gebhart/patrepeval huggingface dataset:
Phosphorylation of KasB Regulates Virulence and Acid-Fastness in Mycobacterium tuberculosis (2014)

Mycobacterium tuberculosis bacilli display two signature features: acid-fast staining and the capacity to induce long-term latent infections in humans. However, the mechanisms governing these two important processes remain largely unknown. Ser/Thr phosphorylation has recently emerged as an important regulatory mechanism allowing mycobacteria to adapt their cell wall structure/composition in response to their environment. Herein, we evaluated whether phosphorylation of KasB, a crucial mycolic acid biosynthetic enzyme, could modulate acid-fast staining and virulence. Tandem mass spectrometry and site-directed mutagenesis revealed that phosphorylation of KasB occurred at Thr334 and Thr336 both in vitro and in mycobacteria. Isogenic strains of M. tuberculosis with either a deletion of the kasB gene or a kasB_T334D/T336D allele, mimicking constitutive phosphorylation of KasB, were constructed by specialized linkage transduction. Biochemical and structural analyses comparing these mutants to the parental strain revealed that both mutant strains had mycolic acids that were shortened by 4-6 carbon atoms and lacked trans-cyclopropanation. Together, these results suggested that in M. tuberculosis, phosphorylation profoundly decreases the condensing activity of KasB. Structural/modeling analyses reveal that Thr334 and Thr336 are located in the vicinity of the catalytic triad, which indicates that phosphorylation of these amino acids would result in loss of enzyme activity. Importantly, the kasB_T334D/T336D phosphomimetic and deletion alleles, in contrast to the kasB_T334A/T336A phosphoablative allele, completely lost acid-fast staining. Moreover, assessing the virulence of these strains indicated that the KasB phosphomimetic mutant was attenuated in both immunodeficient and immunocompetent mice following aerosol infection. This attenuation was characterized by the absence of lung pathology. Overall, these results highlight for the first time the role of Ser/Thr kinase-dependent KasB phosphorylation in regulating the later stages of mycolic acid elongation, with important consequences in terms of acid-fast staining and pathogenicity.
CEST MRI to contrast chondrosarcoma tumors: two contrasts in one acquisition (2018)

\t\nIntroduction Chondrosarcoma (a malignant tumor of cartilage) is poorly vascularized and rich in proteoglycans (PGs).1 If the hypoxic and proteoglycan status of the tumor can be assessed by TEP imaging2 and scintigaphy3,4,5 it requires however 2 separated acquisitions. In this context we propose to develop an MRI strategy based on Chemical Exchange Saturation Transfer (CEST) to simultaneously co-register both hypoxia (pH) and PGs content in vivo. Methods The work hypotheses were tested in phantoms containing chondroitin sulfate A or creatine to validate PGs and pH imaging, respectively. NUDE mice (n=6) were implanted with HEMC-SS cells (human chondrosarcoma) in contact to tibia 7 weeks before imaging. MRI images were acquired at 11.7 T using a 40-mm quadratic volume coil. DWI was first performed to localize the tumor, then WASSR (B1=0,1μT for 1.5s, Δωsat=±1000Hz in 20Hz steps) and CEST Z-spectra (B1=1.5μT for 4s, Δωsat=±3000Hz in 50Hz steps) were acquired based on a RARE protocol.31P MRS was performed thanks to a volume coil. 23Na imaging was recorded by using a 20-mm surface coil. Data were analyzed using an in-house program written in Matlab®R2017a. After correction for B0 inhomogeneity, the CEST maps were generated. Results/Discussion Variations in PGs concentration and in pH (fig. 1) were observed in vitro by CEST MRI by monitoring the magnetization transfer ratio asymmetry at 450 (-OH) and 1000Hz (-NH), respectively. These moieties allow extracting the PG concentration and the pH, respectively. In vivo (fig. 2) results showed an increase of asymmetry at 450Hz in the chondrosarcoma compare to the muscle. This increase of asymmetry is expected as during the pathology development the PG concentration increase. In vivo, we also observed an increase of asymmetry at 1800Hz in the chondrosarcoma associated with acidosis in the hypoxic core. The two CEST images are currently being validated by 23Na imaging (GAG concentration) and 31P MRS (pH). Conclusions CEST MRI can be used as a new strategy for non-invasive assessment of chondrosarcoma. Indeed, CEST MRI offers the possibility to image in the same exam the 2 mains characteristics of this tumor: pH and PGs contain. CEST MRI is able to identify and differentiate zones of hypoxia in-vivo.
Agronomic performance and seed quality of Ethiopian mustard in Saskatchewan (1996)

Ethiopian mustard (Brassica carinata A. Braun) is grown as an oilseed crop in Ethiopia. The agronomic performance and seed quality of 11 B. carinata lines were evaluated for 2 yr in field tests at Saskatoon, Saskatchewan, to asses the potential of Ethiopian mustard as an oilseed crop for the Canadian prairies. The B. carinata accessions were 5 d later flowering and 19 d later maturing than the B. napus cultivar Westar. Seed yields of B. carinata were comparable to those of B. napus in 1984, but were much lower than those of B. napus and B. juncea in 1985. Seed of B. carinata had higher protein and lower oil and crude fibre contents than that of B. napus and B. rapa. The fatty acid composition of the oil of B. carinata seed was typical for that of a high erucic acid Brassica oil. Allyl glucosinolate was the only alkenyl glucosinolate found in B. carinata seed meal. A comparison of near isogenic yellow and brown B. carinata lines indicated that, on average, yellow lines produced heavier seed (+ 0.4 g), higher oil (+ 23 g kg −1 ) and protein (+ 21 g kg −1 ) and lower crude fibre (− 12 g kg −1 ) contents than brown lines. Correlation studies showed that seed weight was positively correlated with oil and protein and negatively correlated with fibre content. The results of this study indicated that none of the 11 lines of B. carinata tested was adapted for immediate production on the Canadian prairies. Earlier-maturing, higher-oil-content lines of B. carinata that produce low erucic acid and low glucosinolate seed must be developed before this species can be grown as an oilseed crop in Canada. Key words:Brassica carinata, agronomic performance, seed quality
Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns (2007)

We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.
Comparison of thymic and peripheral T cell Ly‐2/3 antigens (1984)

Major structural differences occur between the thymic and peripheral T cell forms of the Ly-2/3 antigen. Thymus Ly-2/3 consists of similar amounts of two types of disulfide-linked heterodimer, alpha beta and alpha' beta (Mr alpha = 38000, Mr alpha' = 35000, Mr beta = 30000). In contrast material from peripheral T cells consists almost exclusively of alpha beta dimers. The alpha chains of thymus and peripheral T cells differ also in isoelectric point with the thymic alpha chain being the more acidic. Based on peptide mapping experiments the alpha and alpha' chains of thymus are likely to be alternatively modified forms of the same polypeptide backbone. Individual T cell clones or T cell tumors propagated in vitro exhibit either a typical thymus or a typical peripheral T cell Ly-2/3 polypeptide pattern indicating that the synthesis of both alpha and alpha' chains can occur in the same cell. The heterogeneity of thymic Ly-2/3 can be considerably reduced by removal of sialic acid residues, and after desialylation the alpha chains of thymus and a cloned cytotoxic T lymphocyte (CTL) line cannot be electrophoretically distinguished. If Ly-2 structures affected the antigen specificity of CTL, a different structural variant would be expected in individual clones. The electrophoretic identity of desialylated thymus and CTL alpha chains suggests that Ly-2 does not exhibit clonal variation in polypeptide structure and, therefore, cannot contribute to antigen specificity.
Rimsulfuron Plus Thifensulfuron-Methyl Combinations with Selected Postemergence Broadleaf Herbicides in Corn (Zea mays)1 (2002)

Field studies were conducted in 1995 and 1996 to investigate postemergence (POST) applications of rimsulfuron (12 g ai/ha) plus thifensulfuron-methyl (6 g ai/ha) in tank-mixtures with various acetolactate synthase (ALS)- and non–ALS-inhibitor herbicides for weed control in corn. Rimsulfuron plus thifensulfuron-methyl controlled giant foxtail and common lambsquarters at least 95% but did not control common ragweed. Rimsulfuron plus thifensulfuron-methyl tank-mixed with 20 g ai/ha primisulfuron-methyl, 17 g ai/ha CGA-152005 plus 18 g ai/ha primisulfuron, 18 or 36 g ai/ha halosulfuron-methyl, 18 g ai/ha nicosulfuron, or 280 g ai/ha dicamba controlled giant foxtail at least 89%, common lambsquarters at least 96% and, with the exception of the nicosulfuron combination, controlled common ragweed at least 88%. Rimsulfuron plus thifensulfuron-methyl tank-mixed with flumetsulam (26 g ai/ha) plus clopyralid (69 g ai/ha) plus 2,4-D (140 g ai/ha), atrazine (560 g ai/ha), 2,4-D (280 g/ha), or dicamba (308 g/ha) plus atrazine (588 g/ha) reduced the control of giant foxtail to less than 78% 26 d after treatment (DAT). Corn injury was less than 12% from rimsulfuron plus thifensulfuron-methyl and from mixtures of rimsulfuron plus thifensulfuron-methyl with other herbicides except when rimsulfuron plus thifensulfuron-methyl was mixed with flumetsulam plus clopyralid plus 2,4-D. This combination injured corn 26%. In these studies the appropriate tank-mix partners for rimsulfuron plus thifensulfuron-methyl were primisulfuron, CGA-152005 plus primisulfuron, and halosufluron-methyl.Nomenclature: Atrazine; CGA-152005 (proposed name prosulfuron), 1-(4-methoxy-6-methyl-triazin-2-yl)-3-[2-(3,3,3-trifluoropropyl)-phenylsulfonyl] urea; clopyralid; 2,4-D; dicamba; flumetsulam; halosulfuron-methyl; primisulfuron-methyl; rimsulfuron; thifensulfuron-methyl; common lambsquarters, Chenopodium album L. #3 CHEAL; common ragweed, Ambrosia artemisiifolia L. # AMBEL; giant foxtail, Setaria faberi Herrm. # SETFA; corn, Zea mays L. ‘Pioneer 3394’.Additional index words: Herbicide interaction, weed management.Abbrevations: ALS, acetolactate synthase (EC 4.1.3.18); DAT, days after treatment; MSO, methylated seed oil; NIS, nonionic surfactant; POST, postemergence; UAN, urea ammonium nitrate.
Self-quotient Referential Bilateral Filter and Its Application to Real-Time Face Beautification System (2015)

In this paper, self-quotient referential bilateral filter is introduced. Although bilateral filter is a well-known edge-preserving smoothing filter, it is difficult to handle with light variation. The proposed filter combines bilateral filter and self-quotient filter, and can handle the image with light variation. In our method, we utilize self-quotient image as a reference filter for bilateral filter. Some experimental results are shown to demonstrate the effectiveness of the proposed method. As an application, we also developed a real-time face beautification system combining face detector and the proposed filter. Throughout the experiments, our method has a potential to be used for real-time face beautification system.
Two-color pump-probe interferometry of ultra-fast light-matter interaction (2017)

Two-color side-view probing of light-matter interaction from minute focal volume of a tightly focused fs-laser pump pulse reveals charge dynamics with high 0.9 micrometers optical resolution and approximately ~20 fs temporal resolution in coincidence between pump and probe pulses. Use of two colors is advantageous for probing optically excited plasma regions with different density. Holographical digital focusing and spatial filtering were implemented to obtain the same resolution images for subsequent Fourier analysis. Fast electron removal with time constant ~150 fs was resolved and is consistent with self-trapping. Potential applications of an optical control over a light-induced defect placement with deep-sub-wavelength resolution is discussed.
A Competitive Enzyme Immunoassay for the Pyrrolizidine Alkaloids of the Senecionine Type* (1996)

We developed an immunoassay with antibodies against retrorsine to detect the closely related senecionine, the main alkaloid in various Asteraceae. Sensitivity is about 23 pg (68 fmol) for senecionine. Cross reactivity of monocrotalin, retrorsine N-oxide, senkirkine (< 0.1%), and seneciphylline (3.6-34.5%) was resolved. The alkaloid content in leaves of Petasites hybridus (Asteraceae) was determined to be 3.86 ppm, calculated as senecionine, which was far less than in rhizomes (104.8 ppm). Additionally, we proved specificity by taking immunograms from different parts of Petasites hybridus. The test is a suitable tool for assessing the toxic potential of medicinal plants containing senecionine.
Purification and Characterization of Recombinant Human Lysozyme from Eggs of Transgenic Chickens (2015)

Transgenic chickens as bioreactors have several advantages, such as the simple establishment procedure, correct glycosylation profile of expressed proteins, etc. Lysozyme is widely used in food industry, livestock farming, and medical field as a replacement of antibiotics because of its antibacterial and complement system-modulating activity. In this study, we used RT-PCR, Western blot, and immunofluorescence to detect the expression of recombinant human lysozyme (rhLY) in the transgenic chicken. We demonstrated that the transgene of rhLY was genetically stable across different generations. We next optimized the purification procedure of rhLY from the transgenic eggs by utilizing two steps of cation-exchange chromatography and one gel-filtration chromatography. About 6 mg rhLY with the purity exceeding 90% was obtained from ten eggs, and the purification efficiency was about 75%. The purified rhLY had similar physicochemical and biological properties in molecular mass and antibacterial activity compared to the commercial human lysozyme. Additionally, both of them exhibited thermal stability at 60°C and tolerated an extensive pH range of 2 to 11. In conclusion, our study proved that the transgenic chickens we have previously generated were genetically stable and suitable for the production of active rhLY. We also provided a pipeline for purifying the recombinant proteins from transgenic eggs, which could be useful for other studies.
ChemInform Abstract: THALLIUM IN ORGANIC SYNTHESIS. 62. A CONVENIENT SYNTHESIS OF α‐ARYLSUCCINIC ACIDS (1985)

Abstract Aus den Aroylcarbonsäuren (I) erhält man mit Thalliumnitrat und Methanol/Orthoester die Carbonsäureester (II), aus (III) erhält man unter doppelter Reaktions?lhrung die Bis‐carbonsäureester (IV.).
Calcitriol down-regulates human ether a go-go 1 potassium channel expression in cervical cancer cells. (2010)

EAG1 is a calcitriol target in normal and cancer cells and calcitriol is a potential therapy for cervical cancer.
Bone and gallium scintigraphy in children with rhabdomyosarcoma: A 10‐year review (1994)

Technetium-99m bone and Gallium-67 scintigraphy has been widely used in the management of children with solid tumors. A retrospective review of all patients with rhabdomyosarcoma (RMS) from January 1980 to December 1989 was undertaken in order to determine the sensitivity and specificity of scintigraphy in detection of metastatic disease and to determine optimum frequency of serial scans in follow up. Over the 10-year period, 40 patients were diagnosed and treated for RMS: 22 were newly diagnosed from 1980-1984 and of these 16 had a minimum 5-year disease-free period whilst 6 died of the disease, giving a cure rate of 73%. A total of 271 bone and 236 Gallium-67 scans were performed. With respect to detection of metastatic disease in all tissues, Gallium-67 scans had a sensitivity of 84%, specificity 95% and bone scans had a sensitivity of 70% and specificity 95%. Bone scan sensitivity and specificity for skeletal metastases were 100% and 95%, respectively. Considering only patients with Gallium avid primary tumors, the Gallium-67 scan sensitivity was 94%. Ten patients developed new metastatic disease or primary recurrence after starting therapy, 8/10 within 12 months of diagnosis. Frequent surveillance scanning in the treatment phase, 2 years post-diagnosis, is of value in the early detection of metastases and monitoring disease response to therapy. Surveillance scanning after completion of treatment is more difficult to justify.
Miniaturized opto-fluidic ring resonator for sensitive label-free viral detection (2008)

A rapid, label-free on-line virus detection method has been developed based on opto-fluidic ring resonator (OFRR). The OFRR employs a fused silica capillary with a diameter around 100 &mu;m. The circular cross section of the capillary forms the ring resonator that supports the whispering gallery modes (WGMs). The OFRR wall is only a few micrometers. Thus, the evanescent field of the WGMs extends into the core and interacts with the sample flowing in the core. The WGM spectral position shifts in response to the binding of biomolecules to the OFRR inner surface, providing quantitative and kinetic information about the biomolecule interaction. In this work, M13 filamentous phage and anti-M13 antibody are chosen as a model system to demonstrate the detection and quantification of virus in liquid samples. Anti-M13 antibodies are first covalently attached on the aminosilane coated OFRR surface to provide a bioselective layer. The detection is then performed when the virus concentration varies from 10<sup>11</sup> pfu/mL down to 10<sup>3</sup> pfu/mL. Our experimental results show that the OFRR is capable of detecting M13 at a concentration as low as 1000 pfu/mL. Control experiments are carried out to show the specificity of the detection. A theoretical model is developed to analyze the experimental results. The OFRR are advantageous in virus detection, as it integrates the ring resonator with fluidic channels and provides continuous on-line monitoring capability. It also has great potential for sensitive, rapid, and low-cost micro total analysis devices for biomolecule detection.
ChemInform Abstract: KOMPLEXE VON AROMATEN MIT LEWISSAEURE, STRUKTUR UND REAKTIVITAET 6. MITT. KINETIK DER DURCH ALCL3 KATALYSIERTEN BENZOYLIERUNG (1970)

Abstract Die 2:1‐Komplexe von SbCl 3 mit Aromaten (Benzol, Toluol, o‐ und p‐Xylol) ′ werden mit Benzoylchlorid in Gegenwart von AlCl 3 in 1,2‐Dichlor‐äthan bzw. dem Säurechlorid als Lösungsmittel benzoyliert und die Geschwindigkeitskonstanten bestimmt.
Feedforward noise cancellation in an airduct using generalized FIR filter estimation (2004)

A feedforward control algorithm for active noise control based on the recursive estimation of a generalized finite impulse response (FIR) filter is presented in this paper. The feedforward control algorithm is applied to a commercial air ventilation silencer to provide active noise compensation in an airduct. A generalized FIR filter has the same linear parameter structure as a taped delay FIR filter that is favorable for (recursive) estimation purposes. However, the advantage of the generalized FIR filters lies in the possibility to include prior knowledge of system dynamics in the tapped delay line of the filter. By comparison with a conventional FIR filter implementation it is shown that a significant improvement in noise cancellation is obtained.
Squashing cubes (2004)

The vast majority of geometric meshes used in computer graphics are optimized for rendering, and not deformable object simulation. Despite tools for volume (or surface) (re)meshing of geometric models to support physical simulation, in practice, the construction of physically based deformable models from arbitrary graphical models remains a tedious process for animators. Squashing Cubes (SC) automates the construction of physically based deformable objects from arbitrary geometric models. During preprocess, the geometric model (typically a surface mesh) is voxelized into tiny elastic cubes, i.e., the squashing cubes model. Second, a generic deformable object simulator is used to deform the SC model. Finally, the resulting deformations are interpolated back onto the original model, thus producing the final animation. Such domain embedding schemes are familiar to graphics [Pentland and Williams 1989; Faloutsos et al. 1997]. SC is simple to implement, practical for complex models, supports any geometric representation, and the SC deformable models are trivial to simulate. Although SC geometry is approximate, reasonable approximations of deformation displacement fields can be obtained for many animation purposes. One practical benefit of voxelization is that geometric features and defects smaller than the voxel scale are merged; consequently, intersecting and topologically disconnected polygons (so common in graphical models) are deformed appropriately. SC is especially appealing for complex superstructures, such as the bridge, for which the geometric mesh is not “structurally sound.” For example, the bridge model contains numerous modeling shortcuts, such as improperly attached cables, intersecting geometry, small “gaps,” badly shaped (skinny) triangles, and isolated polygons. In short, Squashing Cubes allows animators to focus on animation, and less on physically based modeling details, such as the engineering of bridges using properly connected beam, truss, and shell elements.
Patterns of plasma levels of catechols in neurogenic orthostatic hypotension (1989)

Patients with neurogenic orthostatic hypotension can have deficits in sympathetic neural function at any of several levels of the sympathetic neuraxis. We determined whether patterns of plasma levels of dopa, norepinephrine, dihydroxyphenylglycol, and dihydroxyphenylacetic acid would distinguish patients with orthostatic hypotension associated with multiple system atrophy, pure autonomic failure, or deficiency of dopamine-beta-hydroxylase. Plasma levels of catechols were normal in most patients with multiple system atrophy, consistent with relatively intact peripheral sympathetic neurons; in contrast, most patients with pure autonomic failure had decreased levels of all four catechols, consistent with degenerative loss of sympathetic nerve endings. Patients with deficiency of dopamine-beta-hydroxylase had increased levels of dopa and dihydroxyphenylacetic acid and markedly decreased levels of norepinephrine and dihydroxyphenylglycol, suggesting compensatory increases in sympathetic nerve activity in the absence of norepinephrine biosynthesis. Subgroups of patients with pure autonomic failure or multiple system atrophy had low levels of norepinephrine with normal levels of dopa, dihydroxyphenylglycol, and dihydroxyphenylacetic acid, consistent with normal catecholamine biosynthesis and decreased postganglionic sympathetic nerve traffic or decreased exocytotic release from sympathetic nerve endings. The results demonstrate the value of examining patterns of plasma levels of catechols to elucidate mechanisms of neurogenic orthostatic hypotension.
Introduction to Airborne Radar (1998)

This book covers the following areas: airborne radar; radar fundamentals; pulse Doppler radar; air-to-air operation; high-resolution ground mapping and imaging; electronic warfare; and representative radar system