gebhart/patrepeval huggingface dataset:
Pharmacology of tamsulosin: Saturation-binding isotherms and competition analysis using cloned α1-adrenergic receptor subtypes (1997)

We conclude that tamsulosin displays selectivity for alpha 1a and alpha 1d ARs. This selectivity may contribute to the tamsulosin efficacy reported in several recent clinical studies in patients with BPH.
Chemosensitivity testing of fresh and continuous tumor cell cultures using lactate dehydrogenase. (1997)

We have examined the use of the LDH (lactate dehydrogenase) assay for chemosensitivity testing in established and primary cultures of sarcoma, leukaemia and ovarian cancer in parallel with the MTT assay. The method we describe is rapid, sensitive and ideal for 96-well plate assays using adherent or suspension cultures. Excellent agreement between the two methods was observed (r = 0.936) using a variety of antitumour agents, with some notable exceptions. In the Bax (human synovial sarcoma) cell line MTT colour production by control cells was very low, thus MTT-->formazan production could not be relied upon as a definitive end point equating with cell number. In contrast, colour production of control cells using the LDH assay was significantly greater and all cultures tested were suitable for titration of chemosensitivity. There was a discrepancy between IC50 values obtained either by cell counting or MTT in the HTB88 (human leiomyosarcoma) line treated with 5-FU (59.9 microM vs > 200 microM, respectively). However, cell counting agreed well with the LDH assay (IC50 47.3 microM). Whilst the MTT assay remains a reliable method for chemosensitivity testing, the LDH assay may prove more appropriate in certain experimental settings.
Spectroscopic and Computational Studies of Ni Superoxide Dismutase:  Electronic Structure Contributions to Enzymatic Function (2005)

Ni-containing superoxide dismutase (NiSOD) is the most recently discovered member of the class of metalloenzymes that detoxify the superoxide radical in aerobic organisms. In this study, we have employed a variety of spectroscopic and computational methods to probe the electronic structure of the NiSOD active site in both its oxidized (NiSOD(ox), possessing a low-spin (S = (1)/(2)) Ni(3+) center) and reduced (NiSOD(red), containing a diamagnetic Ni(2+) center) states. Our experimentally validated computed electronic-structure description for NiSOD(ox) reveals strong sigma-bonding interactions between Ni and the equatorial S/N ligands, which give rise to intense charge-transfer transitions in the near-UV region of the absorption spectrum. Resonance Raman (rR) spectra obtained with laser excitation in this region exhibit two features at 349 and 365 cm(-)(1) that are assigned to Ni-S(Cys) stretching modes. The NiSOD(red) active site also exhibits a high degree of metal-ligand bond covalency as well as filled/filled pi-interactions between Ni and S/N orbitals, which serve to adjust the redox potential of the Ni(2+) center. Comparison of our computational results for NiSOD(red) with those obtained in parallel studies of synthetic [NiS(2)N(2)] complexes reveals that the presence of an anionic N-donor ligand is crucial for promoting metal-based (versus S-based) oxidation of the active site. The implications of our electronic-structure descriptions with respect to the function of NiSOD are discussed, and a comparison of M-S(Cys) bonding in NiSOD and other metalloenzymes with sulfur ligation is provided.
Characterizing the Swimming Properties of Artificial Bacterial Flagella (2009)

Artificial bacterial flagella (ABFs) consist of helical tails resembling natural flagella fabricated by the self-scrolling of helical nanobelts and soft-magnetic heads composed of Cr/Ni/Au stacked thin films. ABFs are controlled wirelessly using a low-strength rotating magnetic field. Self-propelled devices such as these are of interest for in vitro and in vivo biomedical applications. Swimming tests of ABFs show a linear relationship between the frequency of the applied field and the translational velocity when the frequency is lower than the step-out frequency of the ABF. Moreover, the influences of head size on swimming velocity and the lateral drift of an ABF near a solid boundary are investigated. An experimental method to estimate the propulsion matrix of a helical swimmer under a light microscope is developed. Finally, swarm-like behavior of multiple ABFs controlled as a single entity is demonstrated.
Facet degradation of GaN heterostructure laser diodes (2005)

We investigated the degradation of cleaved facets of (Al,In)GaN laser diodes in different atmospheres. We found that operation in water-free atmospheres with sufficient oxygen shows a slow degradation. Operation in atmospheres with water vapor causes a fast degradation and an oxidation on the facet. This deposition is a permanent damage to the laser diode. If the laser diode is operated in pure nitrogen, we find a thick deposition on the facet, which shows high absorption. This deposition can be removed by either high optical output powers or by operation in atmospheres with sufficient oxygen. We also explain the influence of these coatings to the degradation behavior and see these coatings as the reason for unstable kinks in the L–I characteristics during operation.
An optimized densification of the filled oxide for quarter micron shallow trench isolation (STI) (2002)

Densification methods using H/sub 2/O and N/sub 2/ ambient annealing of the filled CVD oxide for quarter micron STI are compared. Although the H/sub 2/O ambient oxidation is more effective in terms of the resistance against the HF etching, volume expansion by the trench sidewall oxidation generates a large amount of stress in the narrow isolation region. However, an N/sub 2/ gas ambient annealing at high temperature shows a low stress and a low HF etch rate which enable us to fabricate the stable quarter micron STI.
A distinct DNA methylation signature defines pediatric pre-B cell acute lymphoblastic leukemia (2012)

Pre-B cell acute lymphoblastic leukemia (ALL) is the most prevalent childhood malignancy and remains one of the highest causes of childhood mortality. Despite this, the mechanisms leading to disease remain poorly understood. We asked if recurrent aberrant DNA methylation plays a role in childhood ALL and have defined a genome-scale DNA methylation profile associated with the ETV6-RUNX1 subtype of pediatric ALL. Archival bone marrow smears from 19 children collected at diagnosis and remission were used to derive a disease specific DNA methylation profile. The gene signature was confirmed in an independent cohort of 86 patients. A further 163 patients were analyzed for DNA methylation of a three gene signature. We found that the DNA methylation signature at diagnosis was unique from remission. Fifteen loci were sufficient to discriminate leukemia from disease-free samples and purified CD34+ cells. DNA methylation of these loci was recurrent irrespective of cytogenetic subtype of pre-B cell ALL. We show that recurrent aberrant genomic methylation is a common feature of pre-B ALL, suggesting a shared pathway for disease development. By revealing new DNA methylation markers associated with disease, this study has identified putative targets for development of novel epigenetic-based therapies.
DNA Damage in Human Spermatozoa Is Highly Correlated with the Efficiency of Chromatin Remodeling and the Formation of 8-Hydroxy-2′-Deoxyguanosine, a Marker of Oxidative Stress1 (2009)

DNA damage in human spermatozoa has been associated with a range of adverse clinical outcomes, including infertility, abortion, and disease in the offspring. We have advanced a two-step hypothesis to explain this damage involving impaired chromatin remodeling during spermiogenesis followed by a free radical attack to induce DNA strand breakage. The objective of the present study was to test this hypothesis by determining whether impaired chromatin protamination is correlated with oxidative base damage and DNA fragmentation in human spermatozoa. DNA fragmentation, chromatin protamination, mitochondrial membrane potential, and formation of the oxidative base adduct, 8-hydroxy-2'-deoxyguanosine (8OHdG), were monitored by flow cytometry/fluorescence microscopy. Impairment of DNA protamination during late spermatogenesis was highly correlated (P < 0.001) with DNA damage in human spermatozoa. The disruption of chromatin remodeling also was associated with a significant elevation in the levels of 8OHdG (P < 0.001), and the latter was itself highly correlated with DNA fragmentation (P < 0.001). The significance of oxidative stress in 8OHdG formation was demonstrated experimentally using H2O2/Fe2+ and by the correlation observed between this base adduct and superoxide generation (P < 0.001). That 8OHdG formation was inversely associated with mitochondrial membrane potential (P < 0.001) suggested a possible role for these organelles in the creation of oxidative stress. These results clearly highlight the importance of oxidative stress in the induction of sperm DNA damage and carry significant implications for the clinical management of this condition.
A new wake-up radio architecture for wireless sensor networks (2014)

The last decades have been really hungry in new ways to reduce energy consumption. That is especially true when talking about wireless sensor networks in general and home multimedia networks in particular, since electrical energy consumption is the bottleneck of the network. One of the most energy-consuming functional block of an equipment is the radio front end, and methods to switch it off during the time intervals where it is not active must be implemented. This paper proposes a wake-up radio circuit which is capable of both addressing and waking up not only a more efficient but also more energy-consuming radio front end. By using a frequency footprint to differentiate each sensor, awaking all the sensors except for the one of interest is avoided. The particularity of the proposed wake-up receiver is that the decision is taken in the radio-frequency part and no baseband treatment is needed.
9.6 A 2.7-to-4.3GHz, 0.16psrms-jitter, −246.8dB-FOM, digital fractional-N sampling PLL in 28nm CMOS (2016)

High-performance phase-locked-loops (PLLs) are key building blocks for many modern ICs. The sub-sampling PLL proposed in [1] uses a reference clock REF to sample a high-frequency VCO and converts phase/timing error into voltage. The steep dv/dt slope of the VCO helps to realize a high phase-detection gain and greatly suppresses the noise of loop components succeeding the phase detector, leading to low in-band phase noise and good PLL Figure-Of-Merit (FOM). However, the original design in [1] is analog and limited to integer-N (int-N) operation. It is desirable to extend it to more versatile fractional-N (frac-N) mode, and to make it digital for greater flexibility and more advanced digital calibration. This work presents a new 28nm CMOS digital frac-N sampling PLL design that achieved 0.16ps rms jitter with 8.2mW and a state-of-the-art frac-N PLL FOM of −246.8dB.
Growth Stage–Based Phenotypic Analysis of Arabidopsis (2001)

With the completion of the Arabidopsis genome sequencing project, the next major challenge is the large-scale determination of gene function. As a model organism for agricultural biotechnology, Arabidopsis presents the opportunity to provide key insights into the way that gene function can affect commercial crop production. In an attempt to aid in the rapid discovery of gene function, we have established a high throughput phenotypic analysis process based on a series of defined growth stages that serve both as developmental landmarks and as triggers for the collection of morphological data. The data collection process has been divided into two complementary platforms to ensure the capture of detailed data describing Arabidopsis growth and development over the entire life of the plant. The first platform characterizes early seedling growth on vertical plates for a period of 2 weeks. The second platform consists of an extensive set of measurements from plants grown on soil for a period of approximately 2 months. When combined with parallel processes for metabolic and gene expression profiling, these platforms constitute a core technology in the high throughput determination of gene function. We present here analyses of the development of wild-type Columbia (Col-0) plants and selected mutants to illustrate a framework methodology that can be used to identify and interpret phenotypic differences in plants resulting from genetic variation and/or environmental stress.
On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy) (2016)

T lymphocytes equipped with clonotypic T cell antigen receptors (TCR) recognize immunogenic peptides only when presented in the context of their own major histocompatibility complex (MHC) molecules. Peptide loading to MHC molecules occurs in intracellular compartments (ER for class I and MIIC for class II molecules) and relies on the interaction of the respective peptides and peptide binding pockets on MHC molecules. Those peptide residues not engaged in MHC binding point towards the TCR screening for possible peptide MHC complex binding partners. Natural or intentional modification of both MHC binding registers and TCR interacting residues of peptides - leading to the formation of altered peptide ligands (APLs) - might alter the way peptides interact with TCRs and hence influence subsequent T cell activation events, and consequently T cell effector functions. This review article summarizes how APLs were detected and first described, current concepts of how APLs modify T cellular signaling, which biological mechanisms might force the generation of APLs in vivo, and how peptides and APLs might be used for the benefit of patients suffering from allergic or autoimmune diseases.
Perspectives on transdermal ultrasound mediated drug delivery. (2007)

The use of needles for multiple injection of drugs, such as insulin for diabetes, can be painful. As a result, prescribed drug noncompliance can result in severe medical complications. Several noninvasive methods exist for transdermal drug delivery. These include chemical mediation using liposomes and chemical enhancers or physical mechanisms such as microneedles, iontophoresis, electroporation, and ultrasound. Ultrasound enhanced transdermal drug delivery offers advantages over traditional drug delivery methods which are often invasive and painful. A broad review of the transdermal ultrasound drug delivery literature has shown that this technology offers promising potential for noninvasive drug administration. From a clinical perspective, few drugs, proteins or peptides have been successfully administered transdermally because of the low skin permeability to these relatively large molecules, although much work is underway to resolve this problem. The proposed mechanism of ultrasound has been suggested to be the result of cavitation, which is discussed along with the bioeffects from therapeutic ultrasound. For low frequencies, potential transducers which can be used for drug delivery are discussed, along with cautions regarding ultrasound safety versus efficacy.
Detection and Imaging of Nitric Oxide with Novel Fluorescent Indicators:  Diaminofluoresceins (1998)

Nitric oxide is a gaseous, free radical which plays a role as an intracellular second messenger and a diffusable intercellular messenger. To obtain direct evidence for NO functions in vivo, we have designed and synthesized diaminofluoresceins (DAFs) as novel fluorescent indicators for NO. The fluorescent chemical transformation of DAFs is based on the reactivity of the aromatic vicinal diamines with NO in the presence of dioxygen. The N-nitrosation of DAFs, yielding the highly green-fluorescent triazole form, offers the advantages of specificity, sensitivity, and a simple protocol for the direct detection of NO (detection limit 5 nM). The fluorescence quantum efficiencies are increased more than 100 times after the transformation of DAFs by NO. Fluorescence detection with visible light excitation and high sensitivity enabled the practical assay of NO production in living cells. Membrane-permeable DAF-2 diacetate (DAF-2 DA) can be used for real-time bioimaging of NO with fine temporal and spatial resolution. The dye was loaded into activated rat aortic smooth muscle cells, where the ester bonds are hydrolyzed by intracellular esterase, generating DAF-2. The fluorescence in the cells increased in a NO concentration-dependent manner.
Effect of Therapeutic Footwear on Foot Reulceration in Patients With Diabetes (2002)

This study of persons without severe foot deformity does not provide evidence to support widespread dispensing of therapeutic shoes and inserts to diabetic patients with a history of foot ulcer. Study shoes and custom cork or preformed polyurethane inserts conferred no significant ulcer reduction compared with control footwear. This study suggests that careful attention to foot care by health care professionals may be more important than therapeutic footwear but does not negate the possibility that special footwear is beneficial in persons with diabetes who do not receive such close attention to foot care by their health care providers or in individuals with severe foot deformities.
Glypican-3 is a useful diagnostic marker for a component of hepatocellular carcinoma in human liver cancer (2009)

Primary liver cancers are classified into three types based on their morphology and cytogenetic characteristics hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular and cholangiocarcinoma (CHC). It is often difficult to distinguish these liver tumors. Glypican-3 (GPC3) is serological and histochemical marker of hepatocellular carcinoma. In order to separate these three types of liver cancers, we analyzed the GPC3 expression in 85 liver resection specimens, including 46 HCCs, 28 ICCs and 11 CHCs. GPC3 immunohistochemical staining was used to distinguish HCC from ICC by comparing with the conventional biomarker, alpha-fetoprotein (AFP). The immunostaining of GPC3 was identified in 78.3% (36/46) of HCCs, 60% (9/15) of well differentiated, 88.9% (16/18) of moderately differentiated and 84.6% (11/13) of poorly differentiated HCCs. It was negative in the ICCs. We confirmed that GPC3 expression is specific to HCC component (8/11, 72.7%) but few samples also showed weakly in ICC component (2/11, 18.2%) of CHC sections among 11 cases compared with HCC biomarkers including AFP and hepatocyto paraffin 1 (HepPar1), and ICC biomarkers cytokeratin (CK) 7 and CK19. Three cases in which the macroscopic features resembled ICC did not express GPC3 even in the pathological HCC component. Most (10/11, 91%) of the pathological cholangiocarcinoma components in CHC showed positive staining for CK7 and CK19. The results of this study suggest that GPC3 is a biomarker that is sensitive and specific to HCC component of CHC, and CK7 and CK19 are markers for pathological cholangiocarcinoma component of CHC.
Lysosomal localization of the neuronal ceroid lipofuscinosis CLN5 protein (2002)

The Finnish variant late infantile neuronal ceroid lipofuscinosis (vLINCL) belongs to the neuronal ceroid lipofuscinosis group of common recessively inherited neurodegenerative disorders. The CLN 5 gene responsible for this brain disorder codes for a novel protein with no homology to previously reported proteins. In this study, we have investigated the biosynthesis and intracellular localization of this protein in transiently transfected BHK-21 cells using a CLN5-specific peptide antibody. Confocal immunofluorescence microscopy showed that wild-type CLN5 is predominantly targeted to lysosomes and immunoprecipitation analysis recognized a 60 kDa polypeptide. The molecular weight of this protein was reduced to 40 kDa by deglycosylation with Endo H and to 38 kDa with PNGase F. The same-sized glycosylated polypeptides were also observed in the media, suggesting that the 60 kDa glycosylated CLN5 polypeptide represents a soluble lysosomal glycoprotein, not an integral transmembrane protein as predicted earlier. The most common human vLINCL mutation blocked the lysosomal targeting of expressed polypeptides. This would imply that the pathogenesis of vLINCL would be associated with the defective lysosomal trafficking, preventing the normal biological function of the corresponding polypeptide.
Non-fucosylated therapeutic antibodies as next-generation therapeutic antibodies (2006)

Most of the existing therapeutic antibodies that have been licensed and developed as medical agents are of the human IgG1 isotype, the molecular weight of which is approximately 150 kDa. Human IgG1 is a glycoprotein bearing two N-linked biantennary complex-type oligosaccharides bound to the antibody constant region (Fc), in which the majority of the oligosaccharides are core fucosylated, and it exercises the effector functions of antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity through the interaction of the Fc with either leukocyte receptors (FcgammaRs) or complement. Recently, therapeutic antibodies have been shown to improve overall survival as well as time to disease progression in a variety of human malignancies, such as breast, colon and haematological cancers, and genetic analysis of FcgammaR polymorphisms of cancer patients has demonstrated that ADCC is a major antineoplasm mechanism responsible for clinical efficacy. However, the ADCC of existing licensed therapeutic antibodies has been found to be strongly inhibited by serum due to nonnpecific IgG competing for binding of the therapeutics to FcgammaRIIIa on natural killer cells, which leads to the requirement of a significant amount of drug and very high costs associated with such therapies. Moreover, enhanced ADCC of non-fucosylated forms of therapeutic antibodies through improved FcgammaRIIIa binding is shown to be inhibited by the fucosylated counterparts. In fact, non-fucosylated therapeutic antibodies, not including the fucosylated forms, exhibit the strongest and most saturable in vitro and ex vivo ADCC among such antibody variants with improved FcgammaRIIIa binding as those bearing naturally occurring oligosaccharide heterogeneities and artificial amino acid mutations, even in the presence of plasma IgG. Robust stable production of completely non-fucosylated therapeutic antibodies in a fixed quality has been achieved by the generation of a unique host cell line, in which the endogenous alpha-1,6-fucosyltransferase (FUT8) gene is knocked out. Thus, the application of non-fucosylated antibodies is expected to be a promising approach as next-generation therapeutic antibodies with improved efficacy, even when administrated at low doses in humans in vivo. Clinical trials using non-fucosylated antibody therapeutics are underway at present.
Insertion site preference of Mu, Tn5, and Tn7 transposons (2012)

Abstract Background Transposons, segments of DNA that can mobilize to other locations in a genome, are often used for insertion mutagenesis or to generate priming sites for sequencing of large DNA molecules. For both of these uses, a transposon with minimal insertion bias is desired to allow complete coverage with minimal oversampling. Findings Three transposons, Mu, Tn5, and Tn7, were used to generate insertions in the same set of fosmids containing Candida glabrata genomic DNA. Tn7 demonstrates markedly less insertion bias than either Mu or Tn5, with both Mu and Tn5 biased toward sequences containing guanosine (G) and cytidine (C). This preference of Mu and Tn5 yields less uniform spacing of insertions than for Tn7, in the adenosine (A) and thymidine (T) rich genome of C. glabrata (39% GC). Conclusions In light of its more uniform distribution of insertions, Tn7 should be considered for applications in which insertion bias is deleterious.