gebhart/patrepeval huggingface dataset:
Poly(?-hydroxyl acids)/hydroxyapatite porous composites for bone-tissue engineering. I. Preparation and morphology (1999)

Tissue engineering has shown great promise for creating biological alternatives for implants. In this approach, scaffolding plays a pivotal role. Hydroxyapatite mimics the natural bone mineral and has shown good bone-bonding properties. This paper describes the preparation and morphologies of three-dimensional porous composites from poly(L-lactic acid) (PLLA) or poly(D,L-lactic acid-co-glycolic acid) (PLGA) solution and hydroxyapatite (HAP). A thermally induced phase separation technique was used to create the highly porous composite scaffolds for bone-tissue engineering. Freeze drying of the phase-separated polymer/HAP/solvent mixtures produced hard and tough foams with a co-continuous structure of interconnected pores and a polymer/HAP composite skeleton. The microstructure of the pores and the walls was controlled by varying the polymer concentration, HAP content, quenching temperature, polymer, and solvent utilized. The porosity increased with decreasing polymer concentration and HAP content. Foams with porosity as high as 95% were achieved. Pore sizes ranging from several microns to a few hundred microns were obtained. The composite foams showed a significant improvement in mechanical properties over pure polymer foams. They are promising scaffolds for bone-tissue engineering. © 1999 John Wiley & Sons, Inc. J Biomed Mater Res, 44, 446–455, 1999.
Patterns of failure following surgical resection of renal cell carcinoma: implications for adjuvant local and systemic therapy. (1994)

LF is rare following surgical management of RCC, and shows no clear causal relationship with the development of DM. Patients die of DM, and not LF. These data do not support the role of adjuvant radiation therapy in this disease. Patients with LN involvement or renal vein extension have a significantly increased risk for developing DM, and are therefore appropriate candidates for trials investigating systemic therapy.
XPS Imaging of Patterned Self-assembled Monolayers Containing Perfluorinated Alkyl Chains (1996)

X-ray photoelectron spectroscopy (E–X) imaging has been applied to the study of perfluorinated self-assembled monolayers (SAM) adsorbed on gold surfaces. Patterned monolayers were formed using a ‘stamping’ procedure which enabled the formation of ‘two-component’ monolayers. TheE–X images yield spatial information, with a30 μm resolution, on the quality and chemical composition of the resulting monolayer structures.
Selective inhibitors of phosphoinositide 3-kinase delta: modulators of B-cell function with potential for treating autoimmune inflammatory diseases and B-cell malignancies (2012)

The delta isoform of the p110 catalytic subunit (p110δ) of phosphoinositide 3-kinase is expressed primarily in hematopoietic cells and plays an essential role in B-cell development and function. Studies employing mice lacking a functional p110δ protein, as well as the use of highly-selective chemical inhibitors of p110δ, have revealed that signaling via p110δ-containing PI3K complexes (PI3Kδ) is critical for B-cell survival, migration, and activation, functioning downstream of key receptors on B cells including the B-cell antigen receptor, chemokine receptors, pro-survival receptors such as BAFF-R and the IL-4 receptor, and co-stimulatory receptors such as CD40 and Toll-like receptors (TLRs). Similarly, this PI3K isoform plays a key role in the survival, proliferation, and dissemination of B-cell lymphomas. Herein we summarize studies showing that these processes can be inhibited in vitro and in vivo by small molecule inhibitors of p110δ enzymatic activity, and that these p110δ inhibitors have shown efficacy in clinical trials for the treatment of several types of B-cell malignancies including chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL). PI3Kδ also plays a critical role in the activation, proliferation, and tissue homing of self-reactive B cells that contribute to autoimmune diseases, in particular innate-like B-cell populations such as marginal zone (MZ) B cells and B-1 cells that have been strongly linked to autoimmunity. We discuss the potential utility of p110δ inhibitors, either alone or in combination with B-cell depletion, for treating autoimmune diseases such as lupus, rheumatoid arthritis, and type 1 diabetes. Because PI3Kδ plays a major role in both B-cell-mediated autoimmune inflammation and B-cell malignancies, PI3Kδ inhibitors may represent a promising therapeutic approach for treating these diseases.
New developments in gastrointestinal stromal tumor (2006)

Continued intense study of gastrointestinal stromal tumor may lead to new paradigms that could revolutionize all of oncology.
Cell-Penetrating Peptides (2002)

Classes of Cell-Penetrating Peptides. Mechanisms of Cell Penetration, Interactions of Cell-Penetrating Peptides with Plasma Membranes and Lipid Models. Applications of Cell-Penetrating Peptides.
Isotype specificity of antigen-specific helper clone in vivo. (1987)

Inoculation of an immortalized clone of radiation leukemia virus (RadLV)-transformed antigen (ovalbumin, OVA)-specific T cells together with the relevant carrier (OVA) into unprimed syngeneic mice results in a preferential increase in the expression of anti-OVA antibodies of the immunoglobulin (Ig)G2b and IgG2a isotypes. Identical boosting of the clone-primed mice further augments the preferential production of anti-OVA antibodies of these two isotypes. The class-related helper activity is not due to nonspecific shift of class expression produced by the injected tumor cells, as a non-helper clone of RadLV-transformed T cells does not change the isotypic pattern of anti-OVA antibodies in the inoculated mice. A carrier-specific activation of the B cells is responsible for the class-restricted function of the helper clone. The isotypic profile of anti-hapten antibodies in mice injected with 2,4-dinitrophenyl (DNP)-bovine serum albumin and OVA-specific helper clone is not altered. On the other hand, mice inoculated with the OVA-specific helper clone and DNP-OVA respond with a preferential elevation of anti-DNP antibodies of the IgG2a and IgG2b isotypes. The preferential class augmentation may result from carrier-specific signals delivered by the helper clone which activate B cells in vivo toward certain CH expression. Alternatively, the observed class pattern may be induced by an isotype noncommited helper clone which triggers selected population of B lymphocytes of defined differentiation status toward secretion of a restricted array of isotypes. Regardless of the mechanism of the clone-dependent class expression, the isotypic profile in most of the experiments clearly demonstrates that an antigen-specific helper clone may be one of the elements which regulates the class of antibodies to be produced in vivo under normal physiologic conditions.
Chromogranin A Fragments Modulate Cell Adhesion (1997)

Although several functions have been suggested for chromogranin A, a glycoprotein secreted by many neuroendocrine cells, the physiological role of this protein and of its proteolytic fragments has not been established. We have found that mixtures of chromogranin A fragments can inhibit fibroblast adhesion. The anti-adhesive activity was converted into pro-adhesive activity by limited trypsin treatment. Pro-adhesive effects were observed also with recombinant N-terminal fragments corresponding to residues 1-78 and 1-115 and with a synthetic peptide encompassing the residues 7-57. These fragments induced adhesion and spreading of fibroblasts on plates coated with collagen I or IV, laminin, fetal calf serum (FCS) but not on bovine serum albumin. The long incubation time required for adhesion assays (4 h) and the FCS requirements for optimal adhesion suggest that the adhesive activity is likely indirect and requires other proteins present in the FCS or made by the cells. These findings suggest that chromogranin A and its fragments could play a role in the regulation of cell adhesion. Since chromogranin A is concentrated and stored within granules and rapidly released by neuroendocrine cells and neurons after an appropriate stimulus, this protein could be important for the local control of cell adhesion by stimulated cells.
Reduced state fair queuing for edge and core routers (2004)

Despite many years of research, fair queuing still faces a number of implementation challenges in high speed routers. In particular, in spite of proposals such as DiffServ, the state needs for even simple schedulers are still large for heavily channelized core routers and for edge routers. An earlier proposal, Stochastic Fair Queuing, reduces state but at the expense of added unfairness between certain flows. Another earlier scheme, Core Stateless Fair Queuing, requires header changes and does not address the state needs of edge routers. By contrast, our paper proposes a randomization technique that removes the need to store deficit counters per flow in Deficit Round Robin and its variants. Even without the counters, we show, using both analysis and simulation, that randomized technique preserves throughput fairness properties of DRR. This randomization technique introduced in this paper can be used to considerably reduce the state requirements of high speed schedulers in edge and core routers, making hardware designs feasible. The randomization idea in this paper can also be applied to other round robin schedulers as well as potentially in entirely different scenarios wherever deficits need to be tracked over time explicitly.
Pruritus in Cutaneous T-cell Lymphomas: Frequent, Often Severe and Difficult to Treat (2010)

Pruritus has a well-known association with Hodgkin's disease and other nodal lymphomas; indeed it often reveals the disease. Pruritus is also an important symptom of cutaneous T-cell lymphomas. Lymphoma-associated itch is thus both frequent and severe, but its pathophysiology remains unclear. Few studies have evaluated the efficacy of therapeutic agents in the management of cutaneous T-cell lymphoma-related pruritus. The main objective of treatment remains disease control. Pruritus management is generally based on the physician's experience. Treatment is very difficult, especially in Sézary syndrome. We present here management strategies for cutaneous lymphoma-associated pruritus.
The bi-directional spike detection in EEG using mathematical morphology and wavelet transform (2003)

Epileptic EEG often contains abnormal spiky activity which is diagnostically important. It is proposed that the multi-resolution wavelet transform with mathematical morphology can be used to detect and extract this activity. Differentiating the geometrical characteristics between spikes and normal EEG activity, the process extracts the target patterns from the EEG data in the multi-resolution domains. Morphological analysis utilizes analytic operations based on a pre-defined structuring element (SE) targeted to specific signal features. In our case the SE is defined as a disk to measure the difference in smoothness between the two components. Discrete wavelet transforms are applied to construct the processed signal. The multi-resolution property of the wavelet transform adapts well to the time-invariant nature of the signal. Combining mathematical morphology and wavelet transforms, this method successfully separates the background activity and transient phenomenon from epileptic EEG. Although the morphological operation is a non-linear process, we show that, with the selected structuring element, this approach has ability to detect both positive and negative going spikes identically.
Identification of a Two-Component Signal Transduction System from Corynebacterium diphtheriae That Activates Gene Expression in Response to the Presence of Heme and Hemoglobin (1999)

Corynebacterium diphtheriae, the causative agent of diphtheria, utilizes various host compounds to acquire iron. The C. diphtheriae hmuO gene encodes a heme oxygenase that is involved in the utilization of heme and hemoglobin as iron sources. Transcription of the hmuO gene in C. diphtheriae is controlled under a dual regulatory mechanism in which the diphtheria toxin repressor protein (DtxR) and iron repress expression while either heme or hemoglobin is needed to activate transcription. In this study, two clones isolated from a C. diphtheriae chromosomal library were shown to activate transcription from the hmuO promoter in Escherichia coli. Sequence analysis revealed that these activator clones each carried distinct genes whose products had significant homology to response regulators of two-component signal transduction systems. Located upstream from each of these response regulator homologs are partial open reading frames that are predicted to encode the C-terminal portions of sensor kinases. The full-length sensor kinase gene for each of these systems was cloned from the C. diphtheriae chromosome, and constructs each carrying one complete sensor kinase gene and its cognate response regulator were constructed. One of these constructs, pTSB20, which carried the response regulator (chrA) and its cognate sensor kinase (chrS), was shown to strongly activate transcription from the hmuO promoter in a heme-dependent manner in E. coli. A mutation in chrA (chrAD50N), which changed a conserved aspartic acid residue at position 50, the presumed site of phosphorylation by ChrS, to an asparagine, abolished heme-dependent activation. These findings suggest that the sensor kinase ChrS is involved in the detection of heme and the transduction of this signal, via a phosphotransfer mechanism, to the response regulator ChrA, which then activates transcription of the hmuO promoter. This is the first report of a bacterial two-component signal transduction system that controls gene expression through a heme-responsive mechanism.
Combined Physical and Genetic Map of the Pseudomonas putida KT2440 Chromosome (1998)

A combined physical and genetic map of the Pseudomonas putida KT2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (PFGE) and Southern hybridization. Circular genome size was estimated at 6.0 Mb by adding the sizes of 19 SwaI, 9 PmeI, 6 PacI, and 6 I-CeuI fragments. A complete physical map was achieved by combining the results of (i) analysis of PFGE of the DNA fragments resulting from digestion of the whole genome with PmeI, SwaI, I-CeuI, and PacI as well as double digestion with combinations of these enzymes and (ii) Southern hybridization analysis of the whole wild-type genome digested with different enzymes and hybridized against a series of probes obtained as cloned genes from different pseudomonads of rRNA group I and Escherichia coli, as P. putida DNA obtained by PCR amplification based on sequences deposited at the GenBank database, and by labeling of macrorestriction fragments of the P. putida genome eluted from agarose gels. As an alternative, 10 random mini-Tn5-Km mutants of P. putida KT2440 were used as a source of DNA, and the band carrying the mini-Tn5 in each mutant was identified after PFGE of a series of complete chromosomal digestions and hybridization with the kanamycin resistance gene of the mini-Tn5 as a probe. We established a circular genome map with an average resolution of 160 kb. Among the 63 genes located on the genetic map were key markers such as oriC, 6 rrn loci (rnnA to -F), recA, ftsZ, rpoS, rpoD, rpoN, and gyrB; auxotrophic markers; and catabolic genes for the metabolism of aromatic compounds. The genetic map of P. putida KT2440 was compared to those of Pseudomonas aeruginosa PAO1 and Pseudomonas fluorescens SBW25. The chromosomal backbone revealed some similarity in gene clustering among the three pseudomonads but differences in physical organization, probably as a result of intraspecific rearrangements.
TRECVID 2008 -- Goals, Tasks, Data, Evaluation Mechanisms and Metrics (2009)

The TREC Video Retrieval Evaluation (TRECVID) 2008 is a TREC-style video analysis and retrieval evaluation, the goal of which remains to promote progress in content-based exploitation of digital video via open, metrics-based evaluation. Over the last 7 years this effort has yielded a\nbetter understanding of how systems can effectively accomplish such processing and how one can reliably benchmark their performance. In 2008, 77 teams (see Table 1) from various research organizations --- 24 from\nAsia, 39 from Europe, 13 from North America, and 1 from Australia --- participated in one or more of five tasks: high-level feature extraction, search (fully automatic, manually assisted, or interactive), pre-production video (rushes) summarization, copy detection, or surveillance event detection. The copy detection and surveillance event detection tasks are being run for the first time in TRECVID.\nThis paper presents an overview of TRECVid in 2008.
A cell culture analogue of rodent physiology: Application to naphthalene toxicology (1995)

The difficulties of large-scale animal testing of compounds has spurred development of in vitro testing methods and physiologically based pharmacokinetic models (PBPK). In existing in vitro methods, tissue interactions occurring in vivo are not reproduced accurately and in PBPKs the a priori prediction of metabolism is difficult. Through development of a multicompartmental, multiple cell type bioreactor system these limitations can be circumvented. A cell culture analogue (CCA) of a PBPK was developed. The CCA contains multiple chambers, each of which represents a tissue or group of similar tissues as specified in the PBPK. Proof-of-concept experiments were done using naphthalene as a model. Naphthalene is converted into naphthalene oxide and the circulation of this reactive metabolite from the liver to lung is a possible mechanism for lung injury. A CCA with liver, lung and other tissue compartments was constructed. This system was used in conjunction with cultured H4IIE rat hepatoma cells and L2 rat lung cells to study the importance of circulated naphthalene metabolites (presumably naphthalene oxides) on lung cell toxicity in rodents. By increasing the number of cells and/or inducing cytochrome P-450 activity in the liver compartment, lung cell mortality was increased. Glutathione depletion in the lung and liver cells was also observed. These results indicate that the CCA is a potentially useful concept for studying the action of compounds with reactive metabolites.
The dual receiver cryptosystem and its applications (2004)

We put forth the notion of a dual receiver cryptosystem and implement it based on bilinear pairings over certain elliptic curve groups. The cryptosystem is simple and efficient yet powerful, as it solves two problems of practical importance whose solutions have proven to be elusive before:(1) A provably secure "combined" public-key cryptosystem (with a single secret key per user in space-limited environment) where the key is used for both decryption and signing and where encryption can be escrowed and recovered, while the signature capability never leaves its owner. This is an open problem proposed by the work of Haber and Pinkas. (2) A puzzle is a method for rate-limiting remote users by forcing them to solve a computational task (the puzzle). Puzzles have been based on cryptographic challenges in the past, but the successful design of embedding a useful cryptographic task inside a puzzle, originally posed by Dwork and Naor, remained an open problem till today. We model and present "useful security puzzles" applicable in two scenarios: a secure fileserver, and an online transaction server (such as a webserver).
A short step and practical synthesis of myo-inositol 1,3,4,5-tetrakisphosphate. (1990)

The reaction of myo-inositol with benzoly chloride gave 1, 3, 4, 5-tetra-O-benzoyl-myo-inositol as a major product which was conveniently converted to myo-inositol 1, 3, 4, 5-tetrakisphosphate. The tetrabenzoate was optically resolved by means of chiral column chromatography using Chiralcel OD.
Piezoelectric Nanogenerators Based on Zinc Oxide Nanowire Arrays (2006)

We have converted nanoscale mechanical energy into electrical energy by means of piezoelectric zinc oxide nanowire (NW) arrays. The aligned NWs are deflected with a conductive atomic force microscope tip in contact mode. The coupling of piezoelectric and semiconducting properties in zinc oxide creates a strain field and charge separation across the NW as a result of its bending. The rectifying characteristic of the Schottky barrier formed between the metal tip and the NW leads to electrical current generation. The efficiency of the NW-based piezoelectric power generator is estimated to be 17 to 30%. This approach has the potential of converting mechanical, vibrational, and/or hydraulic energy into electricity for powering nanodevices.
Rapid detection of the mecA gene in methicillin-resistant staphylococci by enzymatic detection of polymerase chain reaction products (1992)

In order to identify methicillin-resistant staphylococci from clinical sources with ease and reliability, enzymatic detection of polymerase chain reaction (ED-PCR) was applied. ED-PCR is based on the capture of amplified products via biotin-streptavidin affinity and the detection of an incorporated hapten in amplified products with an enzyme-linked antibody. In order to identify methicillin-resistant staphylococci of all species, a 150-bp fragment of the mecA gene was targeted for ED-PCR. After PCR was performed with a pair of biotin and dinitrophenol 5'-labeled primers, the reaction mixture was applied to a microtiter well precoated with streptavidin. Thereafter, bound PCR products were detected colorimetrically with alkaline phosphatase-conjugated anti-dinitrophenol antibody. The extraction of DNA from staphylococcal cells for PCR was simplified so that it could be performed within one tube. The total assay, including PCR, took less than 3 h. The sensitivity of mecA gene detection ranged from greater than 5 x 10(2) CFU per tube for Staphylococcus aureus to greater than 5 x 10(3) CFU per tube for Staphylococcus epidermidis. Genotyping results obtained by ED-PCR of 161 tested strains from the colonies (97 strains of S. aureus and 64 strains of coagulase-negative staphylococci) were compared with the phenotypic susceptibilities of the strains to oxacillin. The results of ED-PCR showed excellent agreement with the MICs of oxacillin with very few exceptions; only one strain of S. aureus and two strains of coagulase-negative staphylococci were found to possess the mecA gene, which was discrepant with their phenotypes. Fifty-five blood culture samples were also tested by ED-PCR. For staphylococcal isolates in 33 of the cultures, oxacillin MICs were >4 microgram/ml; 31 of the 33 staphylococcal isolates were determined by ED-PCR to be mecA gene positive. These results suggest that ED-PCR can be used with reasonable confidence in the clinical microbiological laboratory.
Development and validation of the menorrhagia outcomes questionnaire (1998)

The Menorrhagia Outcomes Questionnaire is a practical and scientifically sound measure of outcome from the woman's perspective following surgical treatment for menorrhagia due to benign disease. It takes less than five minutes to complete, is appropriate for use with different surgical treatments for menorrhagia (eg. hysterectomy, endometrial resection, laser ablation) and is feasible for routine monitoring of large numbers of women by postal survey. Most importantly, this questionnaire has been shown to perform well from a scientific point view, having met standard psychometric criteria for reliability and validity.