gebhart/patrepeval huggingface dataset:
High throughput T‐DNA insertion mutagenesis in rice: a first step towards <i>in silico</i> reverse genetics (2004)

A library of 29,482 T-DNA enhancer trap lines has been generated in rice cv. Nipponbare. The regions flanking the T-DNA left border from the first 12,707 primary transformants were systematically isolated by adapter anchor PCR and sequenced. A survey of the 7480 genomic sequences larger than 30 bp (average length 250 bp), representing 56.4% of the total readable sequences and matching the rice bacterial artificial chromosome/phage artificial chromosome (BAC/PAC) sequences assembled in pseudomolecules allowed the assigning of 6645 (88.8%) T-DNA insertion sites to at least one position in the rice genome of cv. Nipponbare. T-DNA insertions appear to be rather randomly distributed over the 12 rice chromosomes, with a slightly higher insertion frequency in chromosomes 1, 2, 3 and 6. The distribution of 723 independent T-DNA insertions along the chromosome 1 pseudomolecule did not differ significantly from that of the predicted coding sequences in exhibiting a lower insertion density around the centromere region and a higher density in the subtelomeric regions where the gene density is higher. Further establishment of density graphs of T-DNA inserts along the recently released 12 rice pseudomolecules confirmed this non-uniform chromosome distribution. T-DNA appeared less prone to hot spots and cold spots of integration when compared with those revealed by a concurrent assignment of the Tos17 retrotransposon flanking sequences deposited in the National Center for Biotechnology Information (NCBI). T-DNA inserts rarely integrated into repetitive sequences. Based on the predicted gene annotation of chromosome 1, preferential insertion within the first 250 bp from the putative ATG start codon has been observed. Using 4 kb of sequences surrounding the insertion points, 62% of the sequences showed significant similarity to gene encoding known proteins (E-value < 1.00 e(-05)). To illustrate the in silico reverse genetic approach, identification of 83 T-DNA insertions within genes coding for transcription factors (TF) is presented. Based both on the estimated number of members of several large TF gene families (e.g. Myb, WRKY, HD-ZIP, Zinc-finger) and on the frequency of insertions in chromosome 1 predicted genes, we could extrapolate that 7-10% of the rice gene complement is already tagged by T-DNA insertion in the 6116 independent transformant population. This large resource is of high significance while assisting studies unravelling gene function in rice and cereals, notably through in silico reverse genetics.
Compact magnets for magnetic resonance (2009)

Abstract This article provides an introduction to magnetic material properties and an overview of compact permanent magnet designs. The descriptions are focused on portable magnetic resonance instruments, including in‐magnet and open configurations. A few examples are presented for spectroscopy as well as for space‐resolved and relaxation measurements. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 48–59, 2009.
Protection and Deprotection of Fused 2-Amino-4(3H)-pyrimidinones: Conversion of Pterins and 5-Deazapterins to 2,4-Diamino Derivatives (1993)

5-Deazapterins and pterins are readily converted to their 4-deoxy-4-amino derivatives (a lactam-to-amidine conversion) by reaction with 4-chlorophenyl phosphorodichloridate and 1.2.4triazole to give intermediate 4-11'-(1.2.4-triazolyl)] derivatives.followed by reaction with aqueous ammonia.Some anomalous results obtained by application of the Mitsunobu reaction (normally a lactam-to-lactim ether conversion) to 5-deazapterins are detailed.
Cleavage of Rabbit Myelin Basic Protein by Thrombin (1984)

Rabbit myelin basic protein (BP) contains several Arg-X bonds with differing susceptibilities to thrombic cleavage as measured by the yields of the various cleavage products obtained under three different conditions. Under conditions where the thrombin-to-substrate ratio was very low (1 NIH unit/mg BP), the concentration of substrate was relatively low (4 mg BP/ml), and the incubation time was short (2 h), the rabbit BP was cleaved essentially completely and specifically at a single site, the Arg(95)-Thr(96) bond. The BPs of other species (beef, pig, guinea pig, rat) were similarly cleaved, no doubt because all have the same amino acid sequence in this region of the protein. Under conditions in which the enzyme-to-substrate ratio and the substrate concentration were higher (2 NIH units/mg BP, 8 mg BP/ml) and the incubation time was long (24 h), additional, partial cleavages occurred, principally at the Arg(43)-Phe(44) and Arg(128)-Ala(129) bonds, but with some cleavage at the Arg(31)-His(32) and Arg(63)-Thr(64) bonds as well. Under conditions in which all three variables were elevated (5 NIH units/mg peptide, 20 mg peptide/ml, 24 h), more extensive cleavage occurred at the above sites. In peptide (96-168), which we examined in detail, nearly complete cleavage of the Arg(128)-Ala(129) bond occurred, with partial cleavage at the unmethylated Arg(105)-Gly(106), Arg(111)-Phe(112), Arg(150)-Leu(151), and Arg(160)-Ser(161) bonds. The susceptibilities to cleavage of the Arg-X bonds in the BP can be explained with varying degrees of success in terms of the known specificity of thrombin. Cleavage of two of the bonds, Arg(128)-Ala(129) and Arg(160)-Ser(161), suggests the occurrence of a chain reversal or beta-turn in the sequence preceding the scissile bonds. Most cleavages of the BP with thrombin do not occur in the more hydrophobic regions; in particular, the hydrophobic region in the center of the molecule that includes the Phe-Phe(87-88) sequence is left intact.
Targeting Intron Insertion Into DNA (2000)

In work reported on page 452, researchers have found a way to coax certain introns, bits of genetic debris that litter the DNA and interrupt the coding sequences of many genes, to hop into the exact sequences where the researchers want them. The method could enhance all sorts of genetic manipulations, from studying basic gene function to combating viral infections to delivering genes for gene therapy.
Computer Vision System as a Tool to Estimate Pork Marbling (2017)

Currently pork marbling is assessed subjectively in the industry, because of the limited methods and tools that are suitable for the industry. In this dissertation, we are devoted to develop a computer vision system for objective measurement of pork which suits the industrial needs. Experiment 1 examined the possibility of using computer vision system (CVS) to predict marbling in a lab-based experiment using pork samples that were already trimmed of subcutaneous fat and connective tissue. Experiment 2 an industrial scale CVS was built to predict the 3rd and 10th rib pork chop?s marbling. Experiment 3 the industrial scale CVS was tested in the meat plant and images of whole boneless pork loin were collected. The CVS predicted marbling were compared with subjective marbling score using crude fat percentage (CF%) as standard. In experiment 1 subjective marbling score had a correlation of 0.81 with CF% while CVS had a 0.66 correlation. CVS has shown an accuracy of 63% for stepwise regression model and 75% for support vector machine model. These results indicate that CVS has the potential to be used as an tool to predict pork intramuscular fat (IMF)%. In experiment 2 the accuracy of CVS predicting pork chop CF% was 68.6% and subjective marbling was 70.1%. A drop of accuracy in predicting anterior chop CF% for both CVS and objective marbling score was observed when compared to posterior chop, this suggest that there is a discrepancy in accuracy between the anatomy location of samples collected. In experiment 3 the accuracy of CVS predicting boneless whole loin was 58.6% and subjective marbling score was 53.3%. In this research, CVS has demonstrated a consistency of accuracies using different pork samples. CVS has shown higher accuracy when predicting whole boneless loin IMF% when compared to subjective assessment.
Overview of non-intrusive load monitoring and identification techniques (2015)

Load monitoring and identification is a method of determining electrical energy consumption and operation condition of individual appliances based on the analysis of composite load measured from the main power meter in a building. They can supply information such as type of load, electricity consumption detail and the running conditions of the appliances to both the consumer and the utility. The information can be used to formulate load plan strategies for optimal energy utilization. Load monitoring techniques can generally be grouped into intrusive and non-intrusive load monitoring. Intrusive load monitoring provides accurate results and would allow each individual appliance's energy consumption to be communicated to a central hub. However, this method is costly because of the number of equipment to be manufactured and installed. This has prompted the introduction of non-intrusive load monitoring system. Non-intrusive load monitoring is cost effective and convenient means of load monitoring since it requires lower equipment due to fewer components to install and smaller space requirements. This paper is concerned with the overview of different load identification and monitoring techniques for energy management focusing on non-intrusive load monitoring.
A PC-based pulse-width modulator for static converters (1990)

Developments in power control techniques for pulse-width-modulated inverters are often ignored because of lack of time for adequate testing and evaluation. A programmable PC-based pulse-width modulator that is designed to alleviate this problem is described. The modulator is capable of generating, in ready-to-use form, gating signals for most types of carrier or programmable pulse-width modulation (PWM) scheme under open-loop operating conditions and for most types of converter. It can also generate and display associated converter-output voltage and current waveforms and their respective frequency spectra for further evaluation of selected PWM schemes. Therefore, tasks such as the selection of PWM strategy, switching frequencies, and voltage/frequency curves (for variable-speed AC drives under open-loop control) are easier to perform. Moreover, the proposed research and development tool differs from similar devices in that it is user friendly, multipurpose, and versatile. Selected performance features of the developed prototype are demonstrated by presenting the associated experimental waveforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Upregulation of AMPK during cold exposure occurs via distinct mechanisms in brown and white adipose tissue of the mouse (2007)

AMPK (adenosine monophosphate-activated protein kinase), a key regulator of cellular energy metabolism and whole-body energy balance, is present in brown adipose tissue but its role in regulating the acute metabolic state and chronic thermogenic potential of this metabolically unique tissue is unknown. To address this, the AMPK signalling system in brown and white adipose tissue was studied in C57Bl/6 mice under control conditions, during acute and chronic cold exposure, and during chronic adrenergic stimulation. In control mice AMPK activity in brown adipose tissue was higher than in any tissue yet reported (3-fold the level in liver) secondary to a high level of expression of the alpha1 isoform. During the first day of cold, a time of intense non-shivering thermogenesis, AMPK activity remained at basal levels. However, chronic (>7 days) cold caused a progressive increase in brown adipose tissue AMPK activity secondary to increased expression of the alpha1 isoform. To investigate the signalling pathway involved, noradrenaline (norepinephrine) and the beta(3)-adrenergic-specific agonist CL 316, 243 were given for 14 days. This increased uncoupling protein-1 content in brown adipose tissue, but not AMPK activity. In white adipose tissue 15 days of cold increased alpha1 AMPK activity 98 +/- 20%, an effect reproduced by chronic noradrenaline or CL 316 243. We conclude that chronic cold not only increases AMPK activity in brown and white adipose tissue, but that it does so via distinct signalling pathways. Our data are consistent with AMPK acting primarily as a regulator of chronic thermogenic potential in brown adipose tissue, and not in the acute activation of non-shivering thermogenesis.
Adaptive color demosaicing and false color removal (2010)

Color interpolation solutions drastically influence the quality of the whole image generation pipeline, so they must guarantee the rendering of high quality pictures by avoiding typical artifacts such as blurring, zipper effects, and false colors. Moreover, demosaicing should avoid emphasizing typical artifacts of real sensors data, such as noise and green imbalance effect, which would be further accentuated by the subsequent steps of the processing pipeline. We propose a new adaptive algorithm that decides the interpolation technique to apply to each pixel, according to its neighborhood analysis. Edges are effectively interpolated through a directional filtering approach that interpolates the missing colors, selecting the suitable filter depending on edge orientation. Regions close to edges are interpolated through a simpler demosaicing approach. Thus flat regions are identified and low-pass filtered to eliminate some residual noise and to minimize the annoying green imbalance effect. Finally, an effective false color removal algorithm is used as a postprocessing step to eliminate residual color errors. The experimental results show how sharp edges are preserved, whereas undesired zipper effects are reduced, improving the edge resolution itself and obtaining superior image quality.
The Potential Therapeutic Applications of Olfactory Ensheathing Cells in Regenerative Medicine (2014)

Olfactory ensheathing cells (OECs) are unique glia cells restricted to the primary olfactory system including the olfactory mucosa, olfactory nerve, and the outer nerve layer of the olfactory bulb. OECs guide growing olfactory axons from the neurons of the nasal cavity olfactory mucosa to the olfactory bulb to connect both the peripheral nervous system (PNS) and central nervous system (CNS). Based on these specialized abilities of OECs, transplantation of OECs to injury sites has been widely investigated for their potential therapeutic applications in neural repair in different injuries. In this article, we reviewed the properties of OECs and their roles in olfactory regeneration and in treatment of different injuries including spinal cord injury, PNS injury, and stroke and neurodegenerative diseases.
2‐Ene‐1,4‐diols by Dimerization of Terminal Epoxides Using Hindered Lithium Amides. (2005)

Reaction of hindered lithium amides with readily available (enantiopure) terminal epoxides gives 2-ene-1,4-diols via carbenoid dimerization of\nthe corresponding α-lithiated epoxides. d-Mannitol and d-iditol were synthesized using this method in three steps from (<i>S</i>)-tritylglycidyl ether.
NMR Microscopy—Fundamentals, Limits and Possible Applications (1990)

Abstract Alongside the numerous applications of NMR spectroscopy to structural elucidation in analytical chemistry, and to biochemical and morphological studies by NMR tomography, NMR microscopy makes possible a whole new range of applications. These include imaging, the investigation of biological objects such as plants and small animals, and also the observation of microscopic structures and structural changes in polymers and ceramics. NMR spectroscopy can also be conducted combinationally as volume‐selective spectroscopy, whereby it is possible to spatially resolve the NMR‐specific parameters: spin density ϱ, chemical shifts δ, and the relaxation times T 1 and T 2 . The numerous well developed methods available make it possible to study dynamic processes by fast imaging with a temporal resolution in milliseconds. This not only allows the imaging of moving objects without incurring movement artefacts but also the measurement of diffusion constants in isotropic and anisotropic diffusion—in the latter case allowing, in principle, the determination of the complete diffusion tensor. The spatially resolved measurement of the relaxation times yields information on molecular mobility and bonding, e. g. the bonding of water, or other solvents, to polymers, the mobility of fluids in polymers or ceramics, or the three‐dimensional evaluation of pore size in porous materials. In biomedicine, NMR microscopy allows the observation of growth on the cellular level, the study of embryos, and the development of therapeutic methods in animal experiments. It can lead to a drastic reduction in the number of animal experiments, and in combination with volume‐selective spectroscopy gives valuable information on in‐vivo metabolism.
A new rip-up and reroute algorithm for very large scale gate arrays (2002)

A fast rip-up and reroute algorithm for large scale gate arrays is reported. The algorithm combines 'global' and 'local' rip-up and reroute processes to efficiently eliminate the unconnects introduced by an initial routing process. The global process reduces the local wire congestion by ripping up and rerouting global paths. The local process eliminates the unconnects, mainly caused by routing order dependency, by ripping up and rerouting local paths. The effectiveness of our method is demonstrated by our experimental results on industrial sea-of-gates (SOG) circuits and a well-known benchmark circuit.
[Three dimensional bioprinting technology of human dental pulp cells mixtures]. (2013)

In this study, the 3D bioprinting of hDPCs mixtures was realized, thus laying initial foundations for the application of the 3D bioprinting technology in tooth regeneration.
A novel Bcl-2 related gene, Bfl-1, is overexpressed in stomach cancer and preferentially expressed in bone marrow. (1995)

Programmed cell death (apoptosis) is an active process which is genetically encoded and plays an important role in several cellular activities such as embryonic development, deletion of autoreactive T-cells and homeostasis. Several genes regulating apoptosis have been reported, including p53, one of the tumor suppressor genes, c-myc, one of the proto-oncogenes, and various kinds of Bcl-2 related genes. A new cDNA clone which is homologous to Bcl-2, named as Bfl-1 were isolated from a human fetal liver at 22 week of gestation. This clone was identified by computer analysis of random cDNA sequences that were obtained in an effort to expand the expressed sequence tag (EST) databases to be used for human genome analysis. The homology was recognized by 72% amino acid identity to the murine A1 gene, a member of the Bcl-2-related genes. The homology to the BH1 and BH2 domains of Bcl-2 was especially significant, suggesting that Bfl-1 is a new member of the Bcl-2-related genes. Bfl-1 is abundantly expressed in the bone marrow and at a low level in some other tissues. Interestingly, a correlation was noted between the expression level of Bfl-1 gene and the development of stomach cancer in eight sets of clinical samples. It is conceivable that Bfl-1 is involved in the promotion of the cell survival in the stomach cancer development or progression.
Correlation Between Intact Sperm Acrosome Assessed Using the Spermac Stain and Sperm Fertilizing Capacity (1996)

Accurate determination of sperm acrosomal status is important in fertility studies. The objective was to correlate the percentage of intact acrosome assessed using the new Spermac stain with the capacity of sperm to fertilize oocytes. Sperm specimens were processed either by centrifuge wash, 48:95 Percoll gradient or test yolk buffer (TYB) wash, and tested using the zona-free hamster oocyte assay. The results indicated a correlation between the percentage of sperm with intact acrosome reaction and the percentage of sperm penetrating the oocytes in the TYB-washed group. The data suggest the usefulness of the Spermac stain for assessing the acrosomal status and in predicting the fertilizing capacity of the sperm.
Silicon Photo-Diode Using Surface-Plasmon Resonance (2007)

The concept of nano-photodiode, employing surface-plasmon antenna to create sub-wavelength size nearfield, is described in relation to silicon photonics. Response time of the prototype silicon nano-photodiode was much shorter (-20 ps) than that of conventional silicon photodiodes (>1 ns). There are two reasons for the high-speed response: short distance between electrodes (-100 nm) and small electrode area (< 1 μm2). The former is realized by lapping near-field region over depletion region (Schottky barrier) in silicon thereby eliminating time-consuming carrier diffusion process. The latter results in small electrode capacitance and thus reducing response time of the photodiode circuit. This nano-photodiode technology can be applied to other semiconductor materials such as germanium and ternary compound semiconductors.
Site-survey-free wireless localization using mobile phones (2012)

Indoor localization is of great importance for a range of pervasive applications, attracting many research efforts in the past two decades. Most radio-based solutions require a process of site survey, in which radio signatures are collected and stored for further comparison and matching. Site survey involves intensive costs on manpower and time. In this work, we study unexploited RF signal characteristics and leverage user motions to construct radio floor plan that is previously obtained by site survey. On this basis, we design WILL, an indoor localization approach based on off-the-shelf WiFi infrastructure and mobile phones. WILL is deployed in a real building covering over 1600m, and its deployment is easy and rapid since site survey is no longer needed. The experiment results show that WILL achieves competitive performance comparing with traditional approaches.
Fragmented QRS as a Marker of Electrical Dyssynchrony to Predict Inter-Ventricular Conduction Defect by Subsequent Echocardiographic Assessment in Symptomatic Patients of Non-Ischemic Dilated Cardiomyopathy (2016)

Fragmentation of QRS complex is an important predictor of electro-mechanical dyssynchrony. It is also helpful in localizing the dyssynchronous segment. In future, larger studies may be carried out to investigate the role of fQRS as a predictor of response to cardiac resynchronization therapy (CRT) in this subgroup of HF patients with narrow QRS.
Locating and tracking facial speech features (1996)

This paper describes a robust method for extracting visual speech information from the shape of lips to be used for an automatic speechreading (lipreading) systems. Lip deformation is modelled by a statistically based deformable contour model which learns typical lip deformation from a training set. The main difficulty in locating and tracking lips consists of finding dominant image features for representing the lip contours. We describe the use of a statistical profile model which learns dominant image features from a training set. The model captures global intensity variation due to different illumination and different skin reflectance as well as intensity changes at the inner lip contour due to mouth opening and visibility of teeth and tongue. The method is validated for locating and tracking lip movements on a database of a broad variety of speakers.