gebhart/patrepeval huggingface dataset:
Combination photoimmunotherapy with monoclonal antibodies recognizing different epitopes of human epidermal growth factor receptor 2: an assessment of phototherapeutic effect based on fluorescence molecular imaging (2016)

Photoimmunotherapy is a new class of molecular targeted cancer therapy based on a monoclonal antibody (mAb) conjugated to a photosensitizer and irradiation with near-infrared (NIR) light for both imaging and therapy. Here, we sought to determine the feasibility of combining photoimmunotherapy using conjugates of human epidermal growth factor receptor 2 (HER2)-specific mAb-photosensitizer IR700, trastuzumab-IR700 and pertuzumab-IR700. HER2-expressing and non-expressing cells were treated with mAb-IR700 conjugates and irradiated with NIR light. Fluorescence imaging and cytotoxic effects were examined in cultured HER2-expressng cancer cell lines and in a mouse tumor xenograft model. Trastuzumab-IR700 and pertuzumab-IR700 could specifically bind to HER2 without competing, and the combination treatment of both agents yielded stronger HER2-specific IR700 fluorescence signals than with the treatment with either agent singly. A cytotoxicity assay showed that the combination treatment of both trastuzumab-IR700 and pertuzumab-IR700 followed by NIR light irradiation induced stronger cytotoxic effect than with treatment of either agent plus NIR light irradiation. Furthermore, the phototoxic and cytotoxic effects of mAb depended on HER2-specific IR700 signal intensities. Consistent with in vitro studies, in xenograft tumor models also, IR700 fluorescence imaging-guided NIR light irradiation after the combination treatment of trastuzumab-IR700 and pertuzumab-IR700 led to stronger antitumor effects than by treatment with either agent followed by NIR light irradiation. In conclusion, fluorescence molecular imaging can facilitate the assessment of treatment outcomes of molecular targeted photoimmunotherapy, which holds great potential in facilitating better outcomes in cancer patients.
Characterization of the Catalytic Site of the ADP-Ribosyltransferase Clostridium botulinum C2 Toxin by Site-directed Mutagenesis (1998)

The actin ADP-ribosylating Clostridium botulinum C2 toxin is a binary toxin composed of the binding component C2II and the enzyme component C2I. C2I ADP-ribosylates G-actin at arginine 177, resulting in the depolymerization of the actin cytoskeleton. Here, we studied the structure-function relationship of C2I by site-directed mutagenesis. Exchange of Glu389 to glutamine caused the complete loss of ADP-ribosyltransferase and NAD-glycohydrolase activities of C2I. In contrast, exchange of Glu387 to glutamine blocked ADP-ribosyltransferase but not NAD-glycohydrolase activity. Whereas photoaffinity labeling of the double mutant E387Q/E389Q C2I with [carbonyl-14C]NAD was blocked, labeling of the single C2I mutants was reduced (E389Q) or not changed (E387Q). Exchange of the STS motif (amino acid residues 348-350) of C2I caused a decrease in transferase activity by more than 99 (S348A) and 90% (T349V), or did not affect activity (S350A). Exchange of Arg299 and Arg300 to lysine reduced transferase activity to <0.1 and approximately 35% of wild-type activity. The data indicate that the amino acid residues Glu389, Glu387, Ser348, and Arg299, which are conserved in various prokaryotic and eukaryotic arginine-modifying ADP-ribosyltransferases, are essential for ADP-ribosyltransferase activity of the enzyme component of C. botulinum C2 toxin.
Scale-Independent Relational Query Processing (2013)

An increasingly common pattern is for newly-released web applications to succumb to a "Success Disaster".In this scenario, overloaded database machines and resultant high response times destroy a previously good user experience, just as a site is becoming popular.Unfortunately, the data independence provided by a traditional relational database system, while useful for agile development, only exacerbates the problem by hiding potentially expensive queries under simple declarative expressions.The disconnect between expression complexity and runtime cost often leads developers to mistrust the suitability of relational database systems for their web applications in the long term.As a result, developers of these applications are increasingly abandoning relational systems in favor of imperative code written against distributed "NoSQL" key/value stores, losing the many benefits of data independence in the process.While some claim that scalability issues are inherent in the use of the relational model, this thesis challenges that notion by extending standard data independence with the notion of scale independence.In contrast to traditional relational databases, a scale-independent system is capable of providing predictable response time for all of the queries in an application, even as the amount of data grows by orders of magnitude.This predictability is achieved by compile-time enforcement of strict upper bounds on the number of operations that will be performed for all queries.Coupled with a service level objective (SLO) compliance prediction model and a scalable storage architecture, these upper bounds make it easy for developers to write success-tolerant applications that support an arbitrarily large number of users while still providing acceptable performance.Statically bounding the amount of work required to execute a query can be easy for some queries, such as those that perform a lookup of a single record by primary key.However, such simple queries are generally insu cient for the construction of complex, real-world applications.Therefore, to enable successful development of such applications, this thesis defines four levels of scale-independent execution that greatly expand the space of queries that can be guaranteed to be scalable a priori.Each scale-independent execution level leverages increasingly sophisticated techniques, ranging from extra cardinality information in
A critical period in the sensitivity of basal forebrain cholinergic neurones to NGF deprivation (1997)

Cholinergic neurones of basal forebrain (BF) express receptors for nerve growth factor (NGF) and are sensitive to NGF. In many CNS structures, including the BF region, the expression of NGF and its receptors is developmentally regulated. To test whether BF neurones depend on NGF during restricted time windows of postnatal development, we antagonized endogenous NGF by implanting, in the lateral ventricle of the rat, hybridoma cells producing blocking antibodies specific for NGF. Implants were performed at postnatal day 2 (P2), P8 and P15. BF cholinergic neurones were drastically reduced in number only when endogenous NGF was antagonized during the first postnatal week. We conclude that BF cholinergic neurones are sensitive to NGF deprivation only during early postnatal development.
Empirical comparison of cell segmentation algorithms using an annotated dataset (2004)

Three popular algorithms (Viterbi active contour, watershed and a thresholding-based method) for segmenting cell nuclei are compared empirically. This is achieved via a large (20,000) image dataset that has been annotated by three independent nonexpert observers. The Hausdorff distance is used as an error metric and Chalana's modified Williams' index is used to compare each algorithm's output to the observers' data.
Regulation of Longevity inCaenorhabditis elegansby Heat Shock Factor and Molecular Chaperones (2003)

The correlation between longevity and stress resistance observed in long-lived mutant animals suggests that the ability to sense and respond to environmental challenges could be important for the regulation of life span. We therefore examined the role of heat shock factor (HSF-1), a master transcriptional regulator of stress-inducible gene expression and protein folding homeostasis, in the regulation of longevity. Down-regulation of hsf-1 by RNA interference suppressed longevity of mutants in an insulin-like signaling (ILS) pathway that functions in the nervous system of Caenorhabditis elegans to influence aging. hsf-1 was also required for temperature-induced dauer larvae formation in an ILS mutant. Using tissue-specific expression of wild-type or dominant negative HSF-1, we demonstrated that HSF-1 acts in multiple tissues to regulate longevity. Down-regulation of individual molecular chaperones, transcriptional targets of HSF-1, also decreased longevity of long-lived mutant but not wild-type animals. However, suppression by individual chaperones was to a lesser extent, suggesting an important role for networks of chaperones. The interaction of ILS with HSF-1 could represent an important molecular strategy to couple the regulation of longevity with an ancient genetic switch that governs the ability of cells to sense and respond to stress.
MRI contrast agents: Classification and application (Review) (2016)

Magnetic resonance imaging (MRI) contrast agents are categorised according to the following specific features: chemical composition including the presence or absence of metal atoms, route of administration, magnetic properties, effect on the magnetic resonance image, biodistribution and imaging applications. The majority of these agents are either paramagnetic ion complexes or superparamagnetic magnetite particles and contain lanthanide elements such as gadolinium (Gd3+) or transition metal manganese (Mn2+). These elements shorten the T1 or T2 relaxation time, thereby causing increased signal intensity on T1-weighted images or reduced signal intensity on T2-weighted images. Most paramagnetic contrast agents are positive agents. These agents shorten the T1, so the enhanced parts appear bright on T1-weighted images. Dysprosium, superparamagnetic agents and ferromagnetic agents are negative contrast agents. The enhanced parts appear darker on T2-weighted images. MRI contrast agents incorporating chelating agents reduces storage in the human body, enhances excretion and reduces toxicity. MRI contrast agents may be administered orally or intravenously. According to biodistribution and applications, MRI contrast agents may be categorised into three types: extracellular fluid, blood pool and target/organ-specific agents. A number of contrast agents have been developed to selectively distinguish liver pathologies. Some agents are also capable of targeting other organs, inflammation as well as specific tumors.
Core/Multishell Nanowire Heterostructures as Multicolor, High-Efficiency Light-Emitting Diodes (2005)

We report the growth and characterization of core/multishell nanowire radial heterostructures, and their implementation as efficient and synthetically tunable multicolor nanophotonic sources. Core/multishell nanowires were prepared by metal-organic chemical vapor deposition with an n-GaN core and InxGa1-xN/GaN/p-AlGaN/p-GaN shells, where variation of indium mole fraction is used to tune emission wavelength. Cross-sectional transmission electron microscopy studies reveal that the core/multishell nanowires are dislocation-free single crystals with a triangular morphology. Energy-dispersive X-ray spectroscopy clearly shows shells with distinct chemical compositions, and quantitatively confirms that the thickness and composition of individual shells can be well controlled during synthesis. Electrical measurements show that the p-AlGaN/p-GaN shell structure yields reproducible hole conduction, and electroluminescence measurements demonstrate that in forward bias the core/multishell nanowires function as light-emitting diodes, with tunable emission from 365 to 600 nm and high quantum efficiencies. The ability to synthesize rationally III-nitride core/multishell nanowire heterostructures opens up significant potential for integrated nanoscale photonic systems, including multicolor lasers.
Phase II Study of Activated Charcoal to Prevent Irinotecan-Induced Diarrhea (2004)

The administration of AC with irinotecan reduced the incidence of grade 3 to 4 diarrhea and antidiarrheal medication consumption and increased irinotecan dose-intensity. Prophylactic AC may have a role in reducing dose-limiting CID and optimizing irinotecan therapy.
Lymphocyte homing into lymph nodes: in vitro demonstration of the selective affinity of recirculating lymphocytes for high-endothelial venules. (1976)

An in vitro model is described for studying the interaction between lymphocytes and high-endothelial venules (HEV) of lymph nodes. Rat or mouse lymphocytes which were layered over fixed sections of syngeneic lymph nodes adhered selectively to the endothelium of HEV but did not bind to other vascular endothelia. Evidence is presented that adherence to HEV in vitro is a property of recirculating lymphocytes and not a characteristic of cells which are unable to home into lymph nodes in vivo.
Races of Phytophthora sojae on Soybean in Illinois (2000)

Phytophthora root rot of soybean (Glycine max (L.) Merr.), caused by Phytophthora sojae M. J. Kauffmann &amp; J. W. Gerdemann, has been isolated throughout the soybean-producing regions of the United States. Posted 3 June 2000.
Calix[4]arene Salenes: A Bifunctional Receptor for NaH2PO4 (1994)

both anionic and cationic binding sites and is able to complex simultaneously anionic and cationic species.
Suppression of the boron penetration induced Si/SiO/sub 2/ interface degradation by using a stacked-amorphous-silicon film as the gate structure for pMOSFET (1994)

The authors report that the boron penetration through the thin gate oxide into the Si substrate does not only cause a large threshold voltage shift but also induces a large degradation in the Si/SiO/sub 2/ interface. An atomically flat Si/SiO/sub 2/ interface can be easily obtained by using a stacked-amorphous-silicon (SAS) film as the gate structure for p/sup +/ poly-Si gate MOS devices even with the annealing temperature as high as 1000/spl deg/C.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Detection of Irradiated Food—methods and Routine Applications (1993)

Irradiation of food for the purpose of extension of shelf life, control of microbial load, reduction of pathogenic microorganisms and disinfection is regarded by many consumers with suspicion. One reason is the lack of methods within food-controlling laboratories which can detect irradiation treatment and which are applied to control correct labelling. This review describes the potential of various methods to reveal irradiation treatment. Special emphasis is given to the three most successful methods, thermoluminescence, electron spin resonance spectroscopy and detection of volatiles. The possibilities and limitations of applying the methods in routine control are discussed.
Antisense RNA protects mRNA from RNase E degradation by RNA–RNA duplex formation during phage infection (2011)

The ecologically important cyanobacterium Prochlorococcus possesses the smallest genome among oxyphototrophs, with a reduced suite of protein regulators and a disproportionately high number of regulatory RNAs. Many of these are asRNAs, raising the question whether they modulate gene expression through the protection of mRNA from RNase E degradation. To address this question, we produced recombinant RNase E from Prochlorococcus sp. MED4, which functions optimally at 12 mM Mg(2+), pH 9 and 35°C. RNase E cleavage assays were performed with this recombinant protein to assess enzyme activity in the presence of single- or double-stranded RNA substrates. We found that extraordinarily long asRNAs of 3.5 and 7 kb protect a set of mRNAs from RNase E degradation that accumulate during phage infection. These asRNA-mRNA duplex formations mask single-stranded recognition sites of RNase E, leading to increased stability of the mRNAs. Such interactions directly modulate RNA stability and provide an explanation for enhanced transcript abundance of certain mRNAs during phage infection. Protection from RNase E-triggered RNA decay may constitute a hitherto unknown regulatory function of bacterial cis-asRNAs, impacting gene expression.
Internalization and trafficking of guanylyl (guanylate) cyclase/natriuretic peptide receptor A is regulated by an acidic tyrosine-based cytoplasmic motif GDAY (2005)

We have identified a GDAY motif in the C-terminal domain of guanylyl cyclase (guanylate cyclase)/NPRA (natriuretic peptide receptor A) sequence, which serves a dual role as an internalization signal and a recycling signal. To delineate the role of the GDAY motif in receptor internalization and sequestration, we mutated Gly920, Asp921 and Tyr923 to alanine residues (GDAY/AAAA) in the NPRA cDNA sequence. The cDNAs encoding wild-type and mutant receptors were transfected in HEK-293 cells (human embryonic kidney 293 cells). The internalization studies of ligand-receptor complexes revealed that endocytosis of 125I-ANP by HEK-293 cells expressing G920A, Y923A or GDAY/AAAA mutant receptor was decreased by almost 50% (P<0.001) when compared with cells expressing the wild-type receptor. However, the effect of D921A mutation on receptor internalization was minimal. Ligand-mediated down-regulation of G920A, Y923A and GDAY/AAAA mutant receptors was decreased by 35-40% when compared with wild-type NPRA. Subsequently, the recycling of internalized D921A and GDAY/AAAA mutant receptors from the intracellular pool was decreased by more than 40+/-4% when compared with wild-type NPRA. Recycling of G920A and Y923A mutant receptors was also decreased, but to a significantly lesser extent compared with the D921A or GDAY/AAAA mutant receptors. We conclude that the Gly920 and Tyr923 residues within the GDAY consensus motif are necessary for internalization, and that residue Asp921 is important for recycling of NPRA. The current results provide new evidence for a dual role of the GDAY sequence motif in ligand-mediated internalization, recycling and down-regulation of a single-transmembrane receptor protein NPRA.
Dispersion and Separation of Small-Diameter Single-Walled Carbon Nanotubes (2006)

The dispersion of small-diameter single-walled carbon nanotubes (SWNTs) produced by the CoMoCAT method in tetrahydrofuran (THF) with the use of amine was studied. The absorption, photoluminescence, and Raman spectroscopies showed that the dispersion and centrifugation process leads to an effective separation of metallic SWNTs from semiconducting SWNTs. Since this method is simple and convenient, it is highly applicable to an industrial utilization for widespread applications of SWNTs.
Functional Transcription Elongation Complexes from Synthetic RNA-DNA Bubble Duplexes (1992)

A synthetic RNA-DNA bubble duplex construct intended to mimic the nucleic acid framework of a functional transcription elongation complex was designed and assembled. The construct consisted of a double-stranded DNA duplex of variable length (the template and nontemplate strands) containing an internal noncomplementary DNA "bubble" sequence. The 3' end of an RNA oligonucleotide that is partially complementary to the template DNA strand was hybridized within the DNA bubble to form an RNA-DNA duplex with a non-complementary 5'-terminal RNA tail. The addition of either Escherichia coli or T7 RNA polymerase to this construct formed a complex that synthesized RNA with good efficiency from the hybridized RNA primer in a template-directed and processive manner, and displayed other features of a normal promoter-initiated transcription elongation complex. Other such constructs can be designed to examine many of the functional and regulatory properties of transcription systems.
Pyrimido[1,6-a]benzimidazoles: a new class of DNA gyrase inhibitors (1992)

Substituted 4-quinolone- (1, A = CH) and 1,8-naphthyrid-4-one- (1, A = N) 3-carboxylic acids are currently the only classes of clinically useful antibacterial agents exerting their activity by inhibiting the subunit A of DNA gyrase. Pyrimido[1,6-alpha]benzimidazoles 11 have been found to be a new class of inhibitors of this enzyme. The design, synthesis, and biological activity of these compounds are reported.
[DNA methylation and non-small cell lung cancer]. (2010)

Genomic DNA methylation is a major form of epigenetic modification. Hypermethylation could affect the binding of transcription factors to DNA and change the structure of chromatin resulting in silence of tumor suppressor genes, which plays an important role in cancer initiation and progression. In recent years, the study of DNA methylation in lung cancer, mostly in non-small cell lung cancer, has made great progress and become a new target for early detection, risk assessment, prognosis and cancer therapy.
Low Upper Limit to Methane Abundance on Mars (2013)

By analogy with Earth, methane in the Martian atmosphere is a potential signature of ongoing or past biological activity. During the past decade, Earth-based telescopic observations reported "plumes" of methane of tens of parts per billion by volume (ppbv), and those from Mars orbit showed localized patches, prompting speculation of sources from subsurface bacteria or nonbiological sources. From in situ measurements made with the Tunable Laser Spectrometer (TLS) on Curiosity using a distinctive spectral pattern specific to methane, we report no detection of atmospheric methane with a measured value of 0.18 ± 0.67 ppbv corresponding to an upper limit of only 1.3 ppbv (95% confidence level), which reduces the probability of current methanogenic microbial activity on Mars and limits the recent contribution from extraplanetary and geologic sources.
Modified deep dorsal laminectomy in the dog. (1975)

Spinal cord compression subsequent to radical laminectomy was investigated. A modified deep dorsal laminectomy technique was devised to allow extensive exposure and decompression of the canine spinal cord without undue hazard of postoperative fibrotic spinal cord compression. A previously described laminectomy technique was modified by the addition of spinal plating to avoid the occurrence of constrictive fibrosis.
Direct mass determination of hydrogen uptake using a quartz crystal microbalance (2007)

The authors demonstrate the application of a quartz crystal microbalance for direct mass determination of hydrogen uptake in storage materials in the pressure range of 0–40bars. The frequency shift of a quartz crystal coated with hydrogen absorbing materials is affected by the hydrogen mass uptake on the crystal, the pressure and the viscosity of the gases, and the crystal surface roughness, of which the roughness contribution has no analytical expression. Through a control experiment on the same crystal in helium, the roughness contribution in hydrogen can be derived and the frequency shift due to the hydrogen mass uptake can be obtained.
Endovascular stimulation within the left pulmonary artery to induce slowing of heart rate and paroxysmal atrial fibrillation (2002)

These data suggest that stimulation of autonomic nerves in the LPA causes slowing of the heart rate followed by paroxysmal APD/AT/AF simulating the spontaneously occurring paroxysmal AF syndrome, associated with bradycardia, reported in patients.