gebhart/patrepeval huggingface dataset:
A study on the flexible camera calibration method using a grid type frame with different line widths (2003)

With 3D vision measuring, camera calibration is necessary to calculate parameters accurately. In this paper, we present an algorithm for camera calibration using perspective ratio of a grid type frame with different line widths. It can easily estimate camera calibration parameters such as the focal length, scale factor, pose, orientations, and distance, but the radial lens distortion is not modeled. The advantage of this algorithm is that it can estimate the distance of the object. To validate the proposed method, we set experiments with a frame on a rotator at a distance of 1.2 m from the camera and rotate the frame from 60 to 60 degrees. We investigated the distance error affected by the scale factor or different line widths and experimentally found an average scale factor that includes the least distance error with each image. The average scale factor tends to fluctuate with small variation and decreases the distance error. Compared with classical methods that use stereo camera of two or three orthogonal planes, the proposed method is easy to use and flexible.
Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers (2006)

Genomes are becoming heavily annotated with important features. Analysis of these features often employs oligonucleotides that hybridize at defined locations. When the defined location lies in a poor sequence context, traditional design strategies may fail. Locked Nucleic Acid (LNA) can enhance oligonucleotide affinity and specificity. Though LNA has been used in many applications, formal design rules are still being defined. To further this effort we have investigated the effect of LNA on the performance of sequencing and PCR primers in AT-rich regions, where short primers yield poor sequencing reads or PCR yields. LNA was used in three positional patterns: near the 5' end (LNA-5'), near the 3' end (LNA-3') and distributed throughout (LNA-Even). Quantitative measures of sequencing read length (Phred Q30 count) and real-time PCR signal (cycle threshold, C(T)) were characterized using two-way ANOVA. LNA-5' increased the average Phred Q30 score by 60% and it was never observed to decrease performance. LNA-5' generated cycle thresholds in quantitative PCR that were comparable to high-yielding conventional primers. In contrast, LNA-3' and LNA-Even did not improve read lengths or C(T). ANOVA demonstrated the statistical significance of these results and identified significant interaction between the positional design rule and primer sequence.
Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil (2000)

The population dynamics of Archaea after flooding of an Italian rice field soil were studied over 17 days. Anoxically incubated rice field soil slurries exhibited a typical sequence of reduction processes characterized by reduction of nitrate, Fe(3+), and sulfate prior to the initiation of methane production. Archaeal population dynamics were followed using a dual approach involving molecular sequence retrieval and fingerprinting of small-subunit (SSU) rRNA genes. We retrieved archaeal sequences from four clone libraries (30 each) constructed for different time points (days 0, 1, 8, and 17) after flooding of the soil. The clones could be assigned to known methanogens (i.e., Methanosarcinaceae, Methanosaetaceae, Methanomicrobiaceae, and Methanobacteriaceae) and to novel euryarchaeotal (rice clusters I, II, and III) and crenarchaeotal (rice clusters IV and VI) lineages previously detected in anoxic rice field soil and on rice roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983-4989, 1998). During the initiation of methanogenesis (days 0 to 17), we detected significant changes in the frequency of individual clones, especially of those affiliated with the Methanosaetaceae and Methanobacteriaceae. However, these findings could not be confirmed by terminal restriction fragment length polymorphism (T-RFLP) analysis of SSU rDNA amplicons. Most likely, the fluctuations in sequence composition of clone libraries resulted from cloning bias. Clonal SSU rRNA gene sequences were used to define operational taxonomic units (OTUs) for T-RFLP analysis, which were distinguished by group-specific TaqI restriction sites. Sequence analysis showed a high degree of conservation of TaqI restriction sites within the different archaeal lineages present in Italian rice field soil. Direct T-RFLP analysis of archaeal populations in rice field soil slurries revealed the presence of all archaeal lineages detected by cloning with a predominance of terminal restriction fragments characteristic of rice cluster I (389 bp), Methanosaetaceae (280 bp), and Methanosarcinaceae/rice cluster VI (182 bp). In general, the relative gene frequency of most detected OTUs remained rather constant over time during the first 17 days after flooding of the soil. Most minor OTUs (e.g., Methanomicrobiaceae and rice cluster III) and Methanosaetaceae did not change in relative frequency. Rice cluster I (37 to 30%) and to a lesser extent rice cluster IV as well as Methanobacteriaceae decreased over time. Only the relative abundance of Methanosarcinaceae (182 bp) increased, roughly doubling from 15 to 29% of total archaeal gene frequency within the first 11 days, which was positively correlated to the dynamics of acetate and formate concentrations. Our results indicate that a functionally dynamic ecosystem, a rice field soil after flooding, was linked to a relatively stable archaeal community structure.
Biology and Management of Dollar Spot (Sclerotinia homoeocarpa); an Important Disease of Turfgrass (1999)

Turfgrasses have been utilized by humans for >10 centuries to enhance their environment, but the modern turfgrass industry developed primarily during the past three decades, largely in response to increased population growth and urbanization. Turfgrass culture represents an important economic component of horticulture in North America with annual expenditures of $25 to $45 billion in the United States between 1982 and 1993 (Beard and Green, 1994; Gibeault and Cockerham, 1985). In return, turfgrass provides numerous benefits, including functional (e.g., reduction of soil erosion, pollution, and noise), recreational (e.g., provision of recreational surfaces for improved health and safety), and aesthetic benefits (e.g., improved aesthetic value and community pride) (Beard and Green, 1994; Gordon et al., 1996). Because of these economic and environmental benefits, turfgrass and turfgrass health have become increasingly important. Dollar spot (Sclerotinia homoeocarpa F.T. Bennett) is one of the most important diseases that affect turfgrass; it can cause considerable damage, particularly to highly maintained golf course putting greens, closely mown fairways, and bowling greens (Goodman and Burpee, 1991). This disease can also damage less intensively managed turfgrass grown on home lawns, recreational and athletic facilities, and educational or industrial properties. Dollar spot reduces the aesthetic and playing quality of infected turf, and can contribute to weed encroachment and plant death (Fig. 1) (Smith et al., 1989). Dollar spot is a widespread disease that affects many turfgrass species throughout North America, Central America, Australia, New Zealand, Japan, the British Isles, and continental Europe (Couch, 1995; Fenstermacher, 1980; Vargas, 1994). Except for western Canada and the Pacific northwest region of the United States, dollar spot is the most common disease of turf in North America (Couch, 1995). The persistent nature of this disease in turfgrass swards often requires intensive control measures. As a result, more money is spent to manage dollar spot than to control any other turfgrass disease on golf courses (Goodman and Burpee, 1991).
The Canine Factor VIII 3′-Untranslated Region and a Concatemeric Hepatocyte Nuclear Factor 1 Regulatory Element Enhance Factor VIII Transgene Expression In Vivo (2002)

If gene therapy is to be an effective treatment modality for hemophilia A, therapeutic levels and tissue-restricted expression of factor VIII (FVIII) must be achieved through optimization of transgene expression. To this end, we incorporated three types of sequence elements into a canine B domain-deleted FVIII transgene cassette and individually evaluated their effect on FVIII transgene expression. Functional FVIII activity was initially assessed in vitro and hydrodynamic injection of the different transgene constructs into mice was subsequently used as a model to compare in vivo expression of the various modified transgenes. Our results demonstrate that in vitro transgene expression is, in these studies, not a good predictor of in vivo transgene performance. In vivo analysis of a hybrid tissue-restricted promoter element, consisting of a concatemer of five hepatocyte nuclear factor 1 (HNF-1) consensus-binding motifs juxtaposed to the human FVIII proximal promoter, indicates that it is as efficient at mediating expression of the FVIII protein as the cytomegalovirus promoter. Addition of the full-length canine FVIII 3'-UTR also enhances transgene expression of FVIII in vivo. Sequence analysis of the canine FVIII 3'-UTR and human FVIII 3'-UTR indicates that the former lacks instability sequences and may therefore be more effective in stabilizing FVIII mRNA. Subsequent inclusion of FVIII introns 16 and 17 into the natural locations of the transgene disrupted mRNA processing and abolished expression of the FVIII protein. Introduction of intron 17 proximal to the FVIII cDNA did not enhance in vivo expression of canine FVIII from the transgene.
Technical challenges of working with extracellular vesicles (2017)

Extracellular Vesicles (EVs) are gaining interest as central players in liquid biopsies, with potential applications in diagnosis, prognosis and therapeutic guidance in most pathological conditions. These nanosized particles transmit signals determined by their protein, lipid, nucleic acid and sugar content, and the unique molecular pattern of EVs dictates the type of signal to be transmitted to recipient cells. However, their small sizes and the limited quantities that can usually be obtained from patient-derived samples pose a number of challenges to their isolation, study and characterization. These challenges and some possible options to overcome them are discussed in this review.
The role of type II transmembrane serine protease‐mediated signaling in cancer (2016)

Pericellular proteases have long been implicated in carcinogenesis. Previous research focused on these proteins, primarily as extracellular matrix (ECM) protein-degrading enzymes which allowed cancer cells to breach the basement membrane and invade surrounding tissue. However, recently, there has been a shift in the view of cell surface proteases, including serine proteases, as proteolytic modifiers of particular targets, including growth factors and protease-activated receptors, which are critical for the activation of oncogenic signaling pathways. Of the 176 human serine proteases currently identified, a subset of 17, known as type II transmembrane serine proteases (TTSPs). Many have been shown to be relevant to cancer progression since they were first identified as a family around the turn of the century. To this end, altered expression of TTSPs appeared as a trademark of several tumor types. However, the substrates and underlying signaling pathways remained unclear. Localization of these proteins to the cell surface places them in the unique position to mediate signal transduction between the cell and its surrounding environment. Many of the TTSPs have already been shown to play key roles in processes such as postnatal development, tissue homeostasis, and tumor progression, which share overlapping molecular mechanisms. In this review, we summarize the current knowledge regarding the role of the TTSP family in pro-oncogenic signaling.
Bending Strength and Holding Power of Tibial Locking Screws (2001)

The bending strength and holding power of two types of specially designed tibial locking devices, a both-ends-threaded screw and an unthreaded bolt, were studied and compared with four types of commercially available tibial interlocking screws: Synthes, Howmedica, Richards, and Osteo AG. To test bending strength, the devices were inserted into a high molecular weight polyethylene tube and loaded at their midpoint by a materials testing machine to simulate a three point bending test. Single loading yielding strength and cyclic loading fatigue life were measured. To test holding power, the devices were inserted into tubes made of polyurethane foam, and their tips were loaded axially to measure pushout strength. The devices were tested with two different densities of foam materials and two different sizes of pilot holes. Insertion torque and stripping torque of the screws were measured first. Pushout tests were performed with each screw inserted with a tightness equal to 60% of its stripping torque. Test results showed that the yielding strength and the fatigue life were related closely to the inner diameter of the screws. The stripping torque predicted the pushout strength more reliably than did the insertion torque. All tested devices showed greater holding power in the foam with the higher density and with the smaller pilot holes. The both-ends-threaded screw had the highest pushout strength and a satisfactory fatigue strength. The unthreaded bolt had the highest fatigue strength but only fair holding power. Clinical studies of the use of these two types of locking devices are worthwhile.
Pyrrolopyrimidines. Part 5. Reaction of 6‐Amino‐1,3‐dimethylpyrrolo[3,4‐d]pyrimidine‐2,4(1H,3H)‐diones with 1,3‐Diketones. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Blepharospasm and orofacial‐cervical dystonia: Clinical and pharmacological findings in 100 patients (1983)

We evaluated prospectively 100 patients, the largest reported series, with blepharospasm and orofacial-cervical dystonia, or Meige syndrome. The mean age at onset was 51.7 years, and 81% presented between the ages of 40 and 70. Women outnumbered men three to two. Blepharospasm was the initial symptom in 58 patients, but only 23 had involuntary movements localized to the orbicularis oculi. Sixty-one patients had the complete syndrome, blepharospasm and oromandibular dystonia, and 60 had neck or generalized dystonia in addition to the orofacial movements. Twenty-one patients with spasmodic dysphonia were included; in 12 of these patients, spasmodic dysphonia was part of the complete (Meige) syndrome, and 16 of these patients had neck or generalized dystonia or essential tremor. An organic cause of Meige syndrome is supported by a high correlation with essential tremor and other movement disorders and by positive family history in some patients. Response to medication was inconsistent, but 69% of patient trials resulted in some improvement; in 22% the benefit was marked and persistent. Tetrabenazine, lithium, and trihexyphenidyl were most useful for the treatment of oromandibular dystonia, and clonazepam was useful in some patients with blepharospasm.
The value of signs and symptoms in differentiating between bacterial, viral and mixed aetiology in patients with community-acquired pneumonia (2013)

Current diagnostics for community-acquired pneumonia (CAP) include testing for a wide range of pathogens, which is costly and not always informative. We compared clinical and laboratory parameters of patients with CAP caused by different groups of pathogens to evaluate the potential for targeted diagnostics and directed treatment. In a prospective study, conducted between April 2008 and April 2009, adult patients with CAP were tested for the presence of a broad range of possible respiratory pathogens using bacterial cultures, PCR, urinary antigen testing and serology. Of 408 patients with CAP, pathogens were detected in 263 patients (64.5%). Streptococcus pneumoniae and influenza A virus were the most frequently identified bacterial and viral pathogens, respectively. Age had a significant effect on the prediction of aetiology (P = 0.054), with an increase in the relative contribution of viruses with advancing age. Multivariate analyses further showed that the presence of cough increased the likelihood of detecting a viral pathogen [odds ratio (OR) 5.536, 95% confidence interval (CI) 2.130-14.390], the presence of immunodeficiency decreased the likelihood of detecting a bacterial pathogen (OR 0.595, 95 % CI 0.246-1.437) and an increase in pneumonia severity index score increased the likelihood of detecting a pathogen in general. Although several variables were independently associated with the detection of a pathogen group, substantial overlap meant there were no reliable clinical predictors to distinguish aetiologies. Therefore, testing for common respiratory pathogens is still necessary to optimize treatment.
Agrobacterium rhizogenes-mediated transformation of opium poppy, Papaver somniferum L., and California poppy, Eschscholzia californica Cham., root cultures (2000)

An efficient protocol for the establishment of transgenic opium poppy (Papaver somniferum L.) and California poppy (Eschscholzia californica Cham.) root cultures using A. grobacterium rhizogenes is reported. Five strains of A. rhizogenes were tested for their ability to produce hairy roots on wounded opium poppy seedlings and California poppy embryogenic calli. Three of the strains induced hairy root formation on both species, whereas two others either caused the growth of tumorigenic calli or produced no response. To characterize the putative transgenic roots further, explant tissues were co-cultivated with the most effective A: rhizogenes strain (R1000) carrying the pBI121 binary vector. Except for the co-cultivation medium, all formulations included 50 mg l(-1) paromomycin to select for transformants and 200 mg l(-1) timentin to eliminate the Agrobacterium. Four weeks after infection, paromomycin-resistant roots appeared on 92-98% of explants maintained on hormone-free medium. Isolated hairy roots were propagated in liquid medium containing 1.0 mg l(-1) indole-3-acetic acid to promote rapid growth. Detection of the neomycin phosphotransferase gene, high levels of beta-glucuronidase (GUS) transcripts and enzyme activity, and GUS histochemical localization confirmed the integrative transformation of root cultures. Transgenic roots grew faster than wild-type roots, and California poppy roots grew more rapidly than those of opium poppy. With the exception of a less compact arrangement of epidermal cells and more root hairs, transformed roots of both species displayed anatomical features and benzylisoquinoline alkaloid profiles that were virtually identical to those of wild-type roots. Transgenic root cultures of opium poppy and California poppy are a simple, reliable and well-defined model system to investigate the molecular and metabolic regulation of benzylisoquinoline alkaloid biosynthesis, and to evaluate the genetic engineering potential of these important medicinal plants.
Internuclear cyclisation. Part IX. Abnormal reactions of 2-amino-N-methylbenzanilides containing ortho-substituents (1954)

D. H. Hey and D. G. Turpin, J. Chem. Soc., 1954, 2471 DOI: 10.1039/JR9540002471
The Scope of Monetary Policy Actions Authorized under the Federal Reserve Act (2004)

The Federal Reserve Act authorizes the Federal Reserve to undertake various types of discount window loans and open market operations. While the Federal Reserve generally has not found it necessary to use all types of such authority, there could be circumstances in which the Federal Reserve might need to consider utilizing its statutory authority more broadly than it has in the past. We examine the limits imposed by the Federal Reserve Act along two dimensions: those types of counterparties and financial instruments with which the Federal Reserve may conduct monetary policy. In doing so, we develop a theme not commonly pursued in the literature--the ways and extent to which the Federal Reserve Act limits the Federal Reserve from taking credit risk onto its balance sheet. We also provide some historical perspective on how the current powers of the Federal Reserve came to be authorized.
Theiler's virus infection of 129Sv mice that lack the interferon alpha/beta or interferon gamma receptors. (1995)

The Daniels strain of Theiler's virus causes a persistent infection of the white matter of spinal cord of susceptible mice, with chronic inflammation and primary demyelination. Inbred 129Sv mice are resistant to this infection; they present with mild encephalomyelitis and clear the infection within a matter of days. A very different outcome was observed with inbred 129Sv mice whose receptors for interferon alpha/beta or interferon gamma had been inactivated by homologous recombination. The former presented severe encephalomyelitis with acute infection of neurons, particularly in brain and hippocampus, and extensive infection with necrosis of the choroid plexus. Most animals died of this acute disease. The latter, presented the same early encephalomyelitis as the control 129Sv mice. However, they remained persistently infected and developed a very severe late infection of the white matter with extensive primary demyelination. This late disease looked like an exacerbated form of the chronic demyelinating disease observed in susceptible inbred mice such as the SJL/J or FVB strains. Our results show that the two interferon systems play nonredundant roles in the resistance of the 129Sv mouse to the infection by Theiler's virus. They also lend support to the notion that the Ifg gene is involved in the resistance/susceptibility of inbred strains of mice to persistent infection by this picornavirus.
The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. (1993)

G/T mispairs that arise in the DNA of higher eukaryotes as a result of spontaneous hydrolytic deamination of 5-methylcytosine to thymine must be corrected to G/C pairs. We describe here the purification to apparent homogeneity of the enzyme that initiates this repair process by excising the mispaired thymine from the hetero-duplex to generate an apyrimidinic site. The enzymatic activity could be attributed to a 55-kDa polypeptide, which was purified from extracts of HeLa cells by a combination of conventional and DNA-affinity chromatography. The enzyme is a mismatch-specific thymine-DNA N-glycosylase, capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, the enzyme can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable endonucleolytic activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA.