gebhart/patrepeval huggingface dataset:
Avalanche photodiode image sensor in standard BiCMOS technology (2000)

To overcome the transistor-induced noise limitations of solid-state image sensors at low light levels, we investigate a programmable camera concept based on an image sensor that employs the avalanche effect for photogenerated charge carriers. Each pixel consists of an avalanche photodiode (APD), high-voltage stabilization circuitry, and image readout electronics. Special emphasis is placed on the integration and characterization of such an APD image sensor with an unmodified, commercially available BiCMOS process. Experimental results of the first APD camera in BiCMOS technology with 12/spl times/24 pixels shows individually programmable, stable diode gain up to a factor of 1000.
Analysis of the N-glycans of recombinant human Factor IX purified from transgenic pig milk (2008)

Glycosylation of recombinant proteins is of particular importance because it can play significant roles in the clinical properties of the glycoprotein. In this work, the N-glycan structures of recombinant human Factor IX (tg-FIX) produced in the transgenic pig mammary gland were determined. The majority of the N-glycans of transgenic pig-derived Factor IX (tg-FIX) are complex, bi-antennary with one or two terminal N-acetylneuraminic acid (Neu5Ac) moieties. We also found that the N-glycan structures of tg-FIX produced in the porcine mammary epithelial cells differed with respect to N-glycans from glycoproteins produced in other porcine tissues. tg-FIX contains no detectable Neu5Gc, the sialic acid commonly found in porcine glycoproteins produced in other tissues. Additionally, we were unable to detect glycans in tg-FIX that have a terminal Galalpha(1,3)Gal disaccharide sequence, which is strongly antigenic in humans. The N-glycan structures of tg-FIX are also compared to the published N-glycan structures of recombinant human glycoproteins produced in other transgenic animal species. While tg-FIX contains only complex structures, antithrombin III (goat), C1 inhibitor (rabbit), and lactoferrin (cow) have both high mannose and complex structures. Collectively, these data represent a beginning point for the future investigation of species-specific and tissue/cell-specific differences in N-glycan structures among animals used for transgenic animal bioreactors.
Resuscitative hypothermia (1996)

Resuscitative (postinsult) hypothermia is less well studied than protective-preservative (pre- and intra-arrest) hypothermia. The latter is in wide clinical use, particularly for protecting the brain during cardiac surgery. Resuscitative hypothermia was explored in the 1950s and then lay dormant until the 1980s when it was revived. This change occurred through the discoveries of brain damage mitigating effects after cardiac arrest in dogs, and after forebrain ischemia in rats, of mild (34 degrees C) hypothermia (which is safe), and of benefits derived from moderate hypothermia (30 degrees C) after traumatic brain injury or focal brain ischemia in various species. The idea that protection-preservation or resuscitation by hypothermia is mainly explained by its ability to reduce cerebral oxygen demand has been replaced by an increasingly documented synergism of many beneficial mechanisms. Deleterious chemical cascades during and after these insults are suppressed even by mild hypothermia. Prolonged moderate hypothermia carries some risks, e.g., arrhythmias, infection and coagulopathies. These side effects need further study. In global brain ischemia, protective-preservative mild hypothermia provides lasting mitigation of brain damage. Resuscitative mild hypothermia, however, may be beneficial in terms of long-term outcome or may merely delay the inevitable loss of selectively vulnerable neurons. Even if the latter is true, mild hypothermia may extend the therapeutic window for other interventions. This extension of the therapeutic window requires further documentation. After normothermic cardiac arrest of 11 mins in dogs, mild resuscitative hypothermia from 15 mins to 12 hours after reperfusion plus cerebral blood flow promotion normalized functional recovery with the least histologic damage seen thus far. Optimal duration of, and rewarming methods from, resuscitative hypothermia need clarification. The earliest possible induction of mild hypothermia after cardiac arrest seems desirable. Head-neck surface cooling alone is too slow. Among many clinically feasible rapid cooling methods, carotid cold flush and peritoneal cooling look promising. After traumatic brain injury or focal brain ischemia, which seem to still benefit from even later cooling, surface cooling methods may be adequate. Resuscitative hypothermia after cardiac arrest, traumatic brain injury, or focal brain ischemia should be considered for clinical trials.
Utility of Dried Blood Spots for Measurement of Cholesterol and Triglycerides in a Surveillance Study (2010)

Blood samples dried on filter paper can be a successful option for population screening in remote areas, provided preanalytical variations arising due to the method of blood spot preparation and storage are well controlled.
Advances in Research on Zinc Finger Protein (2009)

Zinc finger protein is one of the most important transcription factors in eukaryotes,displaying variable secondary structures and enormous functional diversity with finger-like domain,playing a very important role in regulating the genes.It can be mainly divided into three types of zinc finger protein,including C2H2,C4 and C6 type based on their unique and highly conserved consensus amino acid sequences.Zinc fingers can bind to DNA,RNA,DNA-RNA hybrid and also can involved in protein-protein interactions,regulating the expression of the target genes in transcriptional and translational processes.We mainly described the advances research on the structure,classification of zinc finger protein and its interactions with nucleic acids and protein in recent years.
New building blocks for crystal engineering. Syntheses and crystal structures of oxime-substituted pyridines (2000)

The syntheses and crystal structures of a family of oxime-substituted pyridine ligands [py-C(R)NOH, where R = H, Me, Ph, or NH2] are presented. The compounds are all prepared in good yields by allowing a suitably substituted pyridine to react with hydroxylamine. Their solid-state structures show that the dominating hydrogen bond, a head-to-tail O–H⋯N interaction between the oxime O–H moiety and the pyridine nitrogen atom, is present in each of the seven reported cases. This intermolecular interaction generates infinite chains that are crosslinked into 2D or 3D assemblies by weaker C–H⋯N or C–H⋯O hydrogen bonds.
DIAGNOdent: An Optical Method for Caries Detection (2004)

The onset of caries is characterized by demineralization of dental hard tissues. Optimal fluoridation with respective oral hygiene habits and diet may stop the progression of a lesion and even allow for its remineralization. The aim of modern dentistry must be a preventive approach rather than invasive repair of the disease. This is possible only with early detection and respective preventive measures. Some of today's diagnostic tools are not sensitive enough to detect this early onset of destruction. Tools based on fluorescence could have the possibility to overcome this problem. This overview will focus on today's knowledge of one possible tool, the DIAGNOdent.
The Ig-Like V-Type Domain of Paired Ig-Like Type 2 Receptor Alpha Is Critical for Herpes Simplex Virus Type 1-Mediated Membrane Fusion (2010)

Paired immunoglobulin (Ig)-like type 2 receptor alpha (PILRalpha) and PILRbeta are paired receptors that are highly homologous to each other. When engaged by ligand, PILRalpha is inhibitory whereas PILRbeta is activating. PILRalpha is a newly identified herpes simplex virus type 1 (HSV-1) glycoprotein B (gB) receptor and is associated with membrane fusion and entry activity of HSV-1. PILRalpha is a 303-amino-acid protein with an Ig-like V (variable)-type domain from amino acid 31 to 150, whereas PILRbeta is a 217-amino-acid protein with an Ig-like V-type domain from amino acid 21 to 143. We report that PILRbeta is not a receptor for HSV-1 and HSV-2. Domain swaps between PILRalpha and PILRbeta reveal that the Ig-like V-type domain of PILRalpha, but not PILRbeta, plays a critical role in cell membrane fusion activity and the binding of PILRalpha to gB. Individual replacement of 13 amino acids in PILRalpha showed that most of these mutations had no effect on cell fusion activity. However, mutation of the tryptophan residue at amino acid 139 significantly impaired cell fusion activity for HSV-1 and eliminated binding to gB.
Investigations on 2,7-diamino-9-fluorenol photochemistry (2007)

Photoremovable protecting groups have been long known as useful synthetic tools. They are commonly linked to a substrate of interest to make them unable to react, forming in this manner a “caged compound”. Upon irradiation the protecting group undergoes a photochemical reaction that results in release of the substrate and restores its activity. The main goal of this work was that of identifying a system that would efficiently release alcohol, as this could be readily applied in biology. The idea was based on the photochemistry of 9fluorenol which is well established and known. 2,7-diamino-9-fluorenol was efficiently synthesized and LFP investigations were carried out to clarify the reaction mechanism in different solvents. Transients in the infrared area were observed in the solvents TFE and HFIP but their character remains unclear. We suspect their cationic character, and their formation either via singlet or a very fast triplet state. Our mechanistic studies provided rate constants of formation and decay of the transients in three different solvents (TFE, methanol and water). Two derivatives of 2,7-diamino-9-fluorenol (X = C6H5 and COCH3) were synthesized using a four-step synthetic route. The photorelease of these derivatives was elucidated by employing irradiation experiments and product analysis. The results indicate that 2,7diamino-9-fluorenyl acetate liberates acetic acid efficiently whereas the efficiency rate of release of 2,7-diamino-9-fluorenyl phenyl ether is low.
In vivo synthesis of complexN‐glycans by expression of humanN‐acetylglucosaminyltransferase I in the filamentous fungusTrichoderma reesei (1999)

The human N-acetylglucosaminyltransferase I gene was introduced in the genome of Trichoderma reesei strain VTT-D-80133. Expression was studied after induction from the cellobiohydrolase I promoter. Successful in vivo transfer of GlcNAc was demonstrated by analyzing the neutral N-glycans which were synthesized on cellobiohydrolase I. Final proof of the formation of GlcNAcMan5GlcNAc2 was obtained by NMR analysis.
Sequence specificity of psoralen photobinding to DNA: A quantitative approach (1992)

The effects of different DNA sequences on the photoreaction of various furocoumarin derivatives was investigated from a quantitative point of view using a number of self-complementary oligonucleotides. These contained 5'-TA and 5'-AT residues, having various flanking sequences. The furocoumarins included classical bifunctional derivatives, such as 8-methoxy- and 5-methoxypsoralen, as well as monofunctional compounds, such as angelicin and benzopsoralen. Taking into an account the thermodynamic constant for noncovalent binding of each psoralen to each DNA sequence, the rate constants for the photobinding process to each fragment were evaluated. The extent of photoreaction is greatly affected by the DNA sequence examined. While sequences of the type 5'-(GTAC)n are quite reactive towards all furocoumarins, 5'-TATA exhibited a reduced rate of photobinding using monofunctional psoralens. In addition terminal 5'-TA groups were the least reactive with 5- and 8-methoxypsoralen, but not with angelicin or benzopsoralen. Also 5'-AT-containing fragments exhibited remarkably variable responses toward monofunctional or bifunctional psoralen derivatives. As a general trend the photoreactivity rate of the former is less sequence-sensitive, the ratio between maximum and minimum being less than 2 for the examined fragments. The same ratio is about 3.4 for 8-methoxypsoralen and 6.2 for 5-methoxypsoralen. This approach, in combination with footprinting studies, appears to be quite useful for a quantitative investigation of the process of covalent binding of psoralens to specific sites in DNA.
Light-induced olefin metathesis (2010)

Light activation is a most desirable property for catalysis control. Among the many catalytic processes that may be activated by light, olefin metathesis stands out as both academically motivating and practically useful. Starting from early tungsten heterogeneous photoinitiated metathesis, up to modern ruthenium methods based on complex photoisomerisation or indirect photoactivation, this survey of the relevant literature summarises past and present developments in the use of light to expedite olefin ring-closing, ring-opening polymerisation and cross-metathesis reactions.
Employing web search query click logs for multi-domain spoken language understanding (2011)

Logs of user queries from a search engine (such as Bing or Google) together with the links clicked provide valuable implicit feedback to improve statistical spoken language understanding (SLU) models. In this work, we propose to enrich the existing classification feature set for domain detection with features computed using the click distribution over a set of clicked URLs from search query click logs (QCLs) of user utterances. Since the form of natural language utterances differs stylistically from that of keyword search queries, to be able to match natural language utterances with related search queries, we perform a syntax-based transformation of the original utterances, after filtering out domain-independent salient phrases. This approach results in significant improvements for domain detection, especially when detecting the domains of web-related user utterances.
Amplicon mapping and transcriptional analysis pinpoint cyclin L as a candidate oncogene in head and neck cancer. (2002)

DNA gains targeting the 3q chromosome are common in head and neck squamous cell carcinomas, as well as in lung, ovarian, and cervical cancer. Several candidate oncogenes located on 3q were proposed, i.e., PIK3CA, p63, and eIF-5A2. However, none of these genes was found included in a narrow high-level amplification. Recently, microarray-based comparative genomic hybridization (array CGH) was developed for high-resolution screening of deletions and amplifications in tumor genomes. In this study, by microarray-based comparative genomic hybridization, we found a narrow 3q25.3 high-level amplification in a head and neck cancer cell line. We precisely delimited the 3-Mb length-amplified segment by semiquantitative PCR and measured the transcriptional level of every gene (RefSeq full-length mRNA) located inside this segment by cDNA microarray and quantitative reverse transcription-PCR. Four genes were overexpressed in three head and neck cancer cell lines with increased DNA copy number, compared with a control tongue cell line. We extended the transcriptional analysis of these four genes to 20 head and neck squamous cell carcinomas. Only one gene, cyclin L (ania-6a), is commonly overexpressed in primary tumors compared with corresponding normal tissues. This cyclin was previously pinpointed as a candidate for a role in promoting cell cycle entry. Thus, we propose cyclin L as a candidate oncogene in head and neck cancer.
A review of DNA sequencing techniques (2002)

The four best known DNA sequencing techniques are reviewed. Important practical issues covered are read-length, speed, accuracy, throughput, cost, as well as the automation of sample handling and preparation. The methods reviewed are: (i) the Sanger method and its most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other chemical methods; (iii) the Pyrosequencing method--DNA sequencing in real time by the detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with exonuclease (exonuclease digestion of a single molecule composed of a single strand of fluorescently labelled deoxynucleotides). Each method is briefly described, the current literature is covered, advantages, disadvantages, and the most suitable applications of each method are discussed.
A guided evolutionary computation technique as function optimizer (2002)

In this paper, we present a regionally guided approach to function optimization. The proposed technique is called "Guided Evolutionary Simulated Annealing". It combines the simulated annealing and simulated evolution in a novel way. The technique has a mechanism that the search will focus on more "promising" areas. The solution is evolved under regional guidance. The characteristics of the proposed technique are given. We illustrate the technique with two examples. The results of both examples indicate that the GESA technique yields optimal or near-optimal solutions, superior to a version of simulated evolution and a version of parallel simulated annealing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis and dopamine receptor affinities of 2-(4-fluoro-3-hydroxyphenyl)ethylamine and N-substituted derivatives (1990)

The synthesis of 2-(4-fluoro-3-hydroxyphenyl)ethylamine (26) and of some N,N-dialkyl derivatives (27-30) starting from 4-fluoro-3-hydroxytoluene and their in vitro binding affinities for dopamine (DA) receptor are reported. The amine 26 can be regarded as a molecular modification of DA in which the para hydroxyl group is replaced by fluorine. The new compounds 26-30 were evaluated for their affinity at D-1 and D-2 DA receptor subtypes by displacement of [3H]SCH 23390 (D-1 selective) and [3H]spiperone (D-2 selective). The amine 26 had about 2-fold less affinity for D-1 and D-2 binding sites than DA. The substitution of the amino group with ethyl, n-propyl, and 2-phenylethyl groups decreased the affinity for D-1 binding sites but greatly enhanced the effectiveness on D-2 binding sites. The N-ethyl- (28) and N-n-propyl-N-(2-phenylethyl)-2-(4-fluoro-3- hydroxyphenyl)ethylamine (30) were the most potent members of the series with high selectivity for D-2 binding sites. A similar effect was observed with isomeric N-n-propyl-N-(2-phenylethyl)-2-(3-fluoro-4-hydroxyphenyl)ethylamine (31) which was approximately 65 times more selective for D-2 sites vs D-1 sites. The introduction of a 2-phenylethyl group on the nitrogen atom induce the highest effect, perhaps as a consequence of an increased liposolubility or of binding to a complementary lipophilic site on the receptor.
Patterned Photostimulation with Digital Micromirror Devices to Investigate Dendritic Integration Across Branch Points (2011)

Light is a versatile and precise means to control neuronal excitability. The recent introduction of light sensitive effectors such as channel-rhodopsin and caged neurotransmitters have led to interests in developing better means to control patterns of light in space and time that are useful for experimental neuroscience. One conventional strategy, employed in confocal and 2-photon microscopy, is to focus light to a diffraction limited spot and then scan that single spot sequentially over the region of interest. This approach becomes problematic if large areas have to be stimulated within a brief time window, a problem more applicable to photostimulation than for imaging. An alternate strategy is to project the complete spatial pattern on the target with the aid of a digital micromirror device (DMD). The DMD approach is appealing because the hardware components are relatively inexpensive and is supported by commercial interests. Because such a system is not available for upright microscopes, we will discuss the critical issues in the construction and operations of such a DMD system. Even though we will be primarily describing the construction of the system for UV photolysis, the modifications for building the much simpler visible light system for optogenetic experiments will also be provided. The UV photolysis system was used to carryout experiments to study a fundamental question in neuroscience, how are spatially distributed inputs integrated across distal dendritic branch points. The results suggest that integration can be non-linear across branch points and the supralinearity is largely mediated by NMDA receptors.
Attenuation of the Editing Activity of theEscherichia coliLeucyl-tRNA Synthetase Allows Incorporation of Novel Amino Acids into Proteins in Vivo (2002)

The fidelity of translation is dependent on the specificity of the aminoacyl-tRNA synthetases (aaRSs). The aaRSs that activate the hydrophobic amino acids leucine, isoleucine, and valine employ a proofreading mechanism that hydrolyzes noncognate aminoacyl adenylates and misaminoacylated tRNAs. Discrimination between structurally similar amino acids by these AARSs is believed to operate by a double-sieve principle, wherein a separate editing domain governs hydrolysis on the basis of the size and hydrophilicity of the amino acid side chain. Leucyl-tRNA synthetase (LeuRS) relies on its editing function to correct misaminoacylation of tRNA(Leu) by isoleucine and methionine. Thr252 of Escherichia coli LeuRS has been shown previously to be important in defining the size of the editing cavity. Here we report the isolation and characterization of three LeuRS mutants with point mutations at this position (T252Y, T252L, and T252F). The proofreading activity of the synthetase is significantly impaired when an amino acid bulkier than threonine is introduced. The rate of misaminoacylation of tRNA(Leu) by isoleucine and valine increases with the increasing size of the amino acid substituent at position 252, and the noncognate amino acids norvaline and norleucine are inserted efficiently at the leucine sites of recombinant proteins under conditions of constitutive overexpression of the T252Y mutant in E. coli. In addition, the unsaturated amino acids allylglycine, homoallylglycine, homopropargylglycine, and 2-butynylalanine all support protein synthesis in E. coli hosts harboring the mutant synthetase. These results demonstrate that programmed manipulation of the editing cavity can allow in vivo incorporation of novel protein building blocks.
Nitric oxide and cisplatin resistance: NO easy answers (2006)

Cisplatin is one of the most widely used chemotherapeutic drugs for treating cancer. Initially, platinum-based therapies are very effective in treating a wide array of cancers; however, recurrence and resistance remain the major limitation to curative therapies (1). Although cisplatin resistance is clearly multifactorial in nature, increased levels of cellular thiols are often associated with the cisplatin-resistant phenotype (2). Cellular thiols, which include glutathione (GSH), can sequester cisplatin, leading to a reduction in the levels of cisplatin–DNA damage. DNA is the therapeutic target of cisplatin, and efficacy is a function of cisplatin–DNA adducts inhibiting DNA replication and transcription, ultimately resulting in apoptosis. Reduced efficacy of the cisplatin is often observed in cells with increased GSH levels. Modulating the levels of intracellular thiols has been demonstrated to influence cisplatin cytotoxicity in numerous studies (3). In a report by Bratasz et al. (4) in a recent issue of PNAS, the authors exploited GSH overexpression using a nitric oxide (NO)-prodrug in a cisplatin-resistant ovarian cancer model to potentially counteract and target cisplatin-resistant cells.