gebhart/patrepeval huggingface dataset:
Quantum Dot Glycoconjugates (2015)

This chapter introduces novel and efficient methods for the biological applications of quantum dot glycoconjugates in two sections. In the first section, a brief introduction of quantum dots is presented with interfacial chemistry and various synthesis techniques. The second section focuses on the current detection methods highlighting the quantum dots.
RELATIVE POTENCY OF BOMBESIN‐LIKE PEPTIDES (1975)

The pharmacological activity of two natural bombesin-like peptides, alytesin and litorin, and 25 related synthetic peptides has been compared to that of bombesin. 2 The minimum length of the amino acid chain required for the first appearance of bombesin-like effects was represented by the C-terminal heptapeptide, and the minimum length for maximal effects by the C-terminal nonapeptide. The latter possessed approximately the same activity as bombesin and may be considered a good substitute. 3 Both the tryptophan and histidine residues seemed to be essential for bombesin-like activity. 4 The C-terminal octapeptide was less active than either bombesin or the C-terminal nonapeptide and its action was more rapid in onset and less sustained. 5 Litorin apparently has an intermediate position between bombesin octapeptide and bombesin nonapeptide in the speed and duration of its effects. The relationship between structure and activity is discussed.
Comparison of Antigenic Sites of Subtype-specific Respiratory Syncytial Virus Attachment Proteins (1989)

A panel of 19 monoclonal antibodies (MAbs) were used to probe the antigenic relationships between the G (attachment) proteins of A and B respiratory syncytial virus (RSV) subtypes (GA and GB). At least three and two antigenic sites were present on GA and GB, respectively, including a shared neutralizing site. Most of the antibodies had some degree of complement-independent neutralizing capacity, but in common was a large neutralization-resistant fraction of virus (range 13 to 78%). Passive administration of MAbs to the cross-reactive antigenic site reduced pulmonary virus titres of both A and B subtype virus in the cotton rat model. Protection with subtype-specific MAbs, however, did not always correlate with in vitro neutralizing capacity. The cross-reactive antigenic site appears to be stable to denaturation by polyacrylamide gel electrophoresis and is present on the unglycosylated and partially glycosylated forms of GA and GB by Western blot analysis of infected cell lysates.
Production of clinical form of chronic subdural hematoma in experimental animals (1972)

✓ A method for producing a clinical form of experimental chronic subdural hematoma is reported. When blood is mixed with cerebrospinal fluid and incubated, a peculiar clot is formed which, when inoculated into the subdural space of dogs or monkeys, grows gradually. Histologically the capsule of the hematoma is comparable to that seen in human chronic subdural hematoma. In some animals progressive hemiparesis develops.
Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase (1999)

MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities of ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predict new ERK substrates and design peptide inhibitors of ERK that functioned in vitro and in vivo.
Follicle-Stimulating Hormone Enhances the Development of Preantral Follicles in Juvenile Rats1 (1997)

The stimulatory effects of gonadotropins on antral and preovulatory follicles are well known, but conflicting results have been reported regarding the gonadotropin responsiveness and dependency of preantral follicles. Taking advantage of the relatively uniform development of the first wave of follicles in the postnatal rat ovary, we evaluated the role of endogenous and exogenous gonadotropins on preantral follicle development. Reduction of the high levels of gonadotropins present in juvenile rats by either hypophysectomy (at Day 15) or GnRH antagonist treatment (starting from Day 11 of age) resulted in decreased ovarian weight at Day 19 of age that was associated with a reduced number of developing follicles and increased atresia of remaining follicles. In contrast, treatment with FSHctp (a long-acting FSH agonist) in intact (Days 5-19 of age), hypophysectomized (Days 15-19), or GnRH antagonist-treated (Days 11-19) animals resulted in increased ovarian weight and follicle development as determined histologically and by inhibin-alpha expression. A dose-dependent stimulatory effect of hCG on ovarian weight was seen when animals were cotreated with FSHctp and the GnRH antagonist. At low doses of hCG, augmentation of antral follicle formation occurred, whereas higher doses of hCG led to morphological signs of luteinization. These findings demonstrate the important role of endogenous gonadotropins in preantral follicle development and indicate that preantral follicles are highly responsive to exogenous gonadotropins.
Parallel isoelectric focusing II (2004)

A miniature electrophoretic device is developed on the basis of a new isoelectric focusing (IEF) method, namely parallel isoelectric focusing. We report here the theory and the results of operation of a new parallel isoelectric device (PID). The main advantages and limitations of the method are discussed for miniaturization purposes. It is shown that the method guarantees the fast and complete separation of any complex protein mixtures under acceptable conditions, such as voltage source, temperature, size of the device, and separation process duration. It is shown that the main problem of PID miniaturization is the buffer design, and the relation between Immobiline buffer capacity and solution buffer capacity. The main experimental limitation of PID resolution is protein sensitivity to pH changes.
Chemical Modification of the N-10 Ribityl Side Chain of Flavins EFFECTS ON PROPERTIES OF FLAVOPROTEIN DISULFIDE OXIDOREDUCTASES (1995)

Three flavin derivatives modified at the 2'-position of the flavin N-10 ribityl side chain were synthesized: arabinoflavin, 2'-F-2'-deoxyarabinoflavin, and 2'-deoxyriboflavin. These were converted to the FAD level with FAD synthetase. Apoproteins of lipoamide dehydrogenase, glutathione reductase, and mercuric reductase, a family of flavoprotein oxidoreductases, were reconstituted with these flavins. Significant reduction of the catalytic activities was observed with the modified enzymes. During anaerobic reduction of the modified enzymes with substrate or dithiothreitol, decreased thermodynamic stability of the two-electron reduced enzyme forms (EH2) and the accumulation of the four-electron reduced forms (EH4) noted. This effect was more pronounced in case of arabino-FAD-reconstituted enzymes than with the other two. It was found that NAD+ binding influences the interaction between the flavin and the reduced disulfide in the 2'-F-arabino-FAD-lipoamide dehydrogenase, presumably by altering the relative oxidation-reduction potentials. 19F NMR data were obtained for different forms of the 2'-F-arabino-FAD-lipoamide dehydrogenase, which suggest marked conformational changes from one form to the other. The 19F NMR data for the oxidized forms of all three 2'-F-arabino-FAD proteins suggest that the fluorine experiences very similar chemical environments at the active sites.
Anthocyanin 5‐Aromatic Acyltransferase from <i>Gentiana Triflora</i> (1997)

Acylation with hydroxycinnamic acids stabilizes anthocyanins and makes their colour bluer (bathochromic shift). We purified to homogeneity one acylation enzyme, hydroxycinnamoyl-CoA:anthocyanidin 3,5-diglucoside 5-O-glucoside-6"'-O-hydroxycinnamoyltransferase, from blue petals of Gentiana triflora. It is a single polypeptide protein of 52 kDa with a pI of 4.6. It catalyzes the transfer of the p-coumaric acid and caffeic acid from their CoA esters to the 5-glucosyl moiety of anthocyanidin 3,5-diglucosides but could not use malonyl-CoA as an acyl donor. Neither anthocyanidin 3-monoglucoside nor anthocyanins aromatically acylated at the 3-glucosyl moiety could be acylated by this enzyme. Aromatic acylation of anthocyanidin 3,5-diglucoside by this enzyme caused a bathochromic shift and increased pigment stability in neutral to weakly basic pH. Other anthocyanins from the petals of G. triflora were isolated and their structures were determined by fast-atom-bombardment MS and NMR. The biosynthetic pathway of gentiodelphin, a diacylated anthocyanin accumulating in G. triflora petals, is proposed on the basis of these results.
Conformation Coupled Enzyme Catalysis:  Single-Molecule and Transient Kinetics Investigation of Dihydrofolate Reductase (2005)

Ensemble kinetics and single-molecule fluorescence microscopy were used to study conformational transitions associated with enzyme catalysis by dihydrofolate reductase (DHFR). The active site loop of DHFR was labeled with a fluorescence quencher, QSY35, at amino acid position 17, and the fluorescent probe, Alexa555, at amino acid 37, by introducing cysteines at these sites with site-specific mutagenesis. The distance between the probes was such that approximately 50% fluorescence resonance energy transfer (FRET) occurred. The double-labeled enzyme retained essentially full catalytic activity, and stopped-flow studies of both the forward and reverse reactions revealed that the distance between probes increased prior to hydride transfer. A fluctuation in fluorescence intensity of single molecules of DHFR was observed in an equilibrium mixture of substrates but not in their absence. Ensemble rate constants were derived from the distributions of lifetimes observed and attributed to a reversible conformational change. Studies were carried out with both NADPH and NADPD as substrates, with no measurable isotope effect. Similar studies with a G121V mutant DHFR resulted in smaller rate constants. This mutant DHFR has reduced catalytic activity, so that the collective data for the conformational change suggest that the conformational change being observed is associated with catalysis and probably represents a conformational change prior to hydride transfer. If the change in fluorescence is attributed to a change in FRET, the distance change associated with the conformational change is approximately 1-2 A. These results are correlated with other measurements related to conformation coupled catalysis.
Tire Modeling and Friction Estimation (2007)

New system technologies are continuously improving the performance of vehicles regarding comfort, stability, environmental stresses, and safety. Novel sensors are developed and used together with advanced control algorithms and faster and more accurate actuators to help the driver to maneuver the vehicle in a safer way. The physical traction limit set by the friction between the tires and the road can, however, not be overridden. The behavior of tires is, therefore, an important issue since it determines the possibilities to control the vehicle. One essential task for the vehicle control system is to be able to fully utilize these limits. Another is to assist the driver to choose an adequate driving style, adapted to the actual conditions. A method to derive the tire forces for simultaneous braking, cornering and camber, by combining empirical models for the pure behavior of each of respective action is presented in the thesis. The method is based on the physical foundation brought by the simple, but well-suited brush model theory. The pure-slip tire models can be given as empirical models or as raw tabular data. The implementation is verified to be well-working and computationally sound and good results are obtained in validation with the available empirical data. A new type of on board brush-model based friction-estimator using the local measurements on the vehicle is also proposed. A major invention is the way of collecting the measurements into bins, such that the available data used for optimization is evenly weighted along the force and slip axis. Experimental data has been collected and evaluated to ensure the validity of the brush model during certain conditions. The estimator has been implemented and validated on a personal car. The wheel speed signal is an essential signal in many system applications. Based on problems observed during performed measurements, a few ways to reduce the noise on the signal, without adding any phase shift or time delay, are discussed in the thesis.
Fluorescence Excitation Spectroscopy for the Measurement of Epidermal Proliferation¶ (2001)

Fluorescence excitation spectroscopy was used to assess cellular turnover in human skin by monitoring changes of endogenous fluorescence. Epidermal proliferation was induced with alpha-hydroxy acids. Commercially available glycolic acid creams (8 and 4% wt/wt concentration) and a vehicle cream (placebo) were applied in a randomized double blinded fashion on subjects' forearms, twice daily for 21 days. Excitation spectra were recorded (excitation 250-360 nm, emission 380 nm) at days 0, 1, 3, 7, 10, 11, 14, 17 and 21. The 295 nm excitation band (assigned to tryptophan moieties) was used in this study as a marker for cellular proliferation. To further reduce the day-to-day variability of the skin fluorescence the intensity of the 295 nm band was normalized to the 334 nm band (assigned to collagen crosslinks). The fluorescence emission intensity from placebo-treated skin remained practically unchanged over the period of the measurements while the fluorescence intensity measured from the glycolic acid-treated skin increased monotonically with treatment. The rate of increase of the excitation intensity with treatment was found to be dose dependent. The epidermal 295 nm band may be used as a quantitative marker to monitor the rate of proliferation of epidermal keratinocytes noninvasively.
Topical Cidofovir (2000)

Two children with human immunodeficiency virus 1 (HIV-1) presented to the dermatology clinic for treatment of disseminated molluscum contagiosum (MC). Both children suffered from severe social isolation because of their facial disfigurement. Their MC lesions were refractory to numerous therapeutic modalities, including liquid nitrogen, cantharidin, and 0.05 % tretinoin gel. Both children had MC lesions, elevated viral loads, and low CD4 T-cell counts despite highly active antiretroviral therapy (HAART) for a median of 24 months. Patient 1, an 8-year-old African American boy, had a CD4 T-cell count of 329/μL and a viral load of 727050 (log 5.86) HIV RNA copies/mL. Patient 2, a 4-year-old-Hispanic boy, had a CD4 T-cell count of 168/μL and a viral load of 429976 (log 5.63) HIV RNA copies/mL Both patients exhibited hundreds of umbilicated pearly and skin-colored papules disseminated over the entire body, including the face and perineal area (Figure, A and C).
Acquisition of Chemoresistance and EMT Phenotype Is Linked with Activation of the Endothelin A Receptor Pathway in Ovarian Carcinoma Cells (2011)

Our data provide the first evidence that blockade of ET(A)R-driven EMT can overcome chemoresistance and inhibit tumor progression, improving the outcome of EOC patients' treatment.
The Role and Mechanism of Diacylglycerol-Protein Kinase C1 Signaling in Melanogenesis by Cryptococcus neoformans (2005)

The fungus Cryptococcus neoformans is an opportunistic human pathogen that causes a life-threatening meningoencephalitis by expression of virulence factors such as melanin, a black pigment produced by the cell wall-associated enzyme laccase. In previous studies (Heung, L. J., Luberto, C., Plowden, A., Hannun, Y. A., and Del Poeta, M. (2004) J. Biol. Chem. 279, 21144-21153) we proposed that the sphingolipid enzyme inositol-phosphoryl ceramide synthase 1 (Ipc1) regulates melanin production through the generation of diacylglycerol (DAG), which was found to activate in vitro protein kinase C1 (Pkc1). Here, we investigated the molecular mechanisms by which DAG regulates Pkc1 in vivo and the effect of this regulation on laccase activity and melanin synthesis. To this end we deleted the putative DAG binding C1 domain of C. neoformans Pkc1 and found that the C1 deletion abolished the activation of Pkc1 by DAG. Deletion of the C1 domain repressed laccase activity and, consequently, melanin production. Finally, we show that these biological effects observed in the C1 deletion mutant are mediated by alteration of cell wall integrity and displacement of laccase from the cell wall. These studies define novel molecular mechanisms addressing Pkc1-laccase regulation by the sphingolipid pathway of C. neoformans, with important implications for understanding and targeting the Ipc1-Pkc1-laccase cascade as a regulator of virulence of this important human pathogen.
The 3-(<i>N</i>-<i>tert</i>-Butylcarboxamido)-1-propyl Group as an Attractive Phosphate/Thiophosphate Protecting Group for Solid-Phase Oligodeoxyribonucleotide Synthesis (2002)

Among the various phosphate/thiophosphate protecting groups suitable for solid-phase oligonucleotide synthesis, the 3-(N-tert-butylcarboxamido)-1-propyl group is one of the most convenient, as it can be readily removed, as needed, under thermolytic conditions at neutral pH. The deprotection reaction proceeds rapidly (t(1/2) approximately 100 s) through an intramolecular cyclodeesterification reaction involving the amide function and the release of the phosphate/thiophosphate group as a 2-(tert-butylimino)tetrahydrofuran salt. Incorporation of the 3-(N-tert-butylcarboxamido)-1-propyl group into the deoxyribonucleoside phosphoramidites 1a-d is achieved using inexpensive raw materials. The coupling efficiency of 1a-d in the solid-phase synthesis of d(ATCCGTAGCTAAGGTCATGC) and its phosphorothioate analogue is comparable to that of commercial 2-cyanoethyl deoxyribonucleoside phosphoramidites. These oligonucleotides were phosphate/thiophosphate-deprotected within 30 min upon heating at 90 degrees C in Phosphate-Buffered Saline (PBS buffer, pH 7.2). Since no detectable nucleobase modification or significant phosphorothioate desulfurization occurs, the 3-(N-tert-butylcarboxamido)-1-propyl group represents an attractive alternative to the 2-cyanoethyl group toward the large-scale preparation of therapeutic oligonucleotides.
CD38+ M-MDSC expansion characterizes a subset of advanced colorectal cancer patients (2018)

NCI P01-CA14305603, the American Cancer Society, Scott and Suzi Lustgarten Family Colon Cancer Research Fund, Hansen Foundation, and Janssen Research and Development.
Teratoma in the Orchiectomy Specimen and Volume of Metastasis are Predictors of Retroperitoneal Teratoma in Post-Chemotherapy Nonseminomatous Testis Cancer (2002)

The absence of teratoma in the orchiectomy specimen does not reliably predict the absence of teratoma in the surgical specimen at post-chemotherapy retroperitoneal lymph node dissection. Post-chemotherapy surgery is indicated if retroperitoneal tumor remains after chemotherapy irrespective of the presence or absence of teratoma in the orchiectomy specimen.
Rational Use of Sublingual Opioids in Palliative Medicine (2007)

The sublingual administration of opioid analgesics has been a mainstay in the pain management of homebound dying hospice patients who are no longer able to swallow. It is also a potentially useful route of administration in other situations in which the oral route is not available and other routes are impractical or inappropriate. Potential advantages of the sublingual route include rapid analgesic onset and avoidance of hepatic first-pass metabolism. Pharmacokinetic and pharmacodynamic studies have yielded widely disparate data on sublingual morphine. Other opioids have been less studied. Available data suggests limited sublingual availability of hydrophilic opioids (e.g., morphine, oxycodone, and hydromorphone) and superior absorption of the lipophilic opioids (e.g., methadone and the fentanils). Buprenorphine, a potent, lipophilic, partial mu-opioid receptor agonist, appears promising but awaits further study.
Edge-based rich representation for vehicle classification (2005)

In this paper, we propose an approach to vehicle classification under a mid-field surveillance framework. We develop a repeatable and discriminative feature based on edge points and modified SIFT descriptors, and introduce a rich representation for object classes. Experimental results show the proposed approach is promising for vehicle classification in surveillance videos despite great challenges such as limited image size and quality and large intra-class variations. Comparisons demonstrate the proposed approach outperforms other methods.
Band discontinuity reduction of i-GaInAsP/p-InP for improving 1.55 μm GaInAsP/InP surface emitting laser performances (2002)

The long wavelength GaInAsP/InP surface emitting (SE) laser is becoming important for use in optical fiber networks. We reported a low threshold GaInAsP/InP SE laser grown by chemical beam epitaxy (CBE) with some device characteristics. However, its temperature dependence on threshold and efficiency are inferior to those of short wavelength SE lasers. The auger process and intervalence band absorption were discussed as the primary causes of the worse temperature characteristic. In addition to these, the potential spike at the active layer and p-cladding hetero-interface may require an additional voltage bias to inject holes. Takemoto et al. proposed a band discontinuity reduction (BDR) layer to reduce the spike height. Kazarinov et al. Pointed out that this spike reduces a potential barrier for electron confinement in the active layer and increases an electron overflow to the p-cladding layer. A preliminary calculation shows the carrier overflow may degrade the performance of long wavelength SE lasers. In this study, we investigate the current-voltage characteristic of the hetero-interface and introduce a BDR layer which has an intermediate composition between the active layer and the p-cladding layer in order to improve the temperature characteristic of long wavelength SE lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MMP9 and SCF Protect from Apoptosis in Acute Kidney Injury (2009)

Apoptosis of tubular epithelial cells is a hallmark of acute kidney injury (AKI), but the cellular events preceding apoptosis in this setting are incompletely understood. Because matrix metalloproteinase 9 (MMP9) degrades matrix components involved in cell survival, we studied the role of MMP9 in AKI. In the mouse model of folic acid–induced AKI, we observed a marked increase of MMP9 activity in the S3 segment of the proximal tubule (S3PT), correlating with the apoptotic phase. MMP9 deficiency increased apoptosis and the severity of renal lesions and substantially delayed recovery of renal function. MMP9−/− mice exhibited significant apoptosis in the S3PT and the intercalated cells of the collecting duct (I-CD), whereas wild-type mice exhibited none in these segments. Stem cell factor (SCF), an MMP9 substrate, was identified in the S3PT, and its receptor, c-Kit, was expressed in both the S3PT and I-CD. MMP9 released the soluble form of SCF (sSCF) from kidney cells in vivo and in vitro. In addition, SCF inhibited apoptosis of tubular cells in vitro, rescued MMP9−/− S3PT and I-CD from apoptosis in vivo, and improved renal function. An ischemia-reperfusion model of AKI produced similar results. In patients with AKI, urinary sSCF increased with acute tubular necrosis but not with prerenal azotemia. In conclusion, these data show that MMP9 protects the S3 segment of the proximal tubule and the I-CD from apoptosis in AKI, most likely by releasing sSCF.