error.Conclusions and RelevanceThe results of this comparative effectiveness pilot study suggest that TPFM captures histological characteristics of NMSC that are present in conventional histology, which reveals its potential as a rapid, point-of-care diagnostic alternative that does not need extensive sample preparation or retraining for image evaluation. Further validation of TPFM imaging performed for a larger cohort is needed to fully evaluate its diagnostic accuracy and potential effect within the field.
Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States
Authors: Zhao Lue Ping , Lybrand Terry P. , Gilbert Peter , Madeleine Margaret , Payne Thomas H. , Cohen Seth , Geraghty Daniel E. , Jerome Keith R. , Corey Lawrence 
Published: September 2022

ImportanceWith timely collection of SARS-CoV-2 viral genome sequences, it is important to apply efficient data analytics to detect emerging variants at the earliest time.ObjectiveTo evaluate the application of a statistical learning strategy (SLS) to improve early detection of novel SARS-CoV-2 variants using viral sequence data from global surveillance.Design, Setting, and ParticipantsThis case series applied an SLS to viral genomic sequence data collected from 63 686 individuals in Africa and 531 827 individuals in the United States with SARS-CoV-2. Data were collected from January 1, 2020, to December 28, 2021.Main Outcomes and MeasuresThe outcome was an indicator of Omicron variant derived from viral sequences. Centering on a temporally collected outcome, the SLS used the generalized additive model to estimate locally averaged Omicron caseload percentages (OCPs) over time to characterize Omicron expansion and to estimate when OCP exceeded 10%, 25%, 50%, and 75% of the caseload. Additionally, an unsupervised learning technique was applied to visualize Omicron expansions, and temporal and spatial distributions of Omicron cases were investigated.ResultsIn total, there were 2698 cases of Omicron in Africa and 12 141 in the United States. The SLS found that Omicron was detectable in South Africa as early as December 31, 2020. With 10% OCP as a threshold, it may have been possible to declare Omicron a variant of concern as early as November 4, 2021, in South Africa. In the United States, the application of SLS suggested that the first case was detectable on November 21, 2021.Conclusions and RelevanceThe application of SLS demonstrates how the Omicron variant may have emerged and expanded in Africa and the United States. Earlier detection could help the global effort in disease prevention and control. To optimize early detection, efficient data analytics, such as SLS, could assist in the rapid identification of new variants as soon as they emerge, with or without lineages designated, using viral sequence data from global surveillance.
Engineering the Framework Cobalt and Hierarchical Pores of Aluminophosphates for Enhanced Performance in n‐Butene Skeletal Isomerization
Authors: Li Jianjun , Chen Wenhan , Wang Haolin , Guo Lili , Zhang Nuowei , Zheng Jinbao , Fu Jile , Nitani Hiroaki , Chen Binghui 
Published: September 2022

AbstractAn effective method is proposed to synthesize a hierarchical Co‐doped AlPO4 molecular sieve (CoAIP‐CTAB). For the obtained zeolite, both framework and extra framework Co are firstly established and identified by X‐ray absorption fine structure (XAFS). The percentage of framework Co (P–O–Co–O–P) is estimated to be 82%. Due to the hierarchical structure and abundant Co sites in the framework, CoAIP‐CTAB nanocrystals have shown high catalytic activity and stability for the catalytic conversion of n‐butenes to isobutene at mild temperature (350 °C) without gas dilution. This novel synthesis strategy may inspire the design of similar types of industrial zeolite catalysts for selective reactions.
High Aspect‐ratio Germanium‐Tin Alloy Nanowires: Potential as Highly Efficient Li‐Ion Battery Anodes
Authors: Garcia‐Gil Adrià , Biswas Subhajit , McNulty David , Roy Ahin , Ryan Kevin M. , Nicolosi Valeria , Holmes Justin D. 
Published: September 2022

AbstractHere, the fabrication of a high aspect ratio (>440) Ge1−xSnx nanowires with super‐thin (≈9 nm) diameter, much below the Bohr radius, using a simple solvothermal‐like growth method under supercritical toluene conditions at a reaction temperature of 440 °C is reported. Ge1−xSnx nanowires are grown with varying amounts of Sn in Ge lattice, between 3.1 to 10.2 at%. The growth of the Ge1−xSnx alloy nanowires is achieved without any additional catalysts, and directly on current collector substrates (titanium) for application as Li‐ion battery anodes. The electrochemical performance of the binder‐free Ge1−xSnx nanowires as an anode material for Li‐ion batteries is investigated via galvanostatic cycling and detailed analysis of differential capacity plots. The dimensions of the nanowires, and the amount of Sn in Ge, are critical to achieving a high specific capacity and capacity retention. Ge1−xSnx nanowires with the highest aspect ratios and with the lowest Sn content (3.1 at%) demonstrate exceptional capacity retention of ≈90% and 86% from the 10th to the 100th and 150th cycles respectively, while maintaining a very high specific capacity value of 1176 and 1127 mAh g−1 after the 100 and 150 cycles respectively.
Fe3O4 Nanoparticles Enhanced Amorphous Ferric Silicate/Reduced Graphene Oxide for High‐Performance Lithium‐Ion Storage
Authors: Li Huan , Tang Chunjuan , An Xiuyun , Li Jili , Min Zhiyu , Wang Fang , Liang Chaoxi , Wang Changqing , Han Dongfeng , Liu Jia 
Published: September 2022

AbstractFerric silicate (FS) has been explored as a potential lithium ion batteries candidate for its environment benign, low cost, rich reserves, and high capacity. Despite these advantages, poor electronic conductivity and large volume variation obstruct its practical utilization. To improve its electrochemical performance, a unique hybrid structure with Fe3O4@ferric silicate nanosheets anchored on the reduced graphene oxide (FO@FS/RGO) is fabricated. The disordered amorphous nanosheet structure of FS not only shortens the transferred length for lithium ions but also facilities the Li+ diffusion and can effectively keep the structure integrity. RGO substrate ameliorates the electronic conductivity and slackens the strain upon cycling. Fe3O4 (FO) nanoparticles embedded in FS further boost the electronic conductivity and the lithium storage capability. The synergistic effects bestow the composite superior electrochemical properties. FO@FS/RGO shows high reversible capacity of 1113 mA h g−1 at 0.2 A g−1, an excellent rate performance of 681 mA h g−1 at 2 A g−1, and a splendid cycling stability with a capacity of 859 mA h g−1 at 1 A g−1 after 800 cycles.
Efficient Semitransparent Perovskite Solar Cells Based on Thin Compact Vacuum Deposited CH3NH3PbI3 Films
Authors: Paliwal Abhyuday , Mardegan Lorenzo , Roldan‐Carmona Cristina , Palazon Francisco , Liu Ting‐Yu , Bolink Henk J. 
Published: September 2022

AbstractLead halide perovskite materials are promising candidates for the application of semitransparent solar cells due to their bandgap tunability and high device efficiencies. The high absorption coefficient of these materials, however, makes it difficult to attain high average visible transmittance values without compromising the power conversion efficiencies (PCEs). In this work, a co‐evaporation process is employed to fabricate thin (50 and 100 nm) methylammonium lead iodide (MAPI) perovskite films and integrate them in semitransparent perovskite solar cells (ST‐PSCs). Due to the compact nature of the thin MAPI films, the resultant fully vacuum and room temperature‐processed devices demonstrate high fill factor values approaching 80% and open‐circuit voltage values close to 1100 mV. As a result of this, the ST‐PSCs exhibit PCE's as high as 9% with a photopic average visible transmittance of the full device of 23%.