gebhart/patrepeval huggingface dataset:
Locomotion in the Abalone Haliotis Kamtschatkana: Pedal Morphology and Cost of Transport (1997)

Morphological analyses of pedal sole area and pedal waves were conducted for a range of speeds and body sizes in the abalone Haliotis kamtschatkana. The pedal sole of resting abalone increased in size disproportionately with animal volume (slope of log10-transformed data, b=0.83; expected slope for isometry, b0=0.67) and length (b=2.51; b0=2.0). Pedal wave frequency increased linearly with speed, confirming that abalone increase speed by increasing the velocity of pedal waves. Total area of the pedal sole decreased by 2.1 % for each shell length per minute increase in speed. Likewise, the area of the foot incorporated into pedal waves increased by 1.8 % for each shell length per minute increase in speed. Together, these changes translated into a 50 % decrease in the pedal sole area in contact with the substratum at a maximum escape speed of 15 shell lengths min-1, relative to the pedal sole at rest. The amount of mucus secreted by resting animals during adhesion to the substratum increased isometrically with foot area (slope of log10-transformed data, b=1.08). The amount of mucus secreted during locomotion did not vary with speed, but was less than the amount needed for adhesion. We suggest that these morphological and physiological changes reduce the energy expenditure during locomotion. Cost of transport was investigated for a range of speeds and abalone sizes. The rate of oxygen consumption O2 (in &micro;l O2 g-1 h-1) increased linearly with increasing absolute speed v (in cm min-1): O2=40.1+0.58v-0.15m (r2=0.35, P=0.04), where m is body mass (in g). Minimum cost of transport, calculated from the slope of absolute speed on O2, was 20.3 J kg-1 m-1. Total cost of transport (COTT) and net cost of transport (COTN) were high at low speeds and decreased as speed increased, to minima of 86.0 J kg-1 m-1 and 29.7 J kg-1 m-1, respectively, at speeds measured in the respirometer. Log10-transformation of both cost of transport and speed data yielded linear relationships with the following regression equations: log10COTT=3.35-0.90log10v-0.21log10m (r2=0.89; P<0.006) and log10COTN=2.29-0.69log10v-0.09log10m (r2=0.48; P<0.006), respectively.
SECRETORY LEUKOCYTE PROTEASE INHIBITOR (SLPI) REGULATE THE EMBRYONIC DIFFERENTIATION DURING PERIIMPLANTATION STAGE (2007)

Embryonic implantation is a results of colaboration between blastocyst and uterine endometrium. SLPI detected in the uterine luminal epithelia at the time of implantation. It is curious whether SLPI can work as regulatory factor in embryonic development during periimplantation stages. In here, we demonstrate a novel role for SLPI in preimplantation embryonic developmental progression during preimplantation period. SLPI mRNA was detected from PN stage and showed peak at 8-cell stage and 4.5pc stage. Protein level also showed same patterns. Embryonic development was much more successful when preimplantation stage embryos were exposed to recombinant SLPI: the early stage was much batter than the later stage. SLPI specific antisense-ODN (As-ODN) had not any significant changes in embryonic development until 8-cell stage. However, after 8-cell stage, development to the next stage was delayed and most of the hatching embryos failed to escapes the ZP by the AS-ODN. In addition, after being exposed to the As-ODNs, embryos could not regain the same level of developmental potency displayed by control group. Coincide with those results, SLPI protein was strongly localized in the extracellular metrix (ECM) of the blastomeres in blastocyst but it was hardly detected in the early stage embryos. In addition, SLPI could modulate the expression of other genes, MMP9, neutrophil elastase, and PAI-1. From our results, it is clear that embryo has its own SLPI during early embryonic stage and exogenous SLPI can modulate the embryonic gene expression. We propose that SLPI regulate the embryonic differentiation to morula, blastocyst as an auto-/para-crine factor. (poster)
Crystallization and Properties of p-Hydroxybenzoate Hydroxylase from Pseudomonas putida (1966)

Abstract 1. The inducible p-hydroxybenzoate hydroxylase of Pseudomonas putida which catalyzes the hydroxylation of p-hydroxybenzoate to protocatechuate has been obtained in crystalline form as a protein homogeneous upon ultracentrifugation and electrophoresis. The molecular weight is estimated to be 83,600. 2. The enzyme contains approximately 1 mole of flavin adenine dinucleotide per mole of protein. Reduced nicotinamide adenine dinucleotide phosphate, but not reduced nicotinamide adenine dinucleotide, serves as the hydrogen donor. 3. The enzyme is highly specific for p-hydroxybenzoate. Only four other aromatic compounds could be attacked at rates of less than 5% of the rate with p-hydroxybenzoate in all cases. 4. Under anaerobic conditions, the enzyme can catalyze the reduction of FAD by NADPH. This reaction requires the presence of the aromatic substrate to proceed at a significant rate. 5. The absorption spectrum of the enzyme in the visible region is slightly modified by the presence of the aromatic substrate.
The Skin Produces Urocortin1 (2000)

Since the skin produces POMC peptides, in the present work we investigated local production of urocortin, a peptide related to CRH, the normal endogenous stimulant for POMC. Urocortin immunoreactivity was detected by direct RIA in extracts of human skin, mouse skin (C57BL-6 strain), cultured cells from established lines of human melanoma and squamous cell carcinoma, human keratinocytes (Ha-CaT), and hamster melanomas. Addition of a reverse phase high performance liquid chromatography step before the RIA confirmed the presence of urocortin, as the immunoreactivity eluted at the same retention time as urocortin standard in extracts from HaCaT keratinocytes and mouse skin. Using the tandem technique of liquid chromatography-mass spectrometry, we identified a peptide with the same mass and retention time as the urocortin standard in human skin extracts. The urocortin antigen could be immunolocalized to normal keratinocytes of the epidermis and hair follicle, epithelium of sweat and sebaceous glands, dermal skeletal muscle, and nevocytes; it was also detected in melanoma and basal cell carcinoma cells. RT-PCR amplification of ribonucleic acid from human skin, cultured keratinocytes, and melanoma cells showed a 145-kb fragment from the coding region of exon 2 of the urocortin gene in all of the tested sources. Lastly, sequencing of the amplified fragment confirmed 100% homology with the known sequence of the urocortin gene. In conclusion, we now demonstrate that human skin and mouse skin as well as cultured keratinocytes and melanoma cells exhibit functional expression of the urocortin gene with actual production of urocortin peptide.
Identifying biological themes within lists of genes with EASE (2003)

EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE, and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from "genes to themes."
Terminal 3p deletions in two families—Correlation between molecular karyotype and phenotype (2010)

The 3p deletion syndrome is a rare disorder caused by deletions of different sizes in the 3p25-pter region. It is characterized by growth retardation, developmental delay, mental retardation, dysmorphism, microcephaly, and ptosis. The phenotype of individuals with deletions varies from normal to severe. Most cases occur de novo, but a few familial cases have been reported. We describe two families with terminal 3p deletions and extremely variable clinical features. In family A, the mother and daughter were extremely mildly affected whereas the son had more severe clinical features. In family B, the mother was normal and her son was affected, having some symptoms that had not been described in the 3p deletion syndrome before. The deletions were characterized by genome-wide SNP array analysis and were 9 and 1.1 Mb in size. Sequencing analysis of the CHL1, CNTN4, and CRBN genes did not reveal any masked recessive alleles that might explain the more severe phenotypes in the probands. In family A, the 9 Mb deletion can be considered causal for the 3p deletion syndrome in the proband, but the extremely mild phenotype in the other family members remains unexplained. In family B, the 1.1 Mb terminal deletion encompasses only the CHL1 gene, which is insufficient to cause 3p deletion symptoms; thus the clinical features observed in this family may have a different cause. The variable penetrance of 3p deletions creates challenges in genetic counseling, as the phenotype of the offspring cannot be predicted based on chromosomal and/or genome-wide array analytical findings.
A refined molecular taxonomy of breast cancer (2011)

The current histoclinical breast cancer classification is simple but imprecise. Several molecular classifications of breast cancers based on expression profiling have been proposed as alternatives. However, their reliability and clinical utility have been repeatedly questioned, notably because most of them were derived from relatively small initial patient populations. We analyzed the transcriptomes of 537 breast tumors using three unsupervised classification methods. A core subset of 355 tumors was assigned to six clusters by all three methods. These six subgroups overlapped with previously defined molecular classes of breast cancer, but also showed important differences, notably the absence of an ERBB2 subgroup and the division of the large luminal ER+ group into four subgroups, two of them being highly proliferative. Of the six subgroups, four were ER+/PR+/AR+, one was ER-/PR-/AR+ and one was triple negative (AR-/ER-/PR-). ERBB2-amplified tumors were split between the ER-/PR-/AR+ subgroup and the highly proliferative ER+ LumC subgroup. Importantly, each of these six molecular subgroups showed specific copy-number alterations. Gene expression changes were correlated to specific signaling pathways. Each of these six subgroups showed very significant differences in tumor grade, metastatic sites, relapse-free survival or response to chemotherapy. All these findings were validated on large external datasets including more than 3000 tumors. Our data thus indicate that these six molecular subgroups represent well-defined clinico-biological entities of breast cancer. Their identification should facilitate the detection of novel prognostic factors or therapeutical targets in breast cancer.
The Chromophore Structural Changes during the Photocycle of Phytochrome:  A Combined Resonance Raman and Quantum Chemical Approach (2007)

Phytochromes are sensory photoreceptors that, upon light irradiation, can be transformed between an inactive and an active state. The conversion is initiated by the photoisomerization of the cofactor, a linear methine-bridged tetrapyrrole, followed by conformational relaxations of the chromophore and the protein matrix that finally leads to the formation of the signaling state. To elucidate the underlying molecular processes, resonance Raman spectroscopy combined with quantum chemical calculations constitutes a powerful approach since it allows determination of the chromophore structure in the various states of phytochrome. On the basis of these studies, a molecular model for the photoinduced reaction cycle is derived.
Highly oversampled subband adaptive filters for noise cancellation on a low-resource DSP system (2002)

A real-time subband adaptive noise cancellation system on an ultra low-power miniature DSP system is implemented. The system is targeted at personal communication devices where the speaker may be in a noisy environment. The system is implemented on an ultra low-power DSP system that incorporates a DSP core and an oversampled WOLA filterbank. Pre-emphasis filters are used to increase the convergence rate of a leaky LMS algorithm in the oversampled subband implementation. System performance is also improved relative to a fullband implementation due to benefits arising from using subband adaptive filters instead of fullband filters. A 10 dB reduction of noise power is achieved in tests using various noise conditions. The entire DSP system consumes 2.1 mW and can be realized in a package size of 6.5 x 3.5 x 2.5 mm.
Discriminant Analysis of the Self‐Administered Alcoholism Screening Test (1987)

For a sample of 1156 patients (520 alcoholics and 636 nonalcoholics), discriminant function analyses were performed on the total score, a nine-item version, and a two-item version of the Self-Administered Alcoholism Screening Test (SAAST). With sensitivities set at 90 and 95%, specificities for the total score and nine-item versions ranged from 96.4 to 99.4%. Cross-validation of the nine-item version with the "jackknife" procedure resulted in only one additional misclassification of the 1156 subjects. Separate analyses of the male and female samples revealed that more items entered the discriminant function for women than for men and resulted in a higher, although clinically nonsignificant, percentage of correct classification for women. The results strongly support the use of either the total score or the nine-item version of the SAAST in large-scale screening for alcoholism in a medical patient population.
Suppression of experimental allergic encephalomyelitis in guinea/pigs by liposome-associated human myelin basic protein. (1981)

Human myelin basic protein (MBP) was inserted into phosphatidyl-serine liposomes and Hartley guinea pigs were treated with 1 or 2 injections of MBP-liposomes mixture by the intracardial route before an encephalitogenic challenge with MBP in CFA. Other groups of guinea pigs were pretreated with equivalent amounts of MBP in saline or of MBP in IFA. Of 24 untreated animals, 22 developed EAE and died or had to be sacrificed within 15 days after challenge. Only 4 of 29 guinea pigs treated with either 75 microgram or 112 microgram MBP-liposomes developed clinical signs of the disease. In the group pretreated with MBP in saline, 11 of 15 animals died, whereas in the MBP-IFA group, only 4 out of 10 died. Histologic modifications were also decreased in the MBP-liposomes and MBP-IFA groups, but in many instances, clinical normal guinea pigs showed disseminated perivascular infiltrates in the brain and spinal cord. Delayed hypersensitivity reactions to MBP were positive in all but 1 animal tested. Early T-rosette levels followed essentially the clinical course of the disease: they were drastically decreased 7 days after challenge in the untreated and MBP-saline-treated groups, but remained essentially normal in the MBP-liposomes group throughout the experiment. Lymphocyte transformation tests carried out in parallel with soluble MBP and with MBP-liposomes indicated that animals in certain groups responded preferentially to 1 form or the other of the antigen. Compared with prevailing procedures, the single i.v. injection of a relatively small amount of liposome-associated MBP appears to represent a promising approach for the antigen-specific suppression of EAE.
Survival and multiplication of Vibrio cholerae in the upper bowel of infant mice (1978)

The survival and multiplication of Vibrio cholerae strains of varying virulence in the upper bowel of orally challenged infant mice early in infection has been examined. Analysis of changes in the apparent specific activity (counts per minute per colony-forming unit) of the cell population after 4 h compared with the inoculum indicated that strain CA401 established a viable, multiplying cell population, whereas strains VB12 (a rough variant) and 569B were subject to host bactericidal and bacteriolytic mechanisms. An analysis of parameters which may affect the specific activity is included. We have defined the infective potential of the strains in terms of the changes in specific activity. The relative infective potentials are CA401 greater than 569B greater than VB12.
Synthesis of Meso-Substituted Chlorins via Tetrahydrobilene-a Intermediates (2001)

Chlorin building blocks incorporating a geminal dimethyl group in the reduced ring and synthetic handles in specific patterns at the perimeter of the macrocycle are expected to have utility in biomimetic and materials chemistry. A prior route employed condensation of a dihydrodipyrrin (Western half) and a bromodipyrromethane-monocarbinol (Eastern half), followed by oxidative cyclization of the putative dihydrobilene-a to form the meso-substituted zinc chlorin in yields of approximately 10%. The limited stability of the dihydrodipyrrin precluded study of the chlorin-forming process. We now have refined this methodology. A tetrahydrodipyrrin Western half (2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin) has been synthesized and found to be quite stable. The condensation of the Western half and an Eastern half (100 mM each) proceeded smoothly in CH(3)CN containing 100 mM TFA at room temperature for 30 min. The resulting linear tetrapyrrole, a 2,3,4,5-tetrahydrobilene-a, also is quite stable, enabling study of the conversion to chlorin. Refined conditions for the oxidative cyclization were found to include the following: the tetrahydrobilene-a (10 mM), AgTf (3-5 molar equiv), Zn(OAc)(2) (15 molar equiv), and 2,2,6,6-tetramethylpiperidine (15 molar equiv) in CH(3)CN at reflux exposed to air for 4-6 h, affording the zinc chlorin. The chlorin-forming process could be implemented in either a two-flask process or a one-flask process. The two-flask process was applied to form six zinc chlorins bearing substituents such as pentafluorophenyl, 3,5-di-tert-butylphenyl, TMS-ethyl benzoate, iodophenyl, or ethynylphenyl (deprotection of the TMS-ethynyl group occurred during the oxidative cyclization process). The stepwise yields (isolated) for the condensation and oxidative cyclization processes forming the tetrahydrobilene and zinc chlorin were 32-72% and 27-62%, respectively, giving overall yields of zinc chlorin from the Eastern and Western halves of 12-45%. Taken together, the refinements introduced enable 100-mg quantities of chlorin building blocks to be prepared in a facile and rational manner.
Stable distributions, pseudorandom generators, embeddings and data stream computation (2002)

In this paper we show several results obtained by combining the use of stable distributions with pseudorandom generators for bounded space. In particular: we show how to maintain (using only O(log n//spl epsiv//sup 2/) words of storage) a sketch C(p) of a point p/spl isin/l/sub 1//sup n/ under dynamic updates of its coordinates, such that given sketches C(p) and C(q) one can estimate |p-q|/sub 1/ up to a factor of (1+/spl epsiv/) with large probability. We obtain another sketch function C' which maps l/sub 1//sup n/ into a normed space l/sub 1//sup m/ (as opposed to C), such that m=m(n) is much smaller than n; to our knowledge this is the first dimensionality reduction lemma for l/sub 1/ norm we give an explicit embedding of l/sub 2//sup n/ into l/sub l//sup nO(log n)/ with distortion (1+1/n/sup /spl theta/(1)/) and a non-constructive embedding of l/sub 2//sup n/ into l/sub 1//sup O(n)/ with distortion (1+/spl epsiv/) such that the embedding can be represented using only O(n log/sup 2/ n) bits (as opposed to at least n/sup 2/ used by earlier methods).
Adhesion-induced tyrosine phosphorylation of the p130 SRC substrate (1995)

Adhesion of cells to the extracellular matrix leads to an increase in the tyrosine phosphorylation of a specific set of proteins, three of which have now been identified as the focal adhesion proteins pp125FAK, paxillin and tensin. In addition, we have previously noted the adhesion-induced tyrosine phosphorylation of a fourth protein, with an apparent molecular mass of 130. As in the case of FAK, paxillin and tensin, a 130 kDa protein is also found to be highly tyrosine phosphorylated in Rous sarcoma virus (RSV)-transformed cells. This protein forms a stable complex with pp60src and is directly phosphorylated by activated forms of c-src. Using a monoclonal antibody (mAb 4F4) specific for the src-associated p130 we show that p130 is also phosphorylated in response to cell adhesion. Immunoprecipitation of p130 followed by an anti-phosphotyrosine immunoblot revealed that adhesion of rat embryo fibroblasts (REF52) to fibronectin (FN) led to a significant increase in the phosphotyrosine content of p130. Furthermore, a comparison of cell lysates before and after immunoprecipitation confirmed the absence of tyrosine phosphorylated p130 from lysates immunoprecipitated with mAb 4F4. Immunofluorescence staining of REF52s revealed that p130 is found in focal adhesions as well as along stress fibers in a pattern reminiscent of that exhibited by alpha-actinin. In addition, in many cells, we found significant staining in the nucleus, but evidence is presented that the nuclear staining is not due to tyrosine phosphorylated p130. Finally, unlike pp125FAK, p130 does not appear to be itself a kinase as evidence by immune-complex kinase assays carried out in the presence or absence of exogenous substrates.
Mammalian pancreatic preproglucagon contains three glucagon-related peptides. (1983)

We have isolated cDNA clones encoding bovine pancreatic preproglucagon. Twenty-five putative preproglucagon clones were selected by screening 3,100 clones of a fetal bovine pancreas cDNA library with a synthetic oligodeoxynucleotide probe. The probe was a mixture of synthetic 17-base DNA oligomers constructed to correspond to the six carboxyl-terminal amino acids (residues 24-29) of mature glucagon. Restriction mapping of six of these clones suggested that they represented a single mRNA species. Primary sequence analysis of one clone containing a 1,200-base-pair DNA insert revealed that it contained an essentially full-length copy of glucagon mRNA. Analysis of the cDNA suggested a protein coding sequence of 540 nucleotides and 5'- and 3'-untranslated regions of 90 and 471 nucleotides, respectively. This cDNA sequence encoded a 20-amino acid signal sequence followed by one for glicentin, a 69-amino acid polypeptide containing an internal glucagon moiety that has been found in porcine intestines. Glicentin is followed by two additional glucagon-like peptides, each flanked by paired basic amino acids (Lys, Arg) characteristic of prohormone processing. These polypeptide sequences show striking homology with those for glucagon and other members of the glucagon family of peptides.
Lantibiotics: structure, biosynthesis and mode of action (2001)

The lantibiotics are a group of ribosomally synthesised, post-translationally modified peptides containing unusual amino acids, such as dehydrated and lanthionine residues. This group of bacteriocins has attracted much attention in recent years due to the success of the well characterised lantibiotic, nisin, as a food preservative. Numerous other lantibiotics have since been identified and can be divided into two groups on the basis of their structures, designated type-A and type-B. To date, many of these lantibiotics have undergone extensive characterisation resulting in an advanced understanding of them at both the structural and mechanistic level. This review outlines some of the more recent developments in the biochemistry, genetics and mechanism of action of these peptides.