gebhart/patrepeval huggingface dataset:
Text scanning approach for exact string matching (2010)

Exact string matching algorithms are essential components in practical applications of the computer system. In this research we propose a new concept to solve the problem of exact string matching by scanning text string for the rightmost character of the pattern in preprocessing phase. In matching phase TSPRC (Test Scanning for Pattern Rightmost Character) compares the pattern with text window from both directions simultaneously. Proposed algorithm implemented and compared with existing algorithms. Comparison results demonstrate that TSPRC is efficient than the number of the existing algorithm and take O(1) time complexity in the best case.
Human immunodeficiency virus type‐1‐specific immune responses induced by DNA vaccination are greatly enhanced by mannan‐coated diC14‐amidine (1997)

Use of mannan-coated N-t-butyl-N'-tetradecyl-3-tetradecylamino-propionamidine (diC14-amidine) as an adjuvant for a DNA vaccine encoding glycoprotein 160 of human immunodeficiency virus type-1 (HIV-1) enhanced the antigen-specific immune responses. The role of interferon-gamma (IFN-gamma) and interleukin-12 in the mechanism of adjuvant action was also evaluated. Coating of diC14-amidine with mannan significantly augmented the HIV-specific delayed-type hypersensitivity reaction induced by the immunogenic DNA. HIV-1-specific cytotoxic T lymphocyte activity was also markedly enhanced by the mannan-diC14-amidine cocktail. An immunomodulatory effect of this cocktail was inhibited by treatment with anti-IFN-gamma monoclonal antibody in vivo, which suggests that IFN-gamma plays an important role in inducing cell-mediated immunity by the DNA vaccine containing this adjuvant. The results of both antigen-specific immunoglobulin isotype analysis and cytokine measurement showed that the immunogenic DNA incorporated into mannan-coated diC14-amidine elicits Th1-biased immune responses.
Nanoscale imaging in DNA nanotechnology (2011)

DNA nanotechnology has developed powerful techniques for the construction of precisely defined molecular structures and machines, and nanoscale imaging methods have always been crucial for their experimental characterization. While initially atomic force microscopy (AFM) was the most widely employed imaging method for DNA-based molecular structures, in recent years a variety of other techniques were adopted by researchers in the field, namely electron microscopy (EM), super-resolution fluorescence microscopy, and high-speed AFM. EM is now typically applied for the characterization of compact nanoobjects and three-dimensional (3D) origami structures, as it offers better resolution than AFM and can be used for 3D reconstruction from single-particle analysis. While the small size of DNA nanostructures had previously precluded the application of fluorescence microscopic methods, the development of super-resolution microscopy now facilities the application of fast and powerful optical methods also in DNA nanotechnology. In particular, the observation of dynamical processes associated with DNA nanoassemblies-e.g., molecular walkers and machines-requires imaging techniques that are both fast and allow observation under native conditions. Here single-molecule fluorescence techniques and high-speed AFM are beginning to play an increasingly important role.
Increased Fast ripple to ripple Ratios Correlate with Reduced Hippocampal Volumes and Neuron Loss in Temporal Lobe Epilepsy Patients (2007)

In surgical patients with TLE, higher ratios of FR to ripple discharges are associated with histopathologic changes found in hippocampal sclerosis. These findings support the hypothesis that pathological alterations linked with hippocampal cell loss and synaptic reorganization promote FR and reduce ripple generation.
A Critical Role for B Cells in the Development of Memory CD4 Cells (2000)

Activated B cells express high levels of class II MHC and costimulatory molecules and are nearly as effective as dendritic cells in their APC ability. Yet, their importance as APC in vivo is controversial and their role, if any, in the development of CD4 memory is unknown. We compared responses of CD4 cells from normal and B cell-deficient mice to keyhole limpet hemocyanin over 6 mo and observed diminished IL-2 production by cells primed in the absence of B cells. This was due to lower frequencies of Ag-responsive cells and not to decreased levels of IL-2 secretion per cell. The absence of B cells did not affect the survival of memory CD4 cells since frequencies remained stable. Despite normal dendritic cell function, multiple immunizations of B cell-deficient mice did not restore frequencies of memory cells. However, the transfer of B cells restored memory cell development. Ag presentation was not essential since B cells activated in vitro with irrelevant Ag also restored frequencies of memory cells. The results provide unequivocal evidence that B cells play a critical role in regulating clonal expansion of CD4 cells and, as such, are requisite for the optimal priming of memory in the CD4 population.
Secretory leukocyte protease inhibitor, an inhibitor of neutrophil activation, is elevated in serum in human sepsis and experimental endotoxemia (2000)

Serum SLPI is elevated in human sepsis and experimental endotoxemia. Maximal concentrations of serum SLPI correlate significantly with maximal multiple organ dysfunction scores in patients with sepsis. Secretory leukocyte protease inhibitor may function to limit ongoing neutrophil-mediated tissue injury associated with organ dysfunction.
Purification and Characterization of UDP-N-Acetylglucosamine: -6-D-Mannoside ß-6N-Acetylglucosaminyltransferase(N-Acetylglucosaminyltransferase V) from a Human Lung Cancer Cell Line1 (1993)

A beta 1-6N-acetylglucosaminyltransferase (GnT-V) [EC 2.4.1.155] which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to alpha-D-6-mannoside has been purified up to 20,000-fold from the cultured supernatant of the QG small lung cancer cell line with a 37% yield. The isolation procedure included chromatography on phenyl-Sepharose, hydroxylapatite, UDP-hexanolamine Sepharose, and a biantennary sugar substrate (GnGn-bi-Asn) coupled to activated CH-Sepharose 4B. Sodium dodecyl sulfate gel electrophoresis under non-reducing conditions showed a single band of 73 kDa. Under reducing conditions, however, an additional component of 60 kDa was seen. Peptide mapping analysis indicated that both of these proteins were essentially identical, indicating that the 60-kDa component is probably a proteolytically cleaved form of the 73-kDa protein. Studies on the activity of the enzyme toward a variety of pyridylaminated sugars showed that the enzyme is most active toward triantennary (GnGnGn-tri-PA) and biantennary (GnGn-bi-PA) sugars. The Km values for GnGn-bi-PA and UDP-GlcNAc were 133 microM and 3.5 mM, respectively. These studies represent the first report of the enzymatic properties of a highly purified human GnT-V.
Local immunotherapy of glioma patients with a combination of 2 bispecific antibody fragments and resting autologous lymphocytes: Evidence forin situT-cell activation and therapeutic efficacy (2000)

After adoptive transfer of pre-activated lymphocytes into the operation cavity of glioma patients, tumor regression and improved survival have been reported in some patients. Results were most impressive when bispecific antibodies with tumor × CD3 specificity were also applied. In this study, we attempted to avoid time-consuming pre-activation procedures for adoptively transferred cells by using a combination of bispecific antibodies directed to the EGF receptor (EGFR) on tumor cells and to CD3 and CD28 on T cells. Eleven patients with high-grade malignant glioma received 3 injections of 2 bispecific antibody fragments (EGFR × CD3 and EGFR × CD28) together with freshly isolated autologous lymphocytes via an Ommaya reservoir. Intracavitary fluid aspirated during immunotherapy was examined for markers of T-cell activation. Increased levels of soluble IL-2 receptor and TNF-α were detected in the intracavitary fluid of all patients tested. Two of the 11 treated patients experienced a beneficial response to therapy as defined by a transient contrast enhancement in subsequent MRI scans and prolonged survival. Side effects were transient and consisted of fever, nausea, headache and aggravation of pre-existing neurologic deficits. These adverse effects were most likely due to the antibody construct containing anti-CD3 specificity. Two patients developed cerebral edema and required steroid treatment. © 2001 Wiley-Liss, Inc.
Determining True HER2 Gene Status in Breast Cancers With Polysomy by Using Alternative Chromosome 17 Reference Genes: Implications for Anti-HER2 Targeted Therapy (2011)

Our results support the findings of recent pangenomic studies that true polysomy 17 is uncommon. Additional FISH studies that use probes to the SMS, RARA, and TP53 genes are an effective way to determine the true HER2 amplification status in patients with polysomy 17 and they have important potential implications for guiding HER2-targeted therapy in breast cancer.
View planning for automated three-dimensional object reconstruction and inspection (2003)

Laser scanning range sensors are widely used for high-precision, high-density three-dimensional (3D) reconstruction and inspection of the surface of physical objects. The process typically involves planning a set of views, physically altering the relative object-sensor pose, taking scans, registering the acquired geometric data in a common coordinate frame of reference, and finally integrating range images into a nonredundant model. Efficiencies could be achieved by automating or semiautomating this process. While challenges remain, there are adequate solutions to semiautomate the scan-register-integrate tasks. On the other hand, view planning remains an open problem---that is, the task of finding a suitably small set of sensor poses and configurations for specified reconstruction or inspection goals. This paper surveys and compares view planning techniques for automated 3D object reconstruction and inspection by means of active, triangulation-based range sensors.
Localization and expression of spermadhesin PSP‐I/PSP‐II subunits in the reproductive organs of the boar (2007)

The epithelial localization and expression of the spermadhesin PSP-I and PSP-II subunits were determined in the testis, ductus epididymes (caput, corpus and cauda), seminal vesicles and bulbourethral glands of mature boars, using immunohistochemical, western blotting and RT-PCR methods. Immunohistochemistry showed positive labelling for PSP-I and PSP-II antibodies in the epithelium of seminal vesicles in all males tested. Positive immunolabelling, but with variable intensity, was also present in the epididymal epithelium (caput, corpus and cauda), although varying largely among segments and boars. Immunoreactivity was nearly or completely absent in the seminiferous epithelium and the bulbourethral gland, although SDS-PAGE and western blotting revealed the presence of PSP-I and PSP-II immunoreactive bands in all the tissue extracts, including the testis and the bulbourethral gland. mRNA amplification by RT-PCR using primers specific for PSP-I and PSP-II showed a trend similar to that observed for western blotting, i.e. intensity variation between tissues (even between segments of the same epididymis) and among boars. Our results indicate that the seminal vesicles are the main source of PSP-I and PSP-II spermadhesins, although epididymal segments, testis and the bulbourethral gland also participate in the expression of both proteins.
Vitronectin is not essential for normal mammalian development and fertility. (1995)

Vitronectin (VN) is an abundant glycoprotein present in plasma and the extracellular matrix of most tissues. Though the precise function of VN in vivo is unknown, it has been implicated as a participant in diverse biological processes, including cell attachment and spreading, complement activation, and regulation of hemostasis. The major site of synthesis appears to be the liver, though VN is also found in the brain at an early stage of mouse organogenesis, suggesting that it may play an important role in mouse development. Genetic deficiency of VN has not been reported in humans or in other higher organisms. To examine the biologic function of VN within the context of the intact animal, we have established a murine model for VN deficiency through targeted disruption of the murine VN gene. Southern blot analysis of DNA obtained from homozygous null mice demonstrates deletion of all VN coding sequences, and immunological analysis confirms the complete absence of VN protein expression in plasma. However, heterozygous mice carrying one normal and one null VN allele and homozygous null mice completely deficient in VN demonstrate normal development, fertility, and survival. Sera obtained from VN-deficient mice are completely deficient in "serum spreading factor" and plasminogen activator inhibitor 1 binding activities. These observations demonstrate that VN is not essential for cell adhesion and migration during normal mouse development and suggest that its role in these processes may partially overlap with other adhesive matrix components.
InP Layer Transfer with Masked Implantation (2009)

InP layer transfer with masked implantation was investigated to eliminate ion-implantation induced damage involved in the ion-cut process. InP donor wafers were selectively implanted with hydrogen through a mask at a dose of 8.5 × 10<sup>16</sup> ions/cm<sup>2</sup> at 160 keV. The layers which were subsequently mechanically exfoliated were characterized by large pyramidal protrusions on the surface, associated with the unimplanted regions. This undesirable morphology was bypassed through the inclusion of a selective etch-stop layer. The resulting structures possessed flat surfaces suitable for further bonding. This process enables the transfer of finished devices, unaffected by ion-implantation, onto a variety of desirable substrates.
Clinical assessment and interpretation of abnormal illness behaviour in low back pain (1989)

Patients with chronic low back pain present with a mixture of symptoms and signs. Some are a direct consequence of physical pathology whereas others are attributable to associated and appropriate psychological and behavioural changes. At times the latter may be out of keeping with the degree of physical pathology and thus have specific significance in terms of the affective and cognitive disturbances that are also present and which may be the basis for abnormal illness behaviour. In an attempt to demonstrate more clearly the relationship between physical, psychological and behavioural components of illness, this paper draws on two data sets in patients with low back pain. The first explores the relationship between behavioural symptoms and signs, objective physical impairment, pain and disability and psychometric measures of distress together with scales making up the illness behaviour questionnaire (IBQ) of Pilowsky and Spence. A second data set is used to assess the value of the IBQ in understanding how psychological distress and behavioural signs and symptoms are related to the outcome of surgical treatment. The results gained reveal that behavioural symptoms and signs are directly related to the physical severity of low back disorder, the patient's report of pain and disability and the outcome of surgical treatment. Scores on the IBQ were strongly related to measures of affective disturbance and psychological distress. More specifically the disease affirmation scale of the IBQ, incorporating scales for disease conviction and psychological versus somatic focussing was an important dimension in relation to the behavioural symptoms and signs, thereby confirming results gained by other workers. Disease conviction and lack of response to clinicians' reassurances regarding illness - a situation in which abnormal illness behaviour is often deemed to exist - should not be seen simply as a function of the disease process, but more as a psychological coping mechanism for certain individuals under stress. The significance of this observation is discussed in relation to decisions regarding the overall assessment of chronic pain patients and their treatment.
Oligonucleotide site-directed mutagenesis in Xenopus egg extracts (1988)

Addition of M13mp18 single-stranded DNA annealed with an oligonucleotide to a Xenopus egg extract results in a rapid and efficient incorporation of the oligonucleotide in a complete double-stranded supercoiled molecule. Both the efficiency of DNA synthesis and the recovery of complete double-stranded molecules are increased relative to the reaction carried out by the classical technique using the E. coli Klenow DNA polymerase, DNA ligase, dNTPs, ATP and ions. Site specific mutagenesis was assayed by reverting a point mutation in the lacz region of M13mp18. The color assay described by Messing and sequencing of the DNA extracted from isolated plaques was used to check for the reversion. A 2 hr incubation of the heteroduplex carrying the mutagenic oligonucleotide in the Klenow-ligase-dNTP mixture allows a recovery of 6% mutant phage after transformation of competent cells with the reaction products. Using the Xenopus egg extract, 83% mutant phage were recovered after the same incubation time, in reactions entirely performed in parallel. The Xenopus extract is stable and contains all components required for the assay, including all ionic and protein factors; thus the only addition is the annealed DNA. Such an eukaryotic system is therefore an attractive alternative to the reconstituted prokaryotic DNA polymerase-DNA ligase system for site specific mutagenesis.
Transgenic barley expressing a protein-engineered, thermostable (1,3-1,4)-beta-glucanase during germination. (1996)

The codon usage of a hybrid bacterial gene encoding a thermostable (1,3-1,4)-beta-glucanase was modified to match that of the barley (1,3-1,4)-beta-glucanase isoenzyme EII gene. Both the modified and unmodified bacterial genes were fused to a DNA segment encoding the barley high-pI alpha-amylase signal peptide downstream of the barley (1,3-1,4)-beta-glucanase isoenzyme EII gene promoter. When introduced into barley aleurone protoplasts, the bacterial gene with adapted codon usage directed synthesis of heat stable (1,3-1,4)-beta-glucanase, whereas activity of the heterologous enzyme was not detectable when protoplasts were transfected with the unmodified gene. In a different expression plasmid, the codon modified bacterial gene was cloned downstream of the barley high-pI alpha-amylase gene promoter and signal peptide coding region. This expression cassette was introduced into immature barley embryos together with plasmids carrying the bar and the uidA genes. Green, fertile plants were regenerated and approximately 75% of grains harvested from primary transformants synthesized thermostable (1,3-1,4)-beta-glucanase during germination. All three trans genes were detected in 17 progenies from a homozygous T1 plant.
Vibrio cholerae iron transport systems: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems (1994)

Vibrio cholerae iron transport mutants were tested for their ability to cause disease in an infant mouse model. The mice were challenged with either the wild-type strain, a vibriobactin synthesis mutant, a heme utilization mutant, or double mutants containing both the vibriobactin synthesis defect and the heme utilization defect. When mice were challenged with 10(7) bacteria, the ability of the double mutant to survive in the intestines was greatly reduced and that of the heme utilization mutant was slightly reduced compared with that of the wild type or the vibriobactin synthesis mutant. When the inoculum size was reduced 10-fold, all of the iron transport mutants failed to colonize the intestines and failed to cause diarrhea in the mice, whereas the wild-type strain was not cleared and elicited a diarrheal response. These data indicate that disruption of either the heme utilization or the vibriobactin uptake system reduces the ability of V. cholerae to cause disease. One of the heme utilization mutants, DHH1, was found to be defective also in utilization of vibriobactin and ferrichrome, mimicking the Escherichia coli TonB- phenotype. This mutant was the least virulent of the iron transport mutants tested. Transformation of DHH1 with the recombinant plasmid pHUT4 restored the abilities to use hemin, vibriobactin, and ferrichrome as iron sources, suggesting that pHUT4 encodes a gene(s) involved globally in the iron transport systems. Hybridization of Vibrio DNA with the V. cholerae heme utilization genes demonstrated the presence of DNA homologous to the genes encoding the outer membrane protein HutA and the inner membrane protein HutB in all the V. cholerae strains tested. The probe containing hutA, but not that containing hutB, also hybridized to DNA from Vibrio parahaemolyticus.
Structure−Activity Relationships in Toll-like Receptor-2 Agonistic Diacylthioglycerol Lipopeptides (2010)

The N-termini of bacterial lipoproteins are acylated with a (S)-(2,3-bisacyloxypropyl)cysteinyl residue. Lipopeptides derived from lipoproteins activate innate immune responses by engaging Toll-like receptor 2 (TLR2) and are highly immunostimulatory and yet without apparent toxicity in animal models. The lipopeptides may therefore be useful as potential immunotherapeutic agents. Previous structure-activity relationships in such lipopeptides have largely been obtained using murine cells, and it is now clear that significant species-specific differences exist between human and murine TLR responses. We have examined in detail the role of the highly conserved Cys residue as well as the geometry and stereochemistry of the Cys-Ser dipeptide unit. (R)-Diacylthioglycerol analogues are maximally active in reporter gene assays using human TLR2. The Cys-Ser dipeptide unit represents the minimal part-structure, but its stereochemistry was found not to be a critical determinant of activity. The thioether bridge between the diacyl and dipeptide units is crucial, and replacement by an oxoether bridge results in a dramatic decrease in activity.
Long range propagation of conformational changes in integrin alpha IIb beta 3. (1993)

Integrin adhesion receptors participate in two-way transfer of information across the plasma membrane. For example, cytoplasmic events, such as activation of protein kinase C, cause an increase in the fibrinogen (Fg) binding affinity of the extracellular domain of integrin alpha IIb beta 3 ("inside-out signaling"). Conversely, ligand binding to alpha IIb beta 3 results in the generation of intracellular signals. We used anti-LIBS2, an anti-beta 3 monoclonal antibody, to understand potential mechanisms of this bidirectional signaling. Anti-LIBS2 bound to alpha IIb beta 3 with low affinity (Kd = 7.4 microM), and mimicked inside-out signaling by promoting Fg binding. The affinity of anti-LIBS2 binding was increased 20-fold (Kd = 326 nM) by addition of an Fg-mimetic synthetic peptide, RGDS. Thus, anti-LIBS2 and ligands (Fg and Fg-mimetic peptides) bind cooperatively to integrin alpha IIb beta 3, indicating a functional linkage between the ligand-binding site and the antibody-binding site. The anti-LIBS2-binding site was mapped by its binding to proteolytic and recombinant fragments of the beta 3 subunit. The epitope was located within an 89-residue region immediately adjacent to the transmembrane domain and 400 residues carboxyl-terminal to the known ligand-binding site(s). Electron microscope images of rotary shadowed ternary complexes of Fg, anti-LIBS2, and alpha IIb beta 3 revealed that the ligand-binding site and anti-LIBS2 epitope are separated by about 16 nm. This indicates that propagated long distance conformational changes can occur in alpha IIb beta 3. Such changes are likely to be involved in the bidirectional signaling function of this integral membrane protein.