Abstract：
:There has been a deluge of biological sequence data in the public domain, which makes sequence comparison one of the most fundamental computational problems in bioinformatics. The biologists routinely use pairwise alignment programs to identify similar, or more specifically, related sequences (having common ancestor). It is a well-known fact that almost everything in bioinformatics depends on the inter-relationship between sequence, structure, and function (all encapsulated in the term relatedness), which is far from being well understood. The potential relatedness of two sequences is better judged by statistical significance of the alignment score rather than by the alignment score alone. This chapter presents a summary of recent advances in accurately estimating statistical significance of pairwise local alignment for the purpose of identifying related sequences, by making the sequence comparison process more sequence specific. Comparison of using pairwise statistical significance to rank database sequences, with well-known database search programs like BLAST, PSI-BLAST, and SSEARCH, is also presented. As expected, the sequence-comparison performance (evaluated in terms of retrieval accuracy) improves significantly as the sequence comparison process is made more and more sequence specific. Shortcomings of currently used approaches and some potentially useful directions for future work are also presented.
journal_name
Adv Exp Med Bioljournal_title
Advances in experimental medicine and biologyauthors
Agrawal A,Choudhary A,Huang Xdoi
10.1007/978-1-4419-7046-6_30subject
Has Abstractpub_date
2011-01-01 00:00:00pages
297-306eissn
0065-2598issn
2214-8019journal_volume
696pub_type
杂志文章abstract：:In isolated titin molecules, length changes may occur in discrete steps (Tskhovrebova et al., 1997; Rief et al., 1997). The extent to which such steps are preserved in the intact muscle-filament lattice has remained unclear. We carried out experiments on single isolated insect-flight-muscle myofibrils in which thin fi...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4615-4267-4_18
更新日期：2000-01-01 00:00:00
abstract：:Flaxseed has been used as an edible grain in different parts of the world since ancient times. However, use of flaxseed oil has been limited due to its high content of polyunsaturated fatty acids. Nonetheless, alpha-linolenic acid, dietary fiber and lignans of flaxseed have regained attention. New varieties of flaxsee...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-1-4899-1925-0_26
更新日期：1998-01-01 00:00:00
abstract：:Although nuclear factor-kB (NF-kB) is generally considered to be a pro-inflammatory transcription factor, recent studies indicate that it also plays a critical role in the development of an anti-inflammatory T cell subset called regulatory T (Treg) cells. Two NF-kB proteins, c-Rel and p65, drive the development of Tre...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-1-4614-0106-3_12
更新日期：2012-01-01 00:00:00
abstract：:In the last years we have been able to establish CD26 as an operational marker for a human Th1-like reaction in various granulomatous diseases. Recently, CD30 was described as a marker for a Th2-type reaction, where CD30 is preferentially expressed and its soluble form released by human T cell clones producing Th2-typ...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4757-9613-1_28
更新日期：1997-01-01 00:00:00
abstract：:Although controversial, animal and tissue studies indicate that carotid bodies are sensitive to changes in glucose as well as in oxygen, thereby functioning as metabolic sensors. This study was designed to test the hypothesis that carotid bodies in humans participate in the counter-regulatory response to insulin-induc...
journal_title：Advances in experimental medicine and biology
pub_type： 临床试验,杂志文章
doi：10.1007/978-90-481-2259-2_31
更新日期：2009-01-01 00:00:00
abstract：:Insulin secretion in humans is usually induced by mixed meals, which upon ingestion, increase the plasma concentration of glucose, fatty acids, amino acids, and incretins like glucagon-like peptide 1. Beta-cells can stay in the off-mode, ready-mode or on-mode; the mode-switching being determined by the open state prob...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-3-030-12457-1_37
更新日期：2020-01-01 00:00:00
abstract：:The ability to serially collect blood samples and conduct ultrasound examinations in Asian and African elephants has provided unique opportunities to study the biology of these endangered species. As a result, many unique aspects of elephant reproduction have been identified. For females, there are interesting differe...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-1-4939-0820-2_8
更新日期：2014-01-01 00:00:00
abstract：:The cellular requirements for generating potent human CD8+ CTLs to influenza A virus in vitro have been defined. Furthermore, we have developed improved methods for generating large numbers of DCs from non-proliferating progenitors. These developments have enabled the design of new strategies to elicit CTLs in vivo. F...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4757-9966-8_62
更新日期：1997-01-01 00:00:00
abstract：:Freeze-drying is a popular method to prepare pharmaceutical formulations containing structurally complex active ingredients and drug delivery system carriers. The solidification performed at lower temperature significantly improves storage stability of proteins, peptides, antibiotics, vaccines, and liposomes, which ar...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-981-13-1244-1_20
更新日期：2018-01-01 00:00:00
abstract：:The 1st International Conference on Oral Mucosal Immunity and the Microbiome (OMIM) took place at the Avra Imperial Hotel, Chania, Crete, Greece, between 26th and 30th September 2018, under the auspices of the Aegean Conferences. This was the first Aegean Conference of its kind in thematic oral research, and a unique ...
journal_title：Advances in experimental medicine and biology
pub_type：
doi：10.1007/978-3-030-28524-1_1
更新日期：2019-01-01 00:00:00
abstract：:RPE65 is essential for both rod- and cone-mediated vision. So far, more than 120 disease-associated mutations have been identified in the human RPE65 gene. Differential clinical manifestations suggested that some patients suffer from null mutations while others retain residual RPE65 activity and some useful vision. To...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-3-319-17121-0_45
更新日期：2016-01-01 00:00:00
abstract：:Checkpoint inhibitors are part of the family of immunotherapies and are increasingly being used in a wide variety of cancers. Immune-related adverse events pose a major challenge in the treatment of cancer patients. Pneumonitis is a rare immune-related adverse event that presents in distinct patterns. The goal of this...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-3-030-41008-7_13
更新日期：2020-01-01 00:00:00
abstract：:Cancer development originates in a single mutant cell transformed from a normal cell, including further evolution of pro-tumor cells through additional mutations into malignant cancer tissues. Data from recent studies, however, suggest that most pro-tumor cells do not develop into tumors but remain dormant within or a...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-3-030-23629-8_5
更新日期：2019-01-01 00:00:00
abstract：:The effects of IABP on the contractile state of the in situ canine heart was evaluated under control conditions and conditions of regional ischemia by determining the transient slope of the end-systolic pressure-volume line, T-Emax. For comparison, the conventional index reflecting contractility, dP/dtmax and other re...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：
更新日期：1989-01-01 00:00:00
abstract：:In a primary and secondary MLC the in vitro immunogenicity of allogeneic PHA induced blast cells (which lack i region coded determinants) was compared to that of LPS imduced blast cells. Unlike LPS induced blast lymphocytes (stimulator cells) which induced high cytotoxic activity, PHA induced blast cells were found to...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4613-4355-4_49
更新日期：1976-01-01 00:00:00
abstract：:Progress in studies on the scrapie agent has been hampered by the slow and tedious endpoint titration assays in rodents. A new assay based on incubation period measurements has been developed. The incubation period is defined as the time interval from inoculation to the onset of clinically detectable neurological illn...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4757-0495-2_35
更新日期：1981-01-01 00:00:00
abstract：:Multiple myeloma (MM) is a hematologic malignancy whose progression may account for uncontrolled osteoclastogenesis promoted by the malignant plasma cells within the marrow microenvironment. Osteoclasts are multinucleated cells derived from the fusion of myeloid progenitors such as monocytes/macrophages, in response t...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-94-007-0782-5_5
更新日期：2011-01-01 00:00:00
abstract：:Cottage cheese whey protein concentrates, prepared by preconcentration by ultrafiltration followed by gel permeation to remove low molecular weight materials, have the solubility, stability and flavor that make them suitable for fortification of soft drinks and related products. These concentrates are characterized by...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4684-3366-1_35
更新日期：1978-01-01 00:00:00
abstract：:Rodent and clinical studies have documented that myeloid cell infiltration of tumors is associated with neutrophilia, lymphocytopenia and poor patient outcomes. This contrasts with lymphocyte infiltration of tumors, which is associated with improved outcomes. Lifestyle parameters such as high fat diet s and omega (ω)-...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-3-319-67577-0_10
更新日期：2017-01-01 00:00:00
abstract：:The studies on intact fibers of the frog and fast-twitch skinned fibers of the Syrian hamster suggest the presence of intermediate low-force (weak) and high-force (strong) attachments in the cross-bridge cycle. Our results suggest that the weak and strong attachments may be separately regulated by independent calcium ...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：
更新日期：1988-01-01 00:00:00
abstract：:The adverse effects of trace metals, heat, steam and other conditions encountered in food processing relate to the acceleration of development of rancidity. Measures to retard oxidation of lipids, vitamins, pigments and proteins include elimination of prooxidants, removal of oxygen and use of blends of inhibitors form...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-1-4899-1925-0_16
更新日期：1998-01-01 00:00:00
abstract：:Cardiac rehabilitation is a comprehensive and multidisciplinary program, and exercise training is extremely crucial in the whole program. In the past decades, many researches have shown the beneficial effects of exercise for cardiovascular disease (CVD) is indisputable Nevertheless, only a well-designed exercise presc...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-981-10-4304-8_19
更新日期：2017-01-01 00:00:00
abstract：:The prognosis for hepatocellular carcinoma (HCC) remains poor and has not improved in over two decades. Most patients with advanced HCC who are not eligible for surgery have limited treatment options due to poor liver function or large, unresectable tumors. Although sorafenib is the standard-of-care treatment for thes...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-981-10-4310-9_13
更新日期：2017-01-01 00:00:00
abstract：:Studies have been cazrried out to determine the in vivo and in vitro effects of lithium carbonate in various neutropenic disorders. Addition of lithium to culture of bone marrow from patients with a variety of neutropenic disorders and ANLL in which normal or elevated serum and/or urinary CSA levels were present did n...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4757-0259-0_21
更新日期：1980-01-01 00:00:00
abstract：:Although prevalence estimates are imprecise, growing numbers of women in the United States are living longer with metastatic breast cancer, attributable at least in part to the availability of effective targeted therapies. Women living with metastatic disease are understudied, however, and substantial heterogeneity ex...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-3-319-16366-6_16
更新日期：2015-01-01 00:00:00
abstract：:Laser diffraction and photomicrography have been used to monitor sarcomere length changes in single muscle fibres of the frog, at long sarcomere lengths, during fixed end tetani. In the central 90% of all fibres, changes in sarcomere length were consistently less than 0.25 micron. Sarcomere length showed an initial ra...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-1-4684-4703-3_42
更新日期：1984-01-01 00:00:00
abstract：:We identified a 45 kDa Ca(2+)-dependent Lf binding protein on rat hepatocytes. Dithiobis(sulfosuccimidylproprionate) (DTSSP)-crosslinked 125I-Lf to a 45 kDa adduct in a Ca(2+)-dependent manner on intact cells. The 125I-labeled crosslinked complexes were absent when either surface-bound 125I-Lf was stripped prior to cr...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：
更新日期：1998-01-01 00:00:00
abstract：:Retbindin (Rtbdn) is a novel protein of unknown function found exclusively in the retina. Recently, our group has suggested, from in silico analysis of the peptide sequence and in vitro binding data, that Rtbdn could function to bind riboflavin (RF) and its derivatives flavin adenine dinucleotide (FAD) and flavin mono...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章
doi：10.1007/978-3-319-75402-4_60
更新日期：2018-01-01 00:00:00
abstract：:In this chapter, we will review studies of HER2 in osteosarcoma and discuss the controversies that have existed in this field. Our present understanding of HER2 in the context of osteosarcoma is that it is expressed on a subset of patient samples, but that expression is not prognostic. We will review the two trials th...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-3-030-43032-0_5
更新日期：2020-01-01 00:00:00
abstract：:Observations indicate three different tissues of origin for ovarian carcinoma. The ovarian surface epithelium, oviduct epithelium (TSE), and derivates of the Müllerian duct. This chapter discusses the TSE-related ovarian carcinogenesis (exfoliation theory). Recent evidence from prophylactic removed ovaries and Fallopi...
journal_title：Advances in experimental medicine and biology
pub_type： 杂志文章,评审
doi：10.1007/978-0-387-68969-2_7
更新日期：2008-01-01 00:00:00
