Statistics and dynamics of stiff chains

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 1996.Includes bibliographical references (leaves 66-68).by Siqian He.Sc.D

MMDB: annotating protein sequences with Entrez's 3D-structure database

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ()

Prognostic and recurrent significance of SII in patients with pancreatic head cancer undergoing pancreaticoduodenectomy

BackgroundTo investigate the clinical significance of preoperative inflammatory status in patients with pancreatic head carcinoma (PHC), we performed a single-center study to assess it.MethodWe studied a total of 164 patients with PHC undergoing PD surgery (with or without allogeneic venous replacement) from January 2018 to April 2022. Systemic immune-inflammation index (SII) was the most important peripheral immune index in predicting the prognosis according to XGBoost analysis. The optimal cutoff value of SII for OS was calculated according to Youden index based on the receiver operating characteristic (ROC) curve and the cohort was divided into Low SII group and High SII group. Demographic, clinical data, laboratory data, follow-up data variables were obtained and compared between the two groups. Kaplan-Meier curves, univariable and multivariable Cox regression models were used to determine the association between preoperative inflammation index, nutritional index and TNM staging system with OS and DFS respectively.ResultsThe median follow-up time was 16 months (IQR 23), and 41.4% of recurrences occurred within 1 year. The cutoff value of SII was 563, with a sensitivity of 70.3%, and a specificity of 60.7%. Peripheral immune status was different between the two groups. Patients in High SII group had higher PAR, NLR than those in Low SII group (P <0.01, <0.01, respectively), and lower PNI (P <0.01). Kaplan–Meier analysis showed significantly poorer OS and DFS (P < 0.001, <0.001, respectively) in patients with high SII. By using the multivariable Cox regression model, high SII (HR, 2.056; 95% CI, 1.082–3.905, P=0.028) was significant predictor of OS. Of these 68 high-risk patients who recurrence within one year, patients with widespread metastasis had lower SII and worse prognosis (P <0.01).ConclusionHigh SII was significantly associated with poor prognosis in patients with PHC. However, in patients who recurrence within one year, SII was lower in patients at TNM stage III. Thus, care needs to be taken to differentiate those high-risk patients

CDD: a Conserved Domain Database for protein classification

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system

PubChem3D: a new resource for scientists

<p>Abstract</p> <p>Background</p> <p>PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.</p> <p>Description</p> <p>PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.</p> <p>A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.</p> <p>Conclusions</p> <p>The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.</p

Fabrication of Flame Retarded Cellulose Aerogel with Hydrophobicity via MF/MTMS Double Cross-Linking

In order to overcome the disadvantage of highly flammable and poor mechanical performance of cellulose aerogel, herein, cellulose nanofibrils (CNF) were cross-linked by melamine formaldehyde (MF), and further cross-linked and surface decorated by methyltrimethoxysilane (MTMS) to obtain flame retarded compound aerogels. FT-IR spectra confirmed that cross-linking reaction occurred between MF/MTMS and CNF matrix. The morphological analysis demonstrated that the pore size shrinked, whereas the pore amount of compound aerogels increased after cross-linking, thereby resulting in the improvement of mechanical performance. Via double cross-linking, the compound aerogels also exhibited excellent hydrophobicity (contact angle up to 132.3°) and flame retardant properties. The limited oxygen index (LOI) value of double cross-linked specimen (Si-CNF/MF) increased from 19.5% to 37.1%, and the vertical combustion test (UL-94) reached V-0 grade. Microcalorimetry measurement showed that the peak heat release rate (pHRR) and total heat release (THR) of Si-CNF/MF decreased by 50.6% and 64.3% in comparison with pure CNF aerogel, respectively. The analysis results of char residue showed that both condensed phase and gas phase flame retardant mechanisms occurred during combustion, and synergistic effect existed between MF and MTMS. Moreover, the very low thermal conductivity of compound aerogels permitted their application as heat preservation materials

Cationic Tropidinyl Scandium Catalyst: A Perfectly Acceptable Substitute for Cationic Half-Sandwich Scandium Catalysts in <i>cis</i>-1,4-Polymerization of Isoprene and Copolymerization with Norbornene

Different nonmetallocene rare earth metal alkyl complexes such as monotropidinyl (Trop) scandium dialkyl complex (Trop)­Sc­(CH₂SiMe₃)₂(THF) (<b>1</b>), ditropidinyl yttrium alkyl complex (Trop)₂Y­(CH₂SiMe₃)­(THF) (<b>3</b>) as well as binuclear lutetium alkyl complex bearing one tetradentate dianionic 6-<i>N</i>-methyl-1,4-cycloheptadienyl (NMCH) ligand [(NMCH)­Lu­(CH₂SiMe₃)­(THF)]₂ (<b>2</b>) have been synthesized in high yields via one-pot acid–base reaction by using of the tris­(trimethylsilylmethyl) rare earth metal complexes with the readily available natural product tropidine. The polymerization experiments indicate that the monotropidinyl scandium dialkyl complex <b>1</b> displays reactivity akin to that of the analogous monocyclopentadienyl scandium dialkyl complexes. In the presence of activator and a small amount of AlMe₃, complex <b>1</b> exhibits similar activities (up to 1.6 × 10⁶ g mol_Sc^–1 h^–1) but higher <i>cis</i>-1,4-selectivities (up to 100%) than (C₅H₅)­Sc­(CH₂SiMe₃)₂(THF) (<i>cis</i>-1,4-selectivity as 95%) in the isoprene polymerization, yielding the pure <i>cis</i>-1,4-PIPs with moderate molecular weights (<i>M</i>_n = 0.5–11.2 × 10⁴ g/mol) and bimodal molecular weight distributions (<i>M</i>_w/<i>M</i>_n = 1.48–6.07). Moreover, the complex <b>1</b>/[Ph₃C]­[B­(C₆F₅)₄/Al^<i>i</i>Bu₃ ternary system also shows good comonomer incorporation ability in the copolymerization of isoprene and norbornene similar to the [C₅Me₄(SiMe₃)]­Sc­(η³-CH₂CHCH₂)₂/activator binary system, affording the random isoprene/norbornene copolymers with a wide range of isoprene contents around 57–91 mol % containing <i>cis</i>-1,4 configuration up to 88%