gebhart/patrepeval huggingface dataset:
Identification of the molecular basis for the functional difference between flavonoid 3′‐hydroxylase and flavonoid 3′,5′‐hydroxylase (2007)

Flavonoid 3'-hydroxylase (F3'H) and flavonoid 3',5'-hydroxylase (F3'5'H) are cytochrome P450 enzymes and determine the B-ring hydroxylation pattern of flavonoids by introducing hydroxyl groups at the 3'- or the 3'- and 5'-position, respectively. Sequence identity between F3'H and F3'5'H is generally low since their divergence took place early in the evolution of higher plants. However, in the Asteraceae the family-specific evolution of an F3'5'H from an F3'H precursor occurred, and consequently sequence identity is substantially higher. We used this phenomenon for alignment studies, in order to identify regions which could be involved in determining substrate specificity and functionality. Subsequent construction and expression of chimeric genes indicated that substrate specificity of F3'H and F3'5'H is determined near the N-terminal end and the functional difference between these two enzymes near the C-terminal end. The impact on function of individual amino acids located in substrate recognition site 6 (SRS6) was further tested by site-directed mutagenesis. Most interestingly, a conservative Thr to Ser exchange at position 487 conferred additional 5'-hydroxylation activity to recombinant Gerbera hybrida F3'H, whereas the reverse substitution transformed recombinant Osteospermum hybrida F3'5'H into an F3'H with low remaining 5'-hydroxylation activity. Since the physicochemical properties of Thr and Ser are highly similar, the difference in size appears to be the main factor contributing to functional difference. The results further suggest that relatively few amino acids exchanges were required for the evolutionary extension of 3'- to 3',5'-hydroxylation activity.
Relation between CXCR-4 expression, Flt3 mutations, and unfavorable prognosis of adult acute myeloid leukemia (2004)

Recently it was shown that, analogous to normal hematopoietic cells, the level of CXC chemokine receptor 4 (CXCR-4) expression on acute myeloid leukemia (AML) cells correlates with stromal cell derived factor-1 alpha (SDF-1)-induced chemotaxis. As we speculated that an anomalous organ distribution of AML cells could affect cell survival and thus result in an altered fraction surviving chemotherapy, we examined a possible correlation between patient prognosis and CXCR-4 expression in AML patients. We found that patients with a high CXCR-4 expression in the CD34(+) subset had a significantly reduced survival and a higher probability of relapse, resulting in a median relapse-free survival (RFS) of only 8.3 months. CXCR-4 expression was significantly higher in fetal liver tyrosine kinase-3 (Flt3)/internal tandem duplication (ITD) AML than in Flt3/wild-type (wt) AML. Covariate analysis indicated that the prognostic significance of Flt3/ITDs with respect to RFS was no more apparent when analyzed in conjunction with the expression of CXCR-4 in the CD34(+) subset, suggesting that the poor prognosis of Flt3/ITD AML might be subordinate to the increased CXCR-4 expression. Using a granulocyte colony-stimulating factor receptor (G-CSF-R)-expressing 32D cell line, we observed that SDF-1/CXCR-4 interaction is required for the survival of myeloid differentiating cells, and it also induces a block in G-CSF-induced myeloid differentiation. These data suggest that the SDF-1/CXCR-4 axis may influence therapy responsiveness and defines unfavorable prognosis in AML.
Preparation and Characterization of a Novel Monoclonal Antibody Specific to Human ZNRD1 Protein (2004)

We have efficiently generated the first monoclonal antibody (MAb) against the human ZNRD1 protein, a transcription-associated protein, consisting of two zinc ribbon domains. Hybridomas were screened by indirect enzyme-linked immunosorbent assay (ELISA) using either purified 6 x His-ZNRD1fusion protein or purified 6 x His-OS-9 fusion protein as a control. One MAb named H6 (IgG(1)), effective in detecting the recombinant and cellular protein, was characterized by ELISA and Western immunoblotting. Thus, it binds to native ZNRD1 protein and should be useful in studies of ZNRD1 protein function and expression. By Western immunoblotting analysis of 16 patients with gastric cancer using the MAb, we found ZNRD1 protein was more overexpressed in incision margin than in carcinoma tissue. The results showed that ZNRD1 might be a novel modifier in gastric carcinogenesis.
Amino Acid Profiling of Protein Hydrolysates Using Liquid Chromatography and Fluorescence Detection (1979)

Abstract A liquid chromatography procedure is described for separating the amino acids in protein hydrolysates. The proteins are hydrolyzed with hydrochloric acid and an aliquot of the hydrolysate is derivatized with dansyl chloride reagent. The derivatization procedure takes only 2 minutes using a reaction temperature of 100°C. The dansylated amino acids are chromatographed using a reversed-phase C8 column and a multi-step, nonlinear gradient elution solvent program which is readily achieved using a microprocessor-controlled liquid chromatograph. Chromatography is complete in approximately 40 min. The procedure is useful for characterizing proteins and may also be used to analyse intact dansylated polypeptides. Chromatograms showing the amino acid profile of chymotrypsin, albumin and histone are given.
Approaches for Rapid Materials Discovery Using Combinatorial Methods (1998)

Methods of combinatorial chemistry are discllssed with applicatins to material science. The integration of automated chemical deposition, processing. screening, and data acquisition, storage and analysis is essential to realize the power of this new paradigm for materials research.
The Bittig Reaction of Benzofuranones (1972)

Abstract The cyclisation of appropriately substituted bensane derivatives affords 3-alkyl, 3-aryl and 3(2H)-benzofuraones but other 3-Substituted benzofurans are not directly available by ring closure methods or by electrophilic substitution.2,3 We now report a convenient route to such compounds via the Wittig reaction between 3(2H)-benzofuranones and stable phosphorus ylids.
Synthane gasifier effluent streams. [Effects of coal type and method of feeding] (1977)

A substantial number of experiments have been carried out with the 4-inch SYNTHANE PDU gasifier, primarily using three coals: North Dakota lignite, Illinois No. 6 bituminous and Montana subbituminous coal. These experiments were performed over a wide range of operating conditions using several coal feeding configurations. Operating pressures ranged from 10 to 40 atmospheres and the steam-to-coal and oxygen-to-coal ratios varied from 0.45 to 2.46 and 0.12 to 0.51, respectively. The effluent streams of the gasifier have been analyzed with regard to composition. The most influential factors affecting pollutant yields appear to be coal type and the method of feeding coal to the fluidized bed of the gasifier (i.e. free fall through the carbonizer or by-passing carbonizer using a dip tube). The dip tube feeding of the coal was found to substantially reduce phenol, COD, thiocyanate, cyanide and tar yields associated with the condensate stream. However, dip tube feeding did not make significant changes in the contaminants found in the gas stream. The rank of the coal being gasified was by far the most influential factor affecting the production of possible environmental pollutants. The effect of additives on the yield of contaminants in both the gas and condensate effluent streamsmore » was considered. Due to scatter of the data no significant effect on the production of condensate or gaseous contaminants due to feeding additives with the coal could be observed. Although the data presented is from a small scale SYNTHANE unit and has a significant amount of scatter, it can serve to estimate the production of potential environmental pollutants which must be treated in commercial SYNTHANE gasifiers and those with similar operational principles.« less
Collision Detection for Deformable Objects (2005)

Abstract Interactive environments for dynamically deforming objects play an important role in surgery simulation and entertainment technology. These environments require fast deformable models and very efficient collision handling techniques. While collision detection for rigid bodies is well investigated, collision detection for deformable objects introduces additional challenging problems. This paper focuses on these aspects and summarizes recent research in the area of deformable collision detection. Various approaches based on bounding volume hierarchies, distance fields and spatial partitioning are discussed. In addition, image‐space techniques and stochastic methods are considered. Applications in cloth modeling and surgical simulation are presented.
The reaction of aldolase with 2-methylmaleic anhydride (1970)

1. The reaction of rabbit muscle aldolase with 2-methylmaleic anhydride is described. All the protein amino groups can be reversibly blocked. 2. As the reaction proceeds, the enzyme activity decreases until, at about 50% citraconylation of amino groups, the enzyme is completely inhibited. At this stage, little or no dissociation of the enzyme tetramer is observed and 75% of the activity is recoverable on unblocking the amino groups. 3. At 80% blocking, the enzyme is completely dissociated but little enzymic activity is recoverable after unblocking. Inability to recover activity after citraconylation and unblocking correlates with the onset of dissociation of the citraconyl-aldolase seen on ultracentrifugation. 4. The only irreversible modification of the enzyme primary structure detectable after the citraconylation and unblocking reactions is the partial loss of thiol groups. It is probable that this is responsible for the inability to reform active enzyme from the citraconylated subunit. 5. Other reversible side reactions of maleic anhydride and citraconic anhydride that may occur with proteins are discussed.
Scattering parameter characterization of microwave optoelectronic devices and fiber-optic networks (1991)

A microwave fiber-optic network analyzer test set is proposed that will allow the application of two-port calibration theory to the measurement of optical and optoelectronic components in high frequency fiber-optic links. Formulae for the optoelectronic calibration are presented. A unified approach to optical and optoelectronic two-port calibration theory is covered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Coherent backscattering of light from biological tissues (1990)

The angular and temporal distributions of light scattered around the backward direction from biological tissues are measured. An enhancement of scattered light intensity around the backward direction, which is associated with the weak photon localization, is observed. The transport mean free path l(t) and the absorption length l(a) of the light in biological tissue can be obtained from the angular line shape of the coherent peak. The values l(t) and l(a) can also be obtained from the temporal profile of the scattered pulse.
Efficient Procurement of Epithelial Stem Cells from Human Tissue Specimens Using a Rho-Associated Protein Kinase Inhibitor Y-27632 (2009)

The efficient culture of stem cells from epithelial tissues such as skin and corneas is important for both experimental studies and clinical applications of tissue engineering. We now demonstrate that treatment of human-skin-derived keratinocytes with a Rho-associated protein kinase inhibitor Y-27632 for the initial 6 days of primary culture can increase the number of keratinocytes that possess stem cell properties to form colonies during in vitro culture of freshly isolated cells and subsequent passage (50-fold). Further, we show that Y-27632 treatment can increase the total number of prostate epithelial cells derived from human prostate specimens. Therefore, the use of Y-27632 during primary cultures offers a simple and effective way to prepare a large number of epithelial stem cells from various human epithelial tissues.
NF-κB-Mediated<i>HER2</i>Overexpression inRadiation-Adaptive Resistance (2008)

The molecular mechanisms governing acquired tumor resistance during radiotherapy remain to be elucidated. In breast cancer patients, overexpression of HER2 (human epidermal growth factor receptor 2) is correlated with aggressive tumor growth and increased recurrence. In the present study, we demonstrate that HER2 expression can be induced by radiation in breast cancer cells with a low basal level of HER2. Furthermore, HER2-postive tumors occur at a much higher frequency in recurrent invasive breast cancer (59%) compared to the primary tumors (41%). Interestingly, NF-kappaB is required for radiation-induced HER2 transactivation. HER2 was found to be co-activated with basal and radiation-induced NF-kappaB activity in radioresistant but not radiosensitive breast cancer cell lines after long-term radiation exposure, indicating that NF-kappaB-mediated HER2 overexpression is involved in radiation-induced repopulation in heterogeneous tumors. Finally, we found that inhibition of HER2 resensitizes the resistant cell lines to radiation. Since HER2 is shown to activate NF-kappaB, our data suggest a loop-like HER2-NF-kappaB-HER2 pathway in radiation-induced adaptive resistance in breast cancer cells.
Ultrasound for the Diagnosis of Atrial Tumor (1969)

The correct preoperative diagnosis of a left atrial myxoma was established using the ultrasonic cardiac echogram in this patient. The findings at cardiac catheterization and angiocardiography were not diagnostic. It is suggested that the ultrasonic cardiac echogram is a simple atraumatic method for the diagnosis of an elusive condition.
Functional FEN1 genetic variants contribute to risk of hepatocellular carcinoma, esophageal cancer, gastric cancer and colorectal cancer (2011)

As a DNA repair protein, Flap endonuclease 1 (FEN1) plays crucial parts in preventing carcinogenesis. Two functional germ line variants (-69G > A and 4150G > T) in the FEN1 gene have been associated with DNA damage levels in coke oven workers and lung cancer risk in general populations. However, the role of these genetic variants on gastrointestinal cancer susceptibility is unknown. Therefore, we evaluated the association between these polymorphisms and gastrointestinal cancer risk in two independent case-control cohorts consisted of a total of 1850 gastrointestinal cancer (hepatocellular carcinoma, esophageal cancer, gastric cancer and colorectal cancer) patients and 2222 healthy controls. The impact of these variations on FEN1 expression was also examined using liver, esophagus, stomach and colon normal tissues. It was found that the FEN1 -69GG genotypes were significantly correlated to increased risk for developing gastrointestinal cancer compared with the -69AA genotype in both cohorts [Jinan cohort: odds ratios (OR) = 2.14, 95% confidence interval (CI) = 1.47-2.80, P = 1.0 × 10(-)(6); Huaian cohort: OR = 1.93, 95% CI = 1.37-2.50, P = 0.5 × 10(-6)]. Similar results were observed for 4150G > T polymorphism. In the combined meta-analyses, OR for -69GG or 4150GG genotype was 2.02 (95% CI = 1.59-2.45) or 1.86 (95% CI = 1.45-2.28) compared with -69AA or 4150TT genotype. In vivo FEN1 messenger RNA expression analyses showed that the -69G or 4150G allele carriers had ∼2-fold decreased FEN1 expression in gastrointestinal tissues compared with -69A or 4150T carriers, indicating that lower FEN1 expression may lead to higher risk for malignant transformation of gastrointestinal cells. Our results highlight FEN1 as an important gene in human gastrointestinal oncogenesis and genetic polymorphisms in FEN1 confer susceptibility to gastrointestinal cancers.
Treatment of non-muscle invasive bladder cancer with Bacillus Calmette–Guerin (BCG): Biological markers and simulation studies (2015)

Intravesical Bacillus Calmette-Guerin (BCG) vaccine is the preferred first line treatment for non-muscle invasive bladder carcinoma (NMIBC) in order to prevent recurrence and progression of cancer. There is ongoing need for the rational selection of i) BCG dose, ii) frequency of BCG administration along with iii) synergistic adjuvant therapy and iv) a reliable set of biochemical markers relevant to tumor response. In this review we evaluate cellular and molecular markers pertinent to the immunological response triggered by the BCG instillation and respective mathematical models of the treatment. Specific examples of markers include diverse immune cells, genetic polymorphisms, miRNAs, epigenetics, immunohistochemistry and molecular biology 'beacons' as exemplified by cell surface proteins, cytokines, signaling proteins and enzymes. We identified tumor associated macrophages (TAMs), human leukocyte antigen (HLA) class I, a combination of Ki-67/CK20, IL-2, IL-8 and IL-6/IL-10 ratio as the most promising markers for both pre-BCG and post-BCG treatment suitable for the simulation studies. The intricate and patient-specific nature of these data warrants the use of powerful multi-parametral mathematical methods in combination with molecular/cellular biology insight and clinical input.
High-Speed Hardware Implementation of Fixed and Runtime Variable Window Length 1-D Median Filters (2015)

Nonlinear digital filters play an important role in digital signal processing applications. In this brief, a novel architecture is proposed for the hardware implementation of fixed and runtime variable window length one-dimensional median filters. In the proposed architecture, the maximum working clock frequency is almost independent of the median filter window length, whereas the hardware complexity is proportional to the number of samples in the window. This feature enables the construction of filters with relatively large window lengths with negligible reduction in the maximum clock frequency, whereas in previous architectures, the maximum clock frequency significantly drops as the window length is increased. The benchmark results show the efficiency of the proposed architecture in comparison with state-of-the-art techniques.
Gene expression, synthesis, and secretion of interleukin 18 and interleukin 1β are differentially regulated in human blood mononuclear cells and mouse spleen cells (1999)

Interleukin (IL)-18, formerly called interferon gamma (IFN-gamma)-inducing factor, is biologically and structurally related to IL-1beta. A comparison of gene expression, synthesis, and processing of IL-18 with that of IL-1beta was made in human peripheral blood mononuclear cells (PBMCs) and in human whole blood. Similar to IL-1beta, the precursor for IL-18 requires processing by caspase 1. In PBMCs, mature but not precursor IL-18 induces IFN-gamma; in whole human blood stimulated with endotoxin, inhibition of caspase 1 reduces IFN-gamma production by an IL-1beta-independent mechanism. Unlike the precursor for IL-1beta, precursor for IL-18 was expressed constitutively in PBMCs and in fresh whole blood from healthy human donors. Western blotting of endotoxin-stimulated PBMCs revealed processed IL-1beta in the supernatants via an caspase 1-dependent pathway. However, in the same supernatants, only unprocessed precursor IL-18 was found. Unexpectedly, precursor IL-18 was found in freshly obtained PBMCs and constitutive IL-18 gene expression was present in whole blood of healthy donors, whereas constitutive IL-1beta gene expression is absent. Similar to human PBMCs, mouse spleen cells also constitutively contained the preformed precursor for IL-18 and expressed steady-state IL-18 mRNA, but there was no IL-1beta protein and no spontaneous gene expression for IL-1beta in these same preparations. We conclude that although IL-18 and IL-1beta are likely members of the same family, constitutive gene expression, synthesis, and processing are different for the two cytokines.
Kinetic changes of the anorectum before and after the anal fistula operation (1999)

目的研究直肠肛门瘘手术前后肛肠动力学的变化.方法对37例肛瘘患者手术前后用直肠肛管测压法检测直肠肛门反射(RAR)、肛管最大收缩压(AMCP)、肛管最长收缩时间(ALCT)、直肠静息压(RRP)、肛管静息压(ARP)5项技术指标.对肛瘘手术前后及其低位、高位手术前后、低位与高位术后进行比较,并与30名正常人进行对比.结果术后RAR完全恢复并敏感率提高(P＜0.01),与正常人无差异(P＞0.05);AMCP与术前无差异(P＞0.05),比正常人明显降低(P＜0.01);ALCT与术前无差异(P＞0.05),比正常人延长(P＜0.05);RRP术后降低(P＜0.01),与正常人无差异(P＞0.05);ARP术后降低(P＜0.01),比正常人亦显著降低(P＜0.01).结论肛瘘疾病及肛管内外括约肌损伤的严重程度对肛门的闭紧功能产生直接影响,尤其是高位肛瘘可能引起部分患者的气体或液体失禁.
Electric vehicle charging system (2012)

Singapore being a clean and green city, each individual is willing to take more responsibility for their direct contribution to greenhouse gas emissions. Electrical Vehicle (EV) no longer have to face consumer fear of complete novelty. This growing interest in electric vehicles concepts for private, public and utility services across the world has certainly encouraged many companies and organisations to push various other technologies associated with electric vehicles. The electric vehicle charging system is a new technology that helps users monitor thier electric vehicle charge status and notify users when charge is complete. LabVIEW is used as the main software programming language in creating the GUI display in this project.
Methylphenidate Blood Levels and Therapeutic Response in Children with Attention-Deficit Hyperactivity Disorder I. Effects of Different Dosing Regimens (2006)

The rate of absorption and elimination of d-MPH was dependent on the pattern of administration, particularly on the initial bolus concentration. This suggests that d-MPH may act on the gastrointestinal system to slow absorption of additional d-MPH. There were significant differences among regimens on time course and degree of therapeutic response. Pulsatile administration produced greater improvement than escalating levels.
Role for urinary biomarkers in diagnosis of acute rejection in the transplanted kidney (2015)

Despite the introduction of potent immunosuppressive medications within recent decades, acute rejection still accounts for up to 12% of all graft losses, and is generally associated with an increased risk of late graft failure. Current detection of acute rejection relies on frequent monitoring of the serum creatinine followed by a diagnostic renal biopsy. This strategy is flawed since an alteration in the serum creatinine is a late clinical event and significant irreversible histologic damage has often already occurred. Furthermore, biopsies are invasive procedures that carry their own inherent risk. The discovery of non-invasive urinary biomarkers to help diagnose acute rejection has been the subject of a significant amount of investigation. We review the literature on urinary biomarkers here, focusing on specific markers perforin and granzyme B mRNAs, FOXP3 mRNA, CXCL9/CXCL10 and miRNAs. These and other biomarkers are not yet widely used in clinical settings, but our review of the literature suggests that biomarkers may correlate with biopsy findings and provide an important early indicator of rejection, allowing more rapid treatment and better graft survival.