gebhart/patrepeval huggingface dataset:
Microfluidic immunoassays as rapid saliva-based clinical diagnostics (2007)

At present, point-of-care (POC) diagnostics typically provide a binary indication of health status (e.g., home pregnancy test strip). Before anticipatory use of diagnostics for assessment of complex diseases becomes widespread, development of sophisticated bioassays capable of quantitatively measuring disease biomarkers is necessary. Successful translation of new bioassays into clinical settings demands the ability to monitor both the onset and progression of disease. Here we report on a clinical POC diagnostic that enables rapid quantitation of an oral disease biomarker in human saliva by using a monolithic disposable cartridge designed to operate in a compact analytical instrument. Our microfluidic method facilitates hands-free saliva analysis by integrating sample pretreatment (filtering, enrichment, mixing) with electrophoretic immunoassays to quickly measure analyte concentrations in minimally pretreated saliva samples. Using 20 microl of saliva, we demonstrate rapid (<10 min) measurement of the collagen-cleaving enzyme matrix metalloproteinase-8 (MMP-8) in saliva from healthy and periodontally diseased subjects. In addition to physiologically measurable indicators of periodontal disease, conventional measurements of salivary MMP-8 were used to validate the microfluidic assays described in this proof-of-principle study. The microchip-based POC diagnostic demonstrated is applicable to rapid, reliable measurement of proteinaceous disease biomarkers in biological fluids.
Elevated expression of caveolin is associated with prostate and breast cancer. (1998)

To identify genes associated with prostate cancer progression, we developed a strategy involving the use of differential display-PCR with a panel of genetically matched primary tumor- and metastasis-derived mouse prostate cancer cell lines. We isolated a cDNA fragment with homology to the mouse caveolin-1 gene. Northern blotting with this fragment revealed increased caveolin expression in metastasis-derived cell lines relative to primary tumor-derived cell lines. Western blotting with a polyclonal caveolin antibody confirmed increased caveolin protein in metastasis-derived mouse cell lines and expression in three of four human prostate cancer cell lines. Immunohistochemical analysis of a human prostate cancer cell line demonstrated a prominent granular pattern of caveolin accumulation. Subsequent analysis of mouse and human prostate specimens revealed minimal caveolin expression in normal epithelium with abundant staining of smooth muscle and endothelium. The frequency of caveolin-positive cells was increased in prostate cancer with markedly increased accumulation of caveolin and a granular staining pattern in lymph node metastatic deposits. In human breast cancer specimens, increased caveolin staining was detected in intraductal and infiltrating ductal carcinoma as well as nodal disease. Caveolin therefore appears to be associated with human prostate cancer progression and is also present in primary and metastatic human breast cancer.
Isolation and characterization of human umbilical cord mesenchymal stem cells with hematopoiesis-supportive function and other potentials. (2006)

We have established a protocol to isolate abundant MSC from human umbilical cords with a 100% success rate. The comparative study indicates that UC is an excellent alternative to BM as a source of MSC for cell therapies.
Isoforms of Murine and Human Serum Amyloid P Component (1998)

Isoelectric focusing (IEF) and immunofixation of murine serum amyloid P component (SAP), purified and in serum, showed a distinct and strain-dependent isoform pattern with up to seven bands (pI 5.1-5.7). Neuraminidase treatment caused a shift of the isoforms to more basic pI values, but did not affect their number. When the acute-phase response was analysed in three mouse strains, CBA/J and C3H/HeN initially showed seven SAP isoforms in serum and C57BL/6 J three or four. The responses in all three strains peaked at day 2 and were normalized within 14 days. On days 2 and 4, CBA/J and C3H/HeN mice showed one more acidic isoform and an increase in the concentration of the most basic isoform. C57BL/6 J mice exhibited two to three new isoforms during the acute-phase response. This appears to be the first demonstration of the physiological existence of SAP isoforms. In contrast, demonstration of isoforms of human SAP required the presence of urea and higher SAP concentrations. TEF and immunofixation of SAP monomers showed five to eight isoforms, ranging from pI 4.7-5.7. IEF of SAP in human serum resulted in a less distinct pattern and more acidic isoforms. As with murine SAP, neuraminidase treatment caused a shift of the isoforms, but no reduction in isoform number. Two-dimensional gel electrophoresis confirmed the existence of multiple isoforms of human SAP monomers.
Mutational analysis of the structure and functions of hepatitis C virus RNA–dependent RNA polymerase (2001)

The hepatitis C virus (HCV) nonstructural protein 5B (NS5B) is an RNA-dependent RNA polymerase (RdRP), a central catalytic enzyme for HCV replication. To further understand the structure and functions of NS5B, we introduced a series of 27 clustered and 19 point substitution mutations within and outside the well-known motifs conserved among RdRP by alanine scanning and investigated effects of these mutants on enzymatic activity of NS5B. Surprisingly, most of the mutations (22 of 27 clustered mutants) do not affect RdRP activity at all, indicating that the side chains of the corresponding amino acid residues are dispensable for the catalytic activity. On the other hand, 4 mutants, cm20t, cm194t, cm2t, and cm3t, are defective in RdRP activity. By further analysis with point mutations within these regions, E18, Y191, C274, Y276, and H502 were determined to be critical for the RdRP activity. Y276 was also shown to be critical for RNA template/primer association, although 3 amino acid sequences were identified to be important for RNA template binding by RNA-filter binding assays. Finally, 4 discontinuous sequences of NS5B (aa139-145, aa149-155, aa 365-371, and aa 382-388) were found to be essential for binding to NS5A as determined by glutathione S-transferase (GST)-pull down assays using GST-NS5A and FLAG-NS5B expressed in cotransfected cells, and GST-pull down assay in vitro. In light of the crystal structure models of NS5B recently reported, our results indicate that the RdRP activity of NS5B requires the longer loop and the helix located at the distal of the thumb, which are unique among RdRPs as well as reverse transcriptases.
Characterization of a novel stable biocatalyst obtained by protein engineering (1999)

Protein engineering is a powerful tool for the improvement of the properties of biocatalysts. Previously we have applied protein engineering technologies to obtain an extremely stable variant of the thermolysin-like protease from Bacillus stearothermophilus [Van den Burg, Vriend, Veltman, Venema and Eijsink (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 2056-2060]. This variant is much more resistant to denaturing conditions (temperature and denaturing agents) than the wild-type enzyme. An extensive enzymic characterization was undertaken to explore the suitability of the variant as a biocatalyst at high temperatures. By comparing a range of variants with increasing thermal stabilities we show that the additivity of the mutations is accompanied by an increase in activity at elevated temperatures in accordance with the Arrhenius law. The results suggest that the constructed protease variants could be suitable alternatives to proteases that are currently used industrially. Our studies demonstrate how protein engineering can be exploited to obtain high-performance biocatalysts.
Role of Isopropyl Myristate, Isopropyl Alcohol and a Combination of Both in Hydrocortisone Permeation across the Human Stratum corneum (2003)

The influence of isopropyl myristate (IPM), isopropyl alcohol (IPA) and a combination of both was studied in view of hydrocortisone (HC) permeation across the human stratum corneum (SC). IPM, IPA and their combination were incorporated into water-containing hydrophilic ointment (WHS), and the resulting effects on HC permeation and on HC accumulation in human SC were investigated as well as the influence of these substances on the microstructure of the SC. Differential scanning calorimetry as well as wide- and small-angle X-ray diffraction show that IPM incorporation into SC results in densely packed bilayer lipids and a loss of order of the corneocyte-bonded lipids. Both effects result in a decreased diffusion coefficient of HC in SC and thus in a decreased permeation rate compared to that of HC from WHS. On the other hand, IPA fluidizes and disrupts the bilayer structure of the intercellular lipids. These effects, concomitant with an increased amount of dissolved HC within the ointment, increase the permeation rate of HC across SC. The combination of both ingredients effects a stronger fluidization and disruption of intercellular lipids than with IPA alone. Therefore, the permeation rate of HC across SC is higher than with IPA alone. Consequently, the IPM and IPA combination acts synergistically on the microstructure of SC.
High-quality audio transform coding at 128 kbits/s (2002)

An approach to wideband digital audio compression of CD-quality signals at data rates of 128 kb/s channel and below is presented. A form of adaptive transform coding, this technique features a nonuniform frequency division and coding scheme to exploit known characteristics of human perception. The algorithm has low computational complexity and can be adapted for use at other bit rates. A windowed overlap-add process is used with the forward/inverse transforms, which have been efficiently implemented using FFTs. Transform coefficients are converted into a subband block-companded format consisting of exponent words and associated mantissas, which are then coded with an adaptive quantizer. A real-time, single-chip programmable digital signal processing (DSP) implementation encodes 480-kHz-sampled stereo audio signals at a variety of bit rates. At 128 kb/s, the coder's subjective performance is appropriate for highest-quality 15-kHz professional audio applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Proteomic analysis of κ‐casein micro‐heterogeneity (2004)

The proteome of bovine milk is dominated by just six gene products that constitute approximately 95% of milk protein. Nonetheless, over 150 protein spots can be readily detected following two-dimensional electrophoresis of whole milk. Many of these represent isoforms of the major gene products produced through extensive post-translational modification. Peptide mass fingerprinting of in-gel tryptic digests (using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) in reflectron mode with alpha-cyano-4-hydroxycinnamic acid as the matrix) identified 10 forms of kappa-casein with isoelectric point (pI) values from 4.47 to 5.81, but could not distinguish between them. MALDI-TOF MS in linear mode, using sinapinic acid as the matrix, revealed a large tryptic peptide (mass > 5990 Da) derived from the C-terminus that contained all the known sites of genetic variance, phosphorylation and glycosylation. Two genetic variants present as singly or doubly phosphorylated forms could be distinguished using mass data alone. Glycoforms containing a single acidic tetrasaccharide were also identified. The differences in electrophoretic mobility of these isoforms were consistent with the addition of the acidic groups. While more extensively glycosylated forms were also observed, substantial loss of N-acetylneuraminic acid from the glycosyl group was evident in the MALDI spectra such that ions corresponding to the intact glycopeptide were not observed and assignment of the glycoforms was not possible. However, by analysing the pI shifts observed on the two-dimensional gels in conjunction with the MS data, the number of N-acetylneuraminic acid residues, and hence the glycoforms present, could be determined.
Cytotoxic sugar analogues of an optimized novobiocin scaffold (2010)

Studies on the natural product, novobiocin, have elucidated specific modifications that increase Hsp90 inhibition. Through diversification of the sugar appendage, coumarin core and benzamide side chain of novobiocin, structurally unique scaffolds have been synthesized. These structural adaptations have produced potent cytotoxic agents, such as KU135, which are prepared more simply than those that contain the noviose sugar. These analogues have been evaluated against two cancer cell lines and demonstrated low micromolar anti-proliferative activity.
Further studies on the interaction of nitric oxide with transition-metal alkyls (1981)

The interaction of nitric oxide with peralkyl compounds of Zn, Cu, Re, Cr, Mo, W, and Zr and with the phosphine complexes Ni(η-C5H5)Me(PPh3), CoMe3(PMe3)3, and RhMe(PPh3)3, and RhMe(PPh3)3 has been studied. In addition to N-alkyl-N-nitrosohydroxylaminate, ON(R)NO, complexes normally formed from diamagnetic alkyls, and η2 or bridged nitrosoalkane, ONR, compounds usually obtained from paramagnetic alkyls, complexes with MO or M–O–M groups may be formed from the latter or from the interaction of NO with certain diamagnetic complexes that may give para-magnetic intermediates, e.g. by dissociation. Among new compounds characterised by i.r. and n.m.r. spectra are the tetrameric {Cu[ON(CH2SiMe3)NO]}4, the nitric oxide adduct of hexamethylrhenium, ReMe6(NO), the complex Re2O3Me4(ONMe)2, and the oxo-compounds of molybdenum and tungsten of stoicheiometry M2O3(NO)2(ONR)2, R = CH2SiMe3 or CH2CMe3. The interaction of molybdenum and tungsten hexacarbonyls with nitrobenzene and nitromethane gives oxo-species with ONR groups.
HSP72 protects against obesity-induced insulin resistance (2008)

Patients with type 2 diabetes have reduced gene expression of heat shock protein (HSP) 72, which correlates with reduced insulin sensitivity. Heat therapy, which activates HSP72, improves clinical parameters in these patients. Activation of several inflammatory signaling proteins such as c-jun amino terminal kinase (JNK), inhibitor of kappaB kinase, and tumor necrosis factor-alpha, can induce insulin resistance, but HSP 72 can block the induction of these molecules in vitro. Accordingly, we examined whether activation of HSP72 can protect against the development of insulin resistance. First, we show that obese, insulin resistant humans have reduced HSP72 protein expression and increased JNK phosphorylation in skeletal muscle. We next used heat shock therapy, transgenic overexpression, and pharmacologic means to overexpress HSP72 either specifically in skeletal muscle or globally in mice. Herein, we show that regardless of the means used to achieve an elevation in HSP72 protein, protection against diet- or obesity-induced hyperglycemia, hyperinsulinemia, glucose intolerance, and insulin resistance was observed. This protection was tightly associated with the prevention of JNK phosphorylation. These findings identify an essential role for HSP72 in blocking inflammation and preventing insulin resistance in the context of genetic obesity or high-fat feeding.
Retinal Thickness and Subnormal Retinal Oxygenation Response in Experimental Diabetic Retinopathy (2005)

The lack of increased thickness in 3-month-old diabetic rats in vivo raises the possibility that intracellular swelling is unlikely to underlie subnormal DeltaPo2 in experimental diabetes. In diabetic rats, the spatial disconnect between subnormal DeltaPo2 pansuperiorly and retinal thinning only superiorly to the optic nerve suggests that neurovascular coupling is perturbed.
Long-term efficacy and safety of androgen receptor inhibitor ODM-201 in ARADES phase I/II trial. (2014)

5079^ Background: ODM-201, is an novel oral androgen receptor (AR) inhibitor that has shown good preclinical efficacy, and has high antitumor activity in metastatic CRPC (mCRPC) patients (pts) (Fizazi et al. 2013). Methods: We report the long-term data in CYP17i-naïve progressive mCRPC pts in the ARADES phase I/II trial and the phase II extension study, in which pts were enrolled into dose levels of 100mg bid, 200mg bid or 700mg bid. Radiographic progression was evaluated either according to RECIST 1.1 for soft tissue or defined by at least 2 new lesions in bone compared to a prior scan. Results: 69 pts had progressive mCRPC; 37 pts were chemotherapy-naïve and 32 chemotherapy-pretreated. The median age was 69 yrs (53-83 yrs). 59 pts (86%) had bone metastases and 12 (17%) had visceral metastases. The median PSA was 99 ng/mL (3-1294) and the CTC count was 5 or more CTCs per 7.5ml in 42% of the pts. Forty-six (67%) pts continued drug over 12 weeks (wks). With a median follow-up of 38 wks the median time to PSA progression was 36 (95% CI: 24–74) wks for chemotherapy-naïve pts, and 21 (95%CI: 16–28) wks for chemotherapy-pretreated pts. The median time to radiographic progression was not reached for chemotherapy-naïve (95% CI: 24–not reached), and was 32 (95% CI: 12–not reached) wks for chemotherapy-pretreated pts. Treatment related AEs occurred in 22/69 (32%) pts. Most commonly reported treatment related AEs in the trial were asthenia/fatigue 6 (9%), decreased appetite 4 (6%), arthralgia 2 (3%), back pain 2 (3%), diarrhea 2 (3%), headache 2 (3%), hot flushes 2 (3%), and myalgia 2(3%), mostly mild to moderate. Conclusions: These data are in line with 12-wk efficacy and safety data reported previously, and show high anticancer activity and favorable tolerability of ODM-201. Clinical trial information: NTC01317641; NTC01429064.
Testosterone replacement therapy improves insulin resistance, glycaemic control, visceral adiposity and hypercholesterolaemia in hypogonadal men with type 2 diabetes (2006)

Testosterone replacement therapy reduces insulin resistance and improves glycaemic control in hypogonadal men with type 2 diabetes. Improvements in glycaemic control, insulin resistance, cholesterol and visceral adiposity together represent an overall reduction in cardiovascular risk.
Fas/FasL-dependent Apoptosis of Alveolar Cells after Lipopolysaccharide-induced Lung Injury in Mice (2001)

To determine the possible contribution of apoptosis in the pathogenesis of acute lung injury (ALI), we investigated Fas antigen (Fas), Fas ligand (FasL), perforin, granzyme A, and granzyme B expressions in a murine model of ALI after intratracheal instillation of Escherichia coli lipopolysaccharide (LPS: 0.3-30 microg) into the left lung. Lung injury, examined by water-to-dry weight ratio and albumin leakage, demonstrated maximal epithelial injury 1 d after 30 microg LPS instillation. Expressions of the proapoptosis molecules' mRNA were dose-dependently up-regulated, with maximal expression in the early phase in the instilled lung and most apparent 1 d after LPS instillation. Negligible mRNA expression of proapoptosis molecules was observed in noninstilled lungs. The terminal deoxynucleotidyl transferase-mediated dUTP biotin nick end labeling (TUNEL) demonstrated positive signals in neutrophils and macrophages as well as in alveolar wall cells of the instilled lung 1 d after LPS instillation. Immunohistochemistry demonstrated that Fas was up-regulated in alveolar and inflammatory cells and FasL-positive inflammatory cells migrated into the air spaces in the LPS-instilled lung. Intratracheal administration of P2 antibody, which is an anti-Fas blocking antibody, attenuated the lung injury after 30 microg LPS instillation without attenuating mRNA expressions of proapoptosis molecules and neutrophil accumulation in the lung. In contrast, concanamycin A, which inhibits the function of perforin, did not alter the outcome after LPS instillation. These results indicate that the Fas/FasL system could be important in the pathogenesis of LPS-induced ALI, and proper regulation of the FasL/Fas system might be important for potential treatment of ARDS.
Advanced endoscopic technologies for colorectal cancer screening (2013)

Colorectal cancer is the third most common cancer in men and the second most common cancer in women worldwide. Diagnosing colorectal has been increasingly successful due to advances in technology. Flexible endoscopy is considered to be an effective method for early diagnosis and treatment of gastrointestinal cancer, making it a popular choice for screening programs. However, millions of people who may benefit from endoscopic colorectal cancer screening fail to have the procedure performed. Main reasons include psychological barriers due to the indignity of the procedure, fear of procedure related pain, bowel preparation discomfort, and potential need for sedation. Therefore, an urgent need for new technologies addressing these issues clearly exists. In this review, we discuss a set of advanced endoscopic technologies for colorectal cancer screening that are either already available or close to clinical trial. In particular, we focus on visual-inspection-only advanced flexible colonoscopes, interventional colonoscopes with alternative propulsion mechanisms, wireless capsule colonoscopy, and technologies for intraprocedural bowel cleansing. Many of these devices have the potential to reduce exam related patient discomfort, obviate the need for sedation, increase diagnostic yield, reduce learning curves, improve access to screening, and possibly avert the need for a bowel preparation.
Identification and Design of Peptides for the Rapid, High-Yield Formation of Nanoparticulate TiO2from Aqueous Solutions at Room Temperature (2008)

Titania (TiO2) nanoparticles are widely used, or are under active development, for a range of applications in (photo)catalysis, photovoltaics, enzyme support, energy storage, and photonics. The peptide-directed room-temperature formation of titania nanoparticles can be an attractive alternative to higher-temperature synthetic methods. However, the influence of the peptide primary structure on the titania precipitation activity at room temperature is not well understood. Through the selective binding of phage-displayed 12-mer peptides to TiO2 substrates, we have identified 20 peptides with an affinity for titania. The average numbers of arginine, lysine, and histidine residues present in these 20 peptides were distinctly higher than for the overall peptide-bearing phage library. Synthetic 16-mer versions of four of these peptides (i.e., 12-mer peptides with C-terminal tetrapeptide tags for quantitative spectrophotometry) induced the formation of 8.1–38.7 mol TiO2/mol peptide after exposure for only 10 min to an otherwise water-stable Ti(IV) complex at room temperature and a pH of 6.3. X-ray diffraction analyses, electron diffraction analyses, and high-resolution transmission electron microscopy revealed that the peptide-induced titania contained fine (<10 nm) anatase and monoclinic β-TiO2 nanocrystals, along with an amorphous phase. The titania yield increased with the number of positive charges carried by these peptides. On the basis of these results, a peptide was designed that exhibited the highest titania formation activity reported to date for a peptide (82.9 mol TiO2/mol peptide), as well as a reduced pH dependence for such titania formation.