bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Cardiovascular Risk Factors and Insulin Resistance in Patients with Subclinical Hypothyroidism
Authors: Shafeek Zeinab , Sawy Abdullah El , Kabbash Ibrahim , Ahwal Loai El , Ayad Nasrat 
Published: April 2023

Background: Overt hypothyroidism is associated with Insulin resistance (IR), accelerated arteriosclerosis and cardiovascular disease (CVD). Although SCH (SCH) is also associated with CVD risk remains controversial.
Objective: The present research aimed to assess risk factors for CVD and IR in SCH cases.
Methods: Case control study was carried out on 90 participants. The research included two groups; group one included 45 SCH cases and group two (controls) included 45 healthy volunteers. We assessed common lipid variables, fasting blood glucose, fasting insulin, HOMA IR, thyroid profile for all participants.
Results: There was highly significant rise in anthropometric measures including body weight, BMI and waist circumference in SCH than controls (P value = <0.001). There was significant rise in systolic and diastolic blood pressure (BP) in SCH than controls (P value = <0.001, 0.001). There was significant rise in triglyceride level, total cholesterol and LDL-C in SCH in comparison to controls (P value = 0.019, <0.001, <0.001) and significant decline in HDL-C in SCH in comparison to controls (P value = 0.011). There was significant positive correlation between TSH level and anthropometric measures, BP, indices of IR, total cholesterol, triglycerides and LDL-C, but significant negative correlation with HDL-C.
Conclusion: Our findings suggest that SCH might increase the risk for CVD which explain the needs for early detection and treatment of such individuals.
In-Vitro Antioxidant, Anti-Arthritis, Anti-inflammatory, Thrombolysis, Anti-bacterial, and in-Vivo Neuropharmacological Activities of Bioactive Metabolites of Solanum americanum Mill.
Authors: Shomudro Hasib Khan , Aboni Anan Mahabub , Jasmeen Tasbira , Sanam Sherejad 
Published: April 2023

Aims: The purpose of this research was to examine the effects of methanol-prepared leaf extracts from the Solanum americanum Mill. plant on a variety of in vitro activities, including antioxidant, anti-Arthritis, anti-inflammatory, thrombolysis, anti-bacterial, and in-vivo neuropharmacological activities.
Study Design: Methanolic extract of Solanum americanum leaf (MESAL) was primarily evaluated via phytochemical screening. The potential for in vitro activities, including antioxidant, anti-arthritis, anti-inflammatory, thrombolysis, and anti-bacterial activity were determined to study due to the pharmacological interest in the plant's chemical constituent. Whether there is statistical significance to the changes seen in its in vivo neuropharmacological characteristics when tested in experimental animals.
Place and Duration of Study: This research was carried out between November 2022 to January 2023 at the Laboratory of Phytochemistry and Pharmacology in the Department of Pharmacy and Laboratory of Microbiology, Stamford University Bangladesh and Bangladesh Council of Scientific and Industrial Research, Dhaka.
Methodology: The plant was subjected to phytochemical screening utilizing a variety of test reagents and potential antioxidant, anti-arthritis, anti-inflammatory, thrombolytic, anti-bacterial, and neuropharmacological activities of MESAL were investigated. Antioxidant, anti-arthritic, anti-inflammatory, thrombolytic, and antibacterial activities were tested at different doses utilizing the DPPH Free Radical Scavenging Assay, Protein Denaturation Assays, Clot Lysis, and the Disk Diffusion Method. Swiss albino mice were tested using open-field and hole-cross methods to measure their locomotion as part of the neuropharmacological study.
Results: The MESAL phytochemical screening findings demonstrated that the plants' chemical compositions varied. Most antioxidant activities were found in MESA, with an IC50 of 11.73 µg/mL compared to Ascorbic acid's IC50 of 28.86 µg/mL. When compared to the standard, the percent inhibition value of MESAL's anti-arthritis activity was significantly higher. With a maximum protein denaturation value of 94.03% at a concentration of 1000µg/mL, MESAL possesses potent anti-inflammatory activity. The value of MESAL in terms of clot lysis is very significant which is 90.257%. While MESAL's antibacterial value is moderate, it is still worth considering. However, the extract was proven to be less effective than Diazepam in improving motor coordination in the Open Field and Hole Cross Tests.
Conclusion: Several pathological conditions, including neurodegenerative diseases, may benefit in the future from the use of plant-derived pharmacological agents due to their neuropharmacological, antioxidant, anti-inflammatory, and anti-arthritic activity, which can replace the use of NSAIDs.
Architectural remodelling in acute and chronic interstitial lung disease: fibrosis or fibroelastosis?
Authors: Negri E M , Montes G S , Saldiva P H N , Capelozzi V L 
Published: July 2002

Aims: Pulmonary fibrosis in acute and chronic lung disease has been much investigated, but little attention has been directed at the elastic tissue in these situations. Our aim was to verify whether elastic deposition accompanies collagen deposition in the repairing process of acute and chronic lung injury.Methods and results: We measured, by image analysis, the content of fibres of the collagenous and elastic systems of the alveolar septum in histological slides sampled from autopsied lungs, using the picrosirius‐polarization method and Weigert's resorcin‐fuchsin stain, respectively. Five groups were studied: I, 10 normal patients; II, 10 patients with cardiogenic pulmonary oedema; III, 23 adult respiratory distress syndrome (ARDS) patients in the early phase; IV, 14 ARDS patients in the late fibroproliferative phase; and V, 10 idiopathic pulmonary fibrosis patients. The first two groups were used as controls. The content of fibres of the collagenous and elastic systems was significantly increased in groups IV and V as compared to the other groups.Conclusions: Our results indicate that deposition of elastic system fibres is present in the fibroproliferative phase of ARDS and in usual interstitial pneumonia and suggest that this event may contribute to the alveolar mechanical dysfunction and remodelling that occur in acute and chronic interstitial lung disease.
FKHR-L1 can act as a critical effector of cell death induced by cytokine withdrawal
Authors: Dijkers Pascale F. , Birkenkamp Kim U. , Lam Eric W.-F. , Thomas N. Shaun B. , Lammers Jan-Willem J. , Koenderman Leo , Coffer Paul J. 
Published: July 2002

Survival signals elicited by cytokines include the activation of phosphatidylinositol 3-kinase (PI3K), which in turn promotes the activation of protein kinase B (PKB). Recently, PKB has been demonstrated to phosphorylate and inactivate forkhead transcription factor FKHR-L1, a potent inducer of apoptosis. To explore the mechanisms underlying the induction of apoptosis after cytokine withdrawal or FKHR-L1 activation, we used a cell line in which FKHR-L1 activity could be specifically induced. Both cytokine withdrawal and FKHR-L1 activation induced apoptosis, which was preceded by an upregulation in p27KIP1 and a concomitant decrease in cells entering the cell cycle. Induction of apoptosis by both cytokine withdrawal and activation of FKHR-L1 correlated with the disruption of mitochondrial membrane integrity and cytochrome c release. This was preceded by upregulation of the pro-apoptotic Bcl-2 family member Bim. Ectopic expression of an inhibitory mutant of FKHR-L1 substantially reduced the levels of apoptosis observed after cytokine withdrawal. Activation of PKB alone was sufficient to promote cell survival, as measured by maintenance of mitochondrial integrity and the resultant inhibition of effector caspases. Furthermore, hematopoietic stem cells isolated from Bim−/− mice exhibited reduced levels of apoptosis upon inhibition of PI3K/PKB signaling.
These data demonstrate that activation of FKHR-L1 alone can recapitulate all known elements of the apoptotic program normally induced by cytokine withdrawal. Thus PI3K/PKB–mediated inhibition of this transcription factor likely provides an important mechanism by which survival factors act to prevent programmed cell death.
Hidden Markov models for detecting remote protein homologies.
Authors: Karplus K , Barrett C , Hughey R 
Published: July 2002

Abstract
MOTIVATION: A new hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (HMM) from the sequence and homologs found using the HMM for database search. SAM-T98 is also used to construct model libraries automatically from sequences in structural databases. METHODS: We evaluate the SAM-T98 method with four datasets. Three of the test sets are fold-recognition tests, where the correct answers are determined by structural similarity. The fourth uses a curated database. The method is compared against WU-BLASTP and against DOUBLE-BLAST, a two-step method similar to ISS, but using BLAST instead of FASTA. RESULTS: SAM-T98 had the fewest errors in all tests-dramatically so for the fold-recognition tests. At the minimum-error point on the SCOP (Structural Classification of Proteins)-domains test, SAM-T98 got 880 true positives and 68 false positives, DOUBLE-BLAST got 533 true positives with 71 false positives, and WU-BLASTP got 353 true positives with 24 false positives. The method is optimized to recognize superfamilies, and would require parameter adjustment to be used to find family or fold relationships. One key to the performance of the HMM method is a new score-normalization technique that compares the score to the score with a reversed model rather than to a uniform null model. AVAILABILITY: A World Wide Web server, as well as information on obtaining the Sequence Alignment and Modeling (SAM) software suite, can be found at http://www.cse.ucsc.edu/research/compbi o/ CONTACT: karplus@cse.ucsc.edu; http://www.cse.ucsc.edu/karplus
Exploiting the past and the future in protein secondary
structure prediction
Authors: Baldi Pierre , Brunak Søren , Frasconi Paolo , Soda Giovanni , Pollastri Gianluca 
Published: July 2002

Abstract
Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network architectures with a fixed, and relatively short, input window of amino acids, centered at the prediction site. Although a fixed small window avoids overfitting problems, it does not permit capturing variable long-rang information.
Results: We introduce a family of novel architectures which can learn to make predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary information, expressed in terms of multiple alignments, both at the input and output levels. While our system currently achieves an overall performance close to 76% correct prediction – at least comparable to the best existing systems – the main emphasis here is on the development of new algorithmic ideas.
Availability: The executable program for predicting protein secondary structure is available from the authors free of charge.
Contact: pfbaldi@ics.uci.edu, gpollast@ics.uci.edu, brunak@cbs.dtu.dk, paolo@dsi.unifi.it
Ontology for immunogenetics: the IMGT-ONTOLOGY
Authors: Giudicelli Véronique , Lefranc Marie-Paule 
Published: July 2002

Abstract
Motivation: IMGT, the international ImMunoGene- Tics database (http://imgt.cines.fr:8104), created by M.-P. Lefranc, is an integrated database specializing in antigen receptors (immunoglobulins and T-cell receptors) and major histocompatibility complex (MHC) of all vertebrate species. IMGT accurate immunogenetics data are based on the standardization of the biological knowledge provided by the ‘ImMunoGeneTics’ IMGT-ONTOLOGY.
The IMGT-ONTOLOGY describes the classification and specification of terms needed for immunogenetics and bioinformatics. IMGT-ONTOLOGY covers four main concepts: ‘IDENTIFICATION’, ‘DESCRIPTION’, ‘CLASSIFICATION’ and ‘OBTENTION’. These concepts allow an extensive and standardized description and characterization of immunoglobulin and T-cell receptor data. The controlled vocabulary and the annotation rules are indispensable to ensure accuracy, consistency and coherence in IMGT. IMGT-ONTOLOGY allows scientists and clinicians to use, for the first time, identical terms with the same meaning in immunogenetics. It provides a semantic repository that will improve interoperability between specialist and generalist databases.
Availability: Controlled vocabulary and annotation rules are described in the IMGT Scientific chart from the IMGT Marie-Paule page at http://imgt.cines.fr:8104
Contact: lefranc@ligm.igh.cnrs.fr
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
Authors: Hertz G Z , Stormo G D 
Published: July 2002

Abstract
MOTIVATION: Molecular biologists frequently can obtain interesting insight by aligning a set of related DNA, RNA or protein sequences. Such alignments can be used to determine either evolutionary or functional relationships. Our interest is in identifying functional relationships. Unless the sequences are very similar, it is necessary to have a specific strategy for measuring-or scoring-the relatedness of the aligned sequences. If the alignment is not known, one can be determined by finding an alignment that optimizes the scoring scheme. RESULTS: We describe four components to our approach for determining alignments of multiple sequences. First, we review a log-likelihood scoring scheme we call information content. Second, we describe two methods for estimating the P value of an individual information content score: (i) a method that combines a technique from large-deviation statistics with numerical calculations; (ii) a method that is exclusively numerical. Third, we describe how we count the number of possible alignments given the overall amount of sequence data. This count is multiplied by the P value to determine the expected frequency of an information content score and, thus, the statistical significance of the corresponding alignment. Statistical significance can be used to compare alignments having differing widths and containing differing numbers of sequences. Fourth, we describe a greedy algorithm for determining alignments of functionally related sequences. Finally, we test the accuracy of our P value calculations, and give an example of using our algorithm to identify binding sites for the Escherichia coli CRP protein. AVAILABILITY: Programs were developed under the UNIX operating system and are available by anonymous ftp from ftp://beagle.colorado.edu/pub/consensus.
MEGA2: molecular evolutionary genetics analysis software
Authors: Kumar Sudhir , Tamura Koichiro , Jakobsen Ingrid B. , Nei Masatoshi 
Published: July 2002

Abstract
Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.
Availability: http://www.megasoftware.net.
Contact: s.kumar@asu.edu
* To whom correspondence should be addressed.
GRIMM: genome rearrangements web server
Authors: Tesler Glenn 
Published: July 2002

Abstract
Summary: Genome Rearrangements In Man and Mouse (GRIMM) is a tool for analyzing rearrangements of gene orders in pairs of unichromosomal and multichromosomal genomes, with either signed or unsigned gene data. Although there are several programs for analyzing rearrangements in unichromosomal genomes, this is the first to analyze rearrangements in multichromosomal genomes. GRIMM also provides a new algorithm for analyzing comparative maps for which gene directions are unknown.
Availability: A web server, with instructions and sample data, is available at http://www-cse.ucsd.edu/groups/bioinformatics/GRIMM.
Contact: gptesler@ucsd.edu
Magma Origin and Evolution of White Island (Whakaari) Volcano, Bay of Plenty, New Zealand
Authors: COLE J. W. , THORDARSON T. , BURT R. M. 
Published: July 2002

Abstract
White Island is an active composite stratovolcano in the Bay of Plenty, New Zealand, that comprises many small volume (&lt;0·1 km3) andesite–dacite lava flows and pyroclastic deposits with phenocryst contents of ∼15–44%. Minor high-Mg basaltic andesite explosive eruptions, such as those of 1976–1992, may have occurred at intervals throughout the history of White Island, but are rarely preserved. These alternate with major episodes of andesite–dacite lava extrusion. The high-Mg magmas form by hydrous melting of mantle, metasomatized by fluids from the dehydrating slab at the slab–mantle wedge interface, that rise rapidly to shallow magma chambers (2–7 km?) where limited mixing and contamination occurs before eruption. Some of this magma remains in the magma chamber where it interacts with the crystal mush, from which it inherits phenocrysts, to form so-called ‘dirty’ lavas. Total phenocryst content of these lavas is correspondingly higher. As more magma is intruded into the chamber, the heat flux will increase and melt fraction will eventually rise to the surface to form high-silica andesite–dacite magma (‘clean’ lavas) with fewer inherited phenocrysts. Similar multi-magma chamber plumbing systems, with complex evolution involving fractionation and contamination, probably occur in most andesite–dacite arc volcanoes.
Palaeogene Continental to Oceanic Magmatism on the SE Greenland Continental Margin at 63°N: a Review of the Results of Ocean Drilling Program Legs 152 and 163
Authors: FITTON J. G. , LARSEN L. M. , SAUNDERS A. D. , HARDARSON B. S. , KEMPTON P. D. 
Published: July 2002

Abstract
Drilling along a 63°N transect off SE Greenland during Ocean Drilling Program (ODP) Legs 152 and 163 recovered a succession of volcanic rocks representing all stages in the break-up of the volcanic rifted margin. The rocks range from pre-break-up continental tholeiitic flood basalt, through syn-break-up picrite, to truly oceanic basalt forming the main part of the seaward-dipping reflector sequence (SDRS). All the lava flows recovered from the transect were erupted in a subaerial environment. 40Ar–39Ar dating shows that the earliest magmas were erupted at ∼61 Ma and has confirmed that the main part of the SDRS was erupted during C24r (56–53 Ma) following continental break-up. Magma represented by the pre-break-up lava flows was stored in crustal reservoirs where it evolved by fractional crystallization and assimilation of continental crust. Trace element and radiogenic isotope data show that the contaminant changed, through time, from lower-crustal granulite to a mixture of granulite and amphibolite, suggesting storage of magma at progressively shallower levels in the crust. The degree of contamination declined rapidly as break-up proceeded, and the youngest rocks sampled in the transect are uncontaminated by continental basement. Variation of, for example, Sc/Zr and Sm/Lu through the succession suggests a shallowing of the top of the mantle melting zone, accompanied by an increase in the average degree of melting with time from ∼4% to ∼12%. These modest degrees of melting imply mantle temperatures only ∼100°C hotter than normal upper mantle. Upwelling mantle must therefore have been fed dynamically to the melt zone to generate the igneous crust of 18 km thickness deduced from seismic and gravity studies. N-MORB-like magmas dominated the earliest part of the succession although a few flows of ‘Icelandic’ basalt were erupted in the pre-break-up phase. In contrast, the post-break-up magmas had an Icelandic mantle source. This suggests that the developing head of the ancestral Iceland plume was compositionally zoned, with a core of Icelandic mantle surrounded by a thick outer zone of hot, depleted upper mantle.
Long-Term Effectiveness of a Peer-Based Intervention to Promote Condom and Contraceptive Use among HIV-Positive and at-Risk Women
Authors: Fogarty Linda A. , Heilig Charles M. , Armstrong Kay , Cabral Rebecca , Galavotti Christine , Gielen Andrea C. , Green Brian M. 
Published: July 2002

Objective. The authors used data from a larger study to evaluate the long-term effects of a peer advocate intervention on condom and contraceptive use among HIV-infected women and women at high risk for HIV infection. Methods. HIV-infected women in one study and women at high risk for HIV infection in a second study were selected from the Women and Infants Demonstration Project and assigned to a standard or an enhanced HIV prevention treatment group. The enhanced intervention included support groups and one-on-one contacts with peer advocates tailored to clients' needs. The authors interviewed women at baseline and at 6-, 12- and 18-months, and measured changes in consistency of condom and contraceptive use and in self-efficacy and perceived advantages and disadvantages of condom and contraceptive use. Results. Of HIV-infected women, the enhanced group had improved consistency in condom use, increased perceived advantages of condom use, and increased level of self-efficacy compared with the standard group. Of women at risk, the enhanced intervention group at six months maintained consistent condom use with a main partner and perceived more benefit of condom use compared with the standard group. These differences diminished at 12 months. Conclusions. The enhanced intervention was generally effective in the HIV+ study. In the at-risk study, however, intervention effects were minimal and short-lived. Factors related to the theory, intervention design, and sample characteristics help explain these differences.