bluuebunny/crossref_metadata_2025_split huggingface dataset:
A knowledge model for analysis and simulation of regulatory

networks
Authors: Rzhetsky Andrey , Koike Tomohiro , Kalachikov Sergey , Gomez Shawn M. , Krauthammer Michael , Kaplan Sabina H. , Kra Pauline , Russo James J. , Friedman Carol 
Published: July 2002

Abstract
Motivation: In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model.
Results: We introduce an ontological model for the representation of biological knowledge related to regulatory networks in vertebrates. We outline a taxonomy of the concepts, define their ‘whole-to-part’ relationships, describe the properties of major concepts, and outline a set of the most important axioms. The ontology is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.
Availability: The knowledge model can be reviewed at http://genome6.cpmc.columbia.edu/tkoike/ontology/
Contact: ar345@columbia.edu
* To whom correspondence should be addressed.
The Human Transcript Database: a catalogue of full length cDNA
inserts
Authors: Bouck John , McLeod Michael P. , Worley Kim , Gibbs Richard A. 
Published: July 2002

Abstract
Summary: Full length cDNA sequences are an important resource for the research community but are currently intermingled with other sequences. We have identified the human full length insert cDNA sequences in GenBank and placed them in a single location, the Human Transcript Database.
Availability: The Human Transcript Database is available at http://www.hgsc.bcm.tmc.edu/HTDB/.
Contact: John Bouck: jbouck@bcm.tmc.edu
Estimating the rate of molecular evolution: incorporating
non-contemporaneous sequences into maximum likelihood phylogenies
Authors: Rambaut Andrew 
Published: July 2002

Abstract
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the dates of isolation. Confidence intervals for these parameters are also estimated.
Results: The approach was applied to a sample of 17 dengue virus serotype 4 sequences, isolated at dates ranging from 1956 to 1994. The rate of substitution for this serotype was estimated to be 7.91 × 10−4 substitutions per site per year (95% confidence intervals of 6.07 × 10−4, 9.86 × 10−4). This is compatible with a date of 1922 (95% confidence intervals of 1900–1936) for the most recent common ancestor of these sequences.
Availability: TipDate can be obtained by WWW from http://evolve.zoo.ox.ac.uk/software. The package includes the source code, manual and example files. Both UNIX and Apple Macintosh versions are available from the same site.
Contact: andrew.rambaut@zoo.ox.ac.uk
Conceptual modelling of genomic information
Authors: Paton Norman W. , Khan Shakeel A. , Hayes Andrew , Moussouni Fouzia , Brass Andy , Eilbeck Karen , Goble Carole A. , Hubbard Simon J. , Oliver Stephen G. 
Published: July 2002

Abstract
Motivation: Genome sequencing projects are making available complete records of the genetic make-up of organisms. These core data sets are themselves complex, and present challenges to those who seek to store, analyse and present the information. However, in addition to the sequence data, high throughput experiments are making available distinctive new data sets on protein interactions, the phenotypic consequences of gene deletions, and on the transcriptome, proteome, and metabolome. The effective description and management of such data is of considerable importance to bioinformatics in the post-genomic era. The provision of clear and intuitive models of complex information is surprisingly challenging, and this paper presents conceptual models for a range of important emerging information resources in bioinformatics. It is hoped that these can be of benefit to bioinformaticians as they attempt to integrate genetic and phenotypic data with that from genomic sequences, in order to both assign gene functions and elucidate the different pathways of gene action and interaction.
Results: This paper presents a collection of conceptual (i.e. implementation-independent) data models for genomic data. These conceptual models are amenable to (more or less direct) implementation on different computing platforms.
Availability: Most of the information models presented here have been implemented by the authors using an object database. The implementation of a public interface to this database is in progress. We hope to have a public release in the autumn of 2000, available from http://img.cs.man.ac.uk/gims.
Contact: norm@cs.man.ac.uk
A comparison of signal sequence prediction methods using a test
set of signal peptides
Authors: Menne Kerstin M.L. , Hermjakob Henning , Apweiler Rolf 
Published: July 2002

Abstract
Summary: We describe the creation of a test set containing secretory and non-secretory proteins. Five existing prediction programs for signal sequences and their cleavage sites are compared on the basis of this test set: SPScan, SigCleave, SignalP V1.1, SignalP V2.0.b2-HMM and SignalP V2.0.b2-NN.
Availability: Detailed results, the test set and the script to create the test set are available at ftp://ftp.ebi.ac.uk/pub/contrib/swissprot/testsets/signal/
Contact: hhe@ebi.ac.uk
Binding of Phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X‐ray crystallography
Authors: Leonidas Demetres D. , Chavali Gayatri B. , Jardine Anwar M. , Li Songlin , Shapiro Robert , Acharya K. Ravi 
Published: July 2002

AbstractHuman angiogenin (Ang) is an unusual homolog of bovine pancreatic RNase A that utilizes its ribonucleolytic activity to induce the formation of new blood vessels. The pyrimidine‐binding site of Ang was shown previously to be blocked by glutamine 117, indicating that Ang must undergo a conformational change to bind and cleave RNA. The mechanism and nature of this change are not known, and no Ang‐inhibitor complexes have been characterized structurally thus far. Here, we report crystal structures for the complexes of Ang with the inhibitors phosphate and pyrophosphate, and the structure of the complex of the superactive Ang variant Q117G with phosphate, all at 2.0 Å resolution. Phosphate binds to the catalytic site of both Ang and Q117G in essentially the same manner observed in the RNase A–phosphate complex, forming hydrogen bonds with the side chains of His 13, His 114, and Gln 12, and the main chain of Leu 115; it makes an additional interaction with the Lys 40 ammonium group in the Ang complex. One of the phosphate groups of pyrophosphate occupies a similar position. The other phosphate extends toward Gln 117, and lies within hydrogen‐bonding distance from the side‐chain amide of this residue as well as the imidazole group of His 13 and the main‐chain oxygen of Leu 115. The pyrimidine site remains obstructed in all three complex structures, that is, binding to the catalytic center is not sufficient to trigger the conformational change required for catalytic activity, even in the absence of the Gln 117 side chain. The Ang–pyrophosphate complex structure suggests how nucleoside pyrophosphate inhibitors might bind to Ang; this information may be useful for the design of Ang antagonists as potential anti‐angiogenic drugs.
Recursive domains in proteins
Authors: Przytycka Teresa , Srinivasan Rajgopal , Rose George D. 
Published: July 2002

AbstractThe domain is a fundamental unit of protein structure. Numerous studies have analyzed folding patterns in protein domains of known structure to gain insight into the underlying protein folding process. Are such patterns a haphazard assortment or are they similar to sentences in a language, which can be generated by an underlying grammar? Specifically, can a small number of intuitively sensible rules generate a large class of folds, including feasible new folds? In this paper, we explore the extent to which four simple rules can generate the known all‐β folds, using tools from graph theory. As a control, an exhaustive set of β‐sandwiches was tested and found to be largely incompatible with such a grammar. The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains.
Involvement of the amino‐terminal β‐hairpin of the Aspergillus ribotoxins on the interaction with membrances and nonspecific ribonuclease activity
Authors: García‐ortega Lucía , Lacadena Javier , Mancheño José M. , Oñaderra Mercedes , Kao Richard , Davies Julian , Olmo Nieves , Martínez Álvaro , Pozo Del , Gavilanes José G. 
Published: July 2002

AbstractRibotoxins are a family of potent cytotoxic proteins from Aspergillus whose members display a high sequence identity (85% for about 150 amino acid residues). The three‐dimensional structures of two of these proteins, α‐sarcin and restrictocin, are known. They interact with phospholipid bilayers, according to their ability to enter cells, and cleave a specific phosphodiester bond in the large subunit of ribosome thus inhibiting protein biosynthesis. Two nonconservative sequence changes between these proteins are located at the amino‐terminal β‐hairpin of α‐sarcin, a characteristic structure that is absent in other nontoxic structurally related microbial RNases. These two residues of α‐sarcin, Lys 11 and Thr 20, have been substituted with the equivalent amino acids in restrictocin. The single mutants (K11L and T20D) and the corresponding K11L/T20D double mutant have been produced in Escherichia coli and purified to homogeneity. The spectroscopic characterization of the purified proteins reveals that the overall native structure is preserved. The ribonuclease and lipid‐perturbing activities of the three mutants and restrictocin have been evaluated and compared with those of α‐sarcin. These proteins exhibit the same ability to specifically inactivate ribosomes, although they show different activity against nonspecific substrate analogs such as poly(A). The mutant variant K11L and restrictocin display a lower phospholipid‐interacting ability correlated with a decreased cytotoxicity. The results obtained are interpreted in terms of the involvement of the amino‐terminal β‐hairpin in the interaction with both membranes and polyadenylic acid.
Development of ferrocene‐appended benzimidazopyridine and pyrroloquinoxaline probes for structure regulated distinct signalling of Fe3+ in aqueous media and HeLa cells
Authors: Srivastava Suman , Thakur Neha , Nayak Namyashree , Garg Neha , Pandey Rampal 
Published: April 2022

AbstractTwo ferrocenyl (Fc) derivatives Fc‐benzimidazopyridine (5) and Fc‐pyrroloquinoxaline (6) have been synthesized through an inexpensive and metal‐free approach and via tailoring the reaction conditions. X‐ray single crystal analysis revealed that same reactants in the presence of different reagents and reaction condition afforded structurally distinct products 5 and 6. Markedly, 5 and 6 act as fluorescent probes for Fe3+ through discrete signalling with high selectivity and ppb level sensitivity. Based on the fluorescence changes, Job's plot, 1H NMR titration and mass spectral studies, it has been proposed that the probe‐metal binding stoichiometry and nitrogen atoms present at different positions in 5 and 6 lead to the distinct fluorescent signalling (turn‐on for 5 and turn‐off for 6). Further, it has been observed that position of donor atom plays major role in fluorescence signalling and probe‐cation stoichiometry. This work reports deeper insights and straightforward comparison between 5 and 6 in terms of exactly opposite fluorescence detection behaviour towards Fe3+ in aqueous media as well as cell lines to the best of our knowledge.
Obtaining biologically active substances from Amaranthus caudatus L. seeds in one technological cycle
Authors: Korabel Ivan M. , Panchak Lidiia V. , Zyn Alina R. , Antonyuk Volodymyr O. 
Published: April 2022

AbstractNowadays, amaranth is a valuable multipurpose crop and a source of a number of very important biologically active substances. The aim of this study was to develop a comprehensive scheme for obtaining fatty oil, triterpenoids and lectin from the seeds of Amaranthus caudatus L. in one technological cycle. Two variants of the lectin and triterpene compound purification method from amaranth seeds were tested. It was determined that the extraction of triterpene compounds should be carried out after purification of the lectin from degreased seeds. The rationality of this sequence of technological operations is explained by the lability of the lectin and the insolubility in water of triterpene compounds from amaranth seeds. The study also presents a scheme for obtaining squalene from amaranth oil by chromatography on silica gel and proposes a more effective affinity sorbent for purification of the lectin. The use of such a sorbent also opens up the possibility of preserving other water‐soluble substances from amaranth seeds. The physicochemical characteristics and carbohydrate specificity of the lectin are described and new data on the results of the interaction of lectin with human and animal erythrocytes are given. The obtained results are discussed in the light of the complex use of raw materials.
Echocardiography‐defined pulmonary hypertension is an adverse prognostic factor for newly diagnosed multiple myeloma patients
Authors: Jian Yuan , Zhou Huixing , Wang Yidan , Zhang Zhiyao , Yang Guangzhong , Geng Chuanying , Tian Ying , Gao Wen , Chen Wenming 
Published: April 2022

AbstractBackgroundPulmonary hypertension (PH) is a common but rarely recognized comorbidity of multiple myeloma (MM) patients, while its prognostic significance for MM has been rarely reported.MethodsWe retrospectively analyzed the clinical characteristics and prognostic value of baseline echocardiography‐defined PH in 426 newly diagnosed MM (NDMM) patients.ResultsEchocardiograph‐defined PH was found in 12.7% (54/426) of NDMM patients, associated with older age, anemia, and renal insufficiency, as well as severe diastolic dysfunction and higher BNP and NT‐pro‐BNP levels. Patients with PH presented with a higher prevalence of atrial fibrillation, while with a similar incidence of thrombosis compared with those without PH. Based on similar treatment regimens and autologous stem cell transplantation (ASCT) rates, patients without PH have deeper and better responses than those with PH (p = 0.002). With the remission of MM, 81.5% of PH was reversible, accompanied by improvement of right ventricular dysfunction and normalization of BNP/NT‐pro‐BNP levels, while could reoccur at MM relapse. Survival analysis revealed that PH was an adverse prognostic factor, associated with reduced progression‐free survival (PFS) (21 vs. 50 months,p < 0.001) and overall survival (OS) (45 vs. 90 months,p = 0.014). Multivariate analysis further verified that baseline PH was an independent predictor for shorter PFS and OS.ConclusionIn conclusion, echocardiography‐defined PH is an adverse prognostic indicator for MM patients and should be routinely evaluated in MM patients at diagnosis to make a precise prognosis.
Pilot Plant Evaluation of NOx Removal by Cobalt Ethylenediamine Solution
Authors: Yang Jie , Yuan Chongrui , Yang Yiting , Zhao Qiancheng , Jiang Yi , Sun Yujie , Chen Li , Nengzi Li-Chao , Liu Shengyu 
Published: April 2022

AbstractThe removal of NOx by cobalt ethylenediamine solution has attracted much attention, but its reaction mechanism is still not clear. In this study, the reaction mechanism was analyzed experimentally and through practical engineering experiments for thirteen consecutive days. The results indicate that the removal of NOx by cobalt ethylenediamine solution can be divided into two steps. For industrial applications, the removal of actual flue gas NO by cobalt ethylenediamine absorbent was investigated by a gas‐liquid countercurrent and concurrent system in a glass fiber factory in Neijiang, Sichuan province in China, indicating that the average removal efficiency of NO and NOx reached 80 % and that of SO2 90 %.
Federated learning‐based IoT: A systematic literature review
Authors: Hosseinzadeh Mehdi , Hemmati Atefeh , Rahmani Amir Masoud 
Published: April 2022

SummaryThe Internet of Things (IoT) has a significant impact on our daily lives as applications, services, devices, and industries become more intelligent. Artificial intelligence (AI) is expected to significantly influence machine learning training on IoT devices without data sharing. Federated learning (FL) is a distributed machine learning method used in many IoT smart devices; however, FL ensures IoT security and privacy. The systematic literature review (SLR) method is used in this paper to review recently published articles in the FL‐based IoT domain. We analyzed 39 papers that were published between 2018 and March 2022. According to the evaluation factors, the accuracy factor has a high percentage in the FL‐based IoT domain by 29%, and the epoch has 23%, the time has 18%, the energy consumption has 9%, the delay has 9%, the communication overhead has 6%, and the privacy has 6%. Finally, we discuss future research challenges and open issues in the context of FL‐based IoT.
Front Cover
Authors: Chen Yongtai , Chu Jinkui , Tang William C. , Zhang Ran , Zhao Mingyu , Xin Benda 
Published: April 2022

Affected by the scattering microenvironment within biological tissues, the emitted polarized light forms a specific two‐dimensional distribution pattern on the imaging focal plane. In the polarization domain, the pursuit of high imaging magnification does not necessarily lead to preponderant image contrast, and may even produce deteriorating results. This study investigates the spatial scale stability of Mueller matrix parameters (MMPs) and analyzes the nonlinear effect of imaging magnification on the MMPs image contrast.Further details can be found in the article by Yongtai Chen, Jinkui Chu, William C. Tang, Ran Zhang, Mingyu Zhao, and Benda Xin (e202100269)
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Inside Cover
Authors: Ma Haigang , Wang Zhiyang , Zuo Chao , Huang Qinghua 
Published: April 2022

Here, a three dimensional confocal photoacoustic dermoscopy (3D‐CPAD) equipped with an autofocusing sono‐opto probe was developed to facilitate the 3D reconstruction of high‐contrast and high‐spatial‐resolution imaging of human skin with multilaminate structures in depth direction. The autofocusing sono‐opto probe mainly integrated an electrowetting‐based varifocal lens to automatically control the acoustic and optical confocal length, and an annular ultrasonic detector with coaxial configuration for receiving photoacoustic signals.Further details can be found in the article by Haigang Ma, Zhiyang Wang, Chao Zuo, and Qinghua Huang (e202100323)
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Metal vs plastic stents for preoperative biliary drainage in patients with periampullary cancer: An updated systematic review and meta‐analysis
Authors: Watanabe Jun , Miki Atsushi , Sasanuma Hideki , Kotani Kazuhiko , Sata Naohiro 
Published: April 2022

AbstractBackground/PurposeMetal stents (MS) are recommended for preoperative biliary drainage (PBD) in patients with periampullary cancer, but whether MS are superior in terms of re‐intervention and direct cost is debatable. This study aimed to compare the effects of MS and PS on the outcomes of patients with periampullary cancer.MethodsFor this random‐effects meta‐analysis, electronic databases were screened for randomized controlled trials (RCTs) published until January 2022. Subgroup analyses were performed basis on the center type and presence of NAC.ResultsIn this meta‐analysis, seven RCTs (440 participants) were included. MS reduced re‐interventions (risk ratio [RR] = 0.42, 95% confidence interval [CI] = 0.25‐0.72) and direct costs (mean difference = −474 USD, 95% CI = −656 to −292). PBD‐related complications (RR = 0.74, 95% CI = 0.32‐1.71) and postoperative complications (RR = 0.73, 95% CI = 0.45‐1.17) did not differ between MS and PS. Compared PS, MS reduced postoperative complications in high‐volume centers (RR = 0.64, 95% CI = 0.49‐0.84) and PBD‐related complications in patients receiving NAC (RR = 0.29, 95% CI = 0.08‐1.08).ConclusionsMetal stents likely reduces re‐interventions and direct costs. Further studies are needed to confirm the effects of MS on the outcomes.
Temperature dependence of exciton–phonon coupling and phonon anharmonicity in ZnTe thin films
Authors: Iqbal Muhammad Faisal , Ain Qurat Ul , Yaqoob Manzar Mushaf , Zhu Peng , Wang Deliang 
Published: April 2022

AbstractIn ZnTe, longitudinal optical (LO) phonons are strongly coupled with free exciton via long‐range order Froehlich interactions. In this study, we ex situ and in situ monitored the effect of annealing temperature on exciton–phonon (e‐ph) coupling in vacuum evaporated ZnTe thin films by resonance Raman scattering experiment. The 350°C air‐annealed thin film exhibited strong e‐ph coupling and nLO phonons up to sixth order were observed in the Raman spectrum. Moreover, a series of (n − 1)LO + TO and (n + 1)LO‐TO combination phonon modes appeared at low and high wavenumber shoulders of the nLO phonon modes, respectively. The phenomenon of e‐ph coupling was in situ monitored by temperature‐dependent Raman scattering experiment for 350°C air‐annealed thin film. During the in situ measurements, the energy of free exciton was decreased and the condition of outgoing resonance was achieved with nLO phonon. The observation of strong overtones phonon scattering and combination phonon modes allowed us to study anharmonic phonon decay of the zone center nLO phonons. The decay of the fundamental 1LO and its overtone 2LO phonon was mainly dominated by three‐phonon process. For higher order LO phonons with n ≥ 3, the four‐phonon process contribution was increased in the decay process with increasing order.
Signal abnormalities of the bladder wall detected by native T1 mapping in patients with overactive bladder
Authors: Yalcin Ahmet , Gultekin Mehmet Hamza , Erdogan Abdullah , Cankaya Bahar Yilmaz 
Published: April 2022

ObjectNative T1 mapping provides tissue‐specific T1 relaxation times, which can be used to identify structural changes in the various organs. The object of this article was to evaluate the bladder wall of patients with overactive bladder using native T1 mapping and compare the relaxation times of patients and healthy controls.Material and methodsSeventeen patients with a diagnosis of overactive bladder and 15 healthy controls were enrolled in this prospective study. All participants underwent pelvic MRI and T1 maps were acquired. Native T1 relaxation times were calculated via regions of interest acquired from the anterosuperior wall of the bladder in all participants. Mean T1 relaxation times of the overactive bladder patients were compared with those of controls.ResultsOveractive bladder patients had statistically significantly higher T1 relaxation times compared with controls (p = 0.004). In the subgroup analysis, there was no statistically significant difference between males (1113.42 ± 62.4) and females (1176.70 ± 100.9) regarding the T1 relaxation times (p = 0.165). There were no correlations between age and T1 relaxation times in patient or control groups (r = 0.057, p = 0.825, and r = 0.052, p = 0.932, respectively).ConclusionNative T1 mapping can identify structural changes in the bladder wall of patients with overactive bladder. This technique has a promising role in the diagnosis of patients with suspected overactive bladder.