gebhart/patrepeval huggingface dataset:
SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system (2020)

Antibodies to the Vel blood group antigen can cause adverse hemolytic reactions unless Vel-negative blood units are transfused. Since the genetic background of Vel-negativity was discovered in 2013, DNA-based typing of the 17-bp deletion causing the phenotype has facilitated identification of Vel-negative blood donors. SMIM1, the gene underlying Vel, encodes a 78-amino acid erythroid transmembrane protein of unknown function. The transmembrane orientation of SMIM1 has been debated since experimental data supported both the N- and C-termini being extracellular. Likewise, computational predictions of its orientation were divided and potential alternatives such as monotopic or dual-topology have been discussed but not investigated. We used a cell-free system to explore the topology of SMIM1 when synthesized in the endoplasmic reticulum (ER). SMIM1 was tagged with an opsin-derived N-glycosylation reporter at either the N- or C-terminus and synthesized in vitro using rabbit reticulocyte lysate supplemented with canine pancreatic microsomes as a source of ER membrane. SMIM1 topology was then determined by assessing the N-glycosylation of its N- or C-terminal tags. Complementary experiments were carried out by expressing the same SMIM1 variants in HEK293T/17 cells and establishing their membrane orientation by immunoblotting and flow cytometry. Our data consistently indicate that SMIM1 has its short C-terminus located extracellularly and that it most likely belongs to the tail-anchored class of membrane proteins with the bulk of the polypeptide located in the cytoplasm. Having established its membrane orientation in an independent model system, future work can now focus on functional aspects of SMIM1 as a potential regulator of erythropoiesis.
mTOR kinase leads to PTEN-loss-induced cellular senescence by phosphorylating p53 (2018)

Loss of PTEN, the major negative regulator of the PI3K/AKT pathway induces a cellular senescence as a failsafe mechanism to defend against tumorigenesis, which is called PTEN-loss-induced cellular senescence (PICS). Although many studies have indicated that the mTOR pathway plays a critical role in cellular senescence, the exact functions of mTORC1 and mTORC2 in PICS are not well understood. In this study, we show that mTOR acts as a critical relay molecule downstream of PI3K/AKT and upstream of p53 in PICS. We found that PTEN depletion induces cellular senescence via p53-p21 signaling without triggering DNA damage response. mTOR kinase, a major component of mTORC1 and mTORC2, directly binds p53 and phosphorylates it at serine 15. mTORC1 and mTORC2 compete with MDM2 and increase the stability of p53 to induce cellular senescence via accumulation of the cell cycle inhibitor, p21. In embryonic fibroblasts of PTEN-knockout mice, PTEN deficiency also induces mTORC1 and mTORC2 to bind to p53 instead of MDM2, leading to cellular senescence. These results collectively demonstrate for the first time that mTOR plays a critical role in switching cells from proliferation signaling to senescence signaling via a direct link between the growth-promoting activity of AKT and the growth-suppressing activity of p53.
Vagus Nerve Stimulation Paired with Tones for the Treatment of Tinnitus: A Prospective Randomized Double-blind Controlled Pilot Study in Humans (2017)

Abstract The aim of the pilot study was to evaluate the effect of Vagus Nerve Stimulation (VNS) paired with sounds in chronic tinnitus patients. All participants were implanted and randomized to a paired VNS (n = 16) or control (n = 14) group. After 6 weeks of home therapy, all participants received paired VNS. The device was used on 96% of days with good compliance. After 6 weeks, the paired VNS group improved on the Tinnitus Handicap Inventory (THI) (p = 0.0012) compared to controls (p = 0.1561). The between-group difference was 10.3% (p = 0.3393). Fifty percent of the participants in the paired VNS group showed clinically meaningful improvements compared to 28% in controls. At one year, 50% of participants had a clinically meaningful response. The therapy had greater benefits for participants with tonal and non-blast induced tinnitus at the end of 6 (24.3% vs. 2%, p = 0.05) and 12 weeks (34% vs. 2%, p = 0.004) compared to controls with 80% and 70% responding at 6 months and 1 year, respectively. Adverse effects were mild and well-tolerated and the therapy had a similar safety profile to VNS for epilepsy. VNS paired with tones may be effective for a subgroup of tinnitus patients and provides impetus for a larger pivotal study.
Comparison of the Performance of the Laccase Bioconversion of Sodium Lignosulfonates in Batch, Continuous and Fed Batch Reactors (2013)

Comparison of the Performance of the Laccase Bioconversion of Sodium Lignosulfonates in Batch, Continuous and Fed Batch Reactors
Development of Photoactivatable Nitroxyl (HNO) Donors Incorporating the (3‐Hydroxy‐2‐naphthalenyl)methyl Phototrigger (2018)

A new family of photoactivatable HNO donors of general structure RSO 2 NHO‐PT [where PT represents the (3‐hydroxy‐2‐naphthalenyl)methyl (3,2‐HMN) phototrigger] has been developed, which rapidly releases HNO. Photogeneration of HNO was demonstrated using the vitamin B 12 derivative aquacobalamin as a trapping agent. The amount of sulfonate RSO 2 – produced was essentially the same as the amount of HNO released upon photolysis, providing a convenient method to indirectly quantify HNO release. Two competing pathways were also observed; a pathway involving O–N bond cleavage leading to release of a sulfonamide, and a pathway resulting in release of the parent N hydroxysulfonamide RSO 2 NHOH (for HNO donors with Me‐ and Ph‐containing leaving groups only). Up to approximately 70 % of the HNO‐generating pathway was observed with the CF 3 ‐containing leaving group, with HNO generation favored for small percentages of aqueous buffer in the acetonitrile/pH 7.00 phosphate buffer solvent mixture. Characterization of the photoproducts obtained from steady‐state irradiation by NMR spectroscopy showed that the desired HNO‐generating pathway was less favored for HNO donors with Me‐ and Ph‐containing leaving groups compared to the CF 3 ‐containing leaving group, suggesting that the excellent CF 3 ‐containing leaving group promotes HNO generation.
CHARACTERISATION OF THE HOST RESPONSE TO PLASMODIUM FALCIPARUM INFECTION. I. CEREBRAL MALARIA (1986)

Cerebral malaria is a major form of complicated malaria consequent upon cerebral damage associated with endothelial cell necrosis. We have used assays of Plasmodium falciparum growth inhibition in vitro to study serum inhibitory factors in patients with cerebral malaria. Serum from children with cerebral malaria inhibited parasite growth in a non-synchronised 72-hour assay to a greater extent than did sera from immune adults or asymptomatic children (p less than 0.001). The high level of non-specific inhibition of parasite growth was particularly evident when sera were tested against three P. falciparum isolates, and contrasted with the inhibitory effect of sera from non-malaria febrile controls. In this study, serum from patients with cerebral malaria was more inhibitory than serum from the other groups (p less than 0.001) and its between-isolate variation, when tested against a panel of P. falciparum isolates in growth assays, was significantly less than that of the other groups tested (p less than 0.005). These results are consistent with the hypothesis of toxin-induced endothelial cell damage, with the sequence of pathogenic events involving host-derived serum factors capable of damaging P. falciparum.
Chemically modified starches. (1991)

Chemically modified starches are widely used for Paper , Textile and Food Industries, etc. This paper explains the basic properties and uses of chemically modified starches .
Effect of Zinc Supplementation on Growth Hormone Secretion, IGF-I, IGFBP-3, Somatomedin Generation, Alkaline Phosphatase, Osteocalcin and Growth in Prepubertal Children with Idiopathic Short Stature (2005)

Controversy exists about the effect of zinc on growth and the GH-IGF system. Zinc supplementation has been shown to stimulate linear growth in zinc-deficient children. However the mechanism of this effect has not been well characterized. Furthermore, the effect of zinc supplementation on non-zinc-deficient short children is unknown. We investigated the effect of zinc supplementation on endogenous GH secretion, serum IGF-I and IGFBP-3 concentrations, IGF-I and IGFBP-3 generation in response to exogenous GH, bone formation markers, and linear growth of non-zinc-deficient children with idiopathic short stature. We analyzed prospectively serum zinc, IGF-I, IGFBP-3, alkaline phosphatase, osteocalcin, and GH response to clonidine test, and performed a somatomedin generation test before and 6 weeks after zinc supplementation in 22 (16 M, 6 F) prepubertal children with idiopathic short stature. Serum IGF-I increased from 67.4+/-70.6 to 98.2+/-77.3 ng/ml (p <0.001), IGFBP-3 from 2326+/-770 to 2758+/-826 ng/ml (p <0.001), alkaline phosphatase from 525+/-136 to 666+/-197 U/l (p <0.0001), and osteocalcin from 16.8+/-10.6 to 25.8+/-12.8 ng/ml (p <0.05) after zinc supplementation despite there being no difference in GH response to clonidine after zinc supplementation (peak GH 11.6+/-6.9 vs 13.4+/-7.8 ng/ml, GH area under the curve during clonidine test 689+/-395 vs 761+/-468, NS). Percent change in IGF-I and IGFBP-3 during the somatomedin generation test was not significantly affected by zinc supplementation (118% vs 136% and 57% vs 44%, respectively). There was no significant correlation between percentage increase in zinc levels and percentage increase in parameters tested. Height SDS or weight SDS did not improve significantly in 17 patients who continued on zinc supplementation for at least 6 months (6-12 months) (-2.59 vs -2.53 SDS and -1.80 vs -1.67 SDS, respectively). Zinc supplementation increased basal IGF-I, IGFBP-3, alkaline phosphatase and osteocalcin without changing GH response to clonidine. Zinc supplementation did not affect sensitivity to exogenous GH as tested by IGF-I and IGFBP-3 generation test. These results suggest a direct stimulatory effect of zinc on serum IGF-IGFBP-3, alkaline phosphatase and osteocalcin. Despite improvements in the above parameters, zinc supplementation to children with idiopathic short stature with normal serum zinc levels did not significantly change height or weight SDS during 6-12 months follow-up.
CCDC 146500: Experimental Crystal Structure Determination (2000)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Experiments on transition enhancement by distributed roughness (1986)

Distributed roughness with nominal height k in a boundary layer with displacement thickness δ* is known to lead to early non-Tollmien–Schlichting–Schubauer (TS) transition when k/δ* exceeds unity in nonaccelerated flows. But could commonly occurring milder random roughness enhance the regular phase-conditioned TS mechanisms and also lead to early transition? The new affirmative answer rests on extensive hot-wire explorations and smoke-wire visualization of flow over smooth and rough walls. The effects appear to be threefold. First, the low-inertia fluid in the valleys between the elements evidently respond more readily to free-stream disturbances. Second, once the TS fluctuations commence, they grow faster. Whether this is caused by continued input from free-stream disturbances along the path or to an increased destabilization of the system or both remains unclear. No inflected mean boundary-layer profiles were registered in careful measurements. Third, there is evidence of roughness-induced three-dimensionalization of the wave fronts which leads to earlier secondary subharmonic instabilities and, hence, to turbulence.
Investigation of interface trap states in TiN/Al2O3/p-Si capacitor by deep level transient spectroscopy (2003)

The minority carrier (electron) capture process and the interface trap density of a TiN/Al2O3/p-Si metal–oxide–semiconductor capacitor were examined by deep level transient spectroscopy (DLTS). It was found that the activation energies of the large peaks detected at higher temperatures with gate bias voltages of 1.8, 1.5, 1.3, and 1.1 V were 0.19, 0.24, 0.29, and 0.37 eV, respectively. These energies were related to the electron-capture process from the conduction band by interface states in the upper half of the Si band gap. The interface state passivation effect of postannealing in a hydrogen ambient was studied from the minority carrier capture process and the usual DLTS signals. The Dit at an energy of 0.35 eV from the valence bandedge decreased from 1×1012 cm−2 eV−1 at the as-fabricated state to 4×1011 cm−2 eV−1 after H2 annealing at 450 °C. It was also found that the Dit at an energy of 0.3 eV from the conduction bandedge decreased to the same amount by the same annealing process.
ChemInform Abstract: TRIFLAMIDES FOR PROTECTION AND MONOALKYLATION OF AMINES AND A NEW GABRIEL SYNTHESIS (1973)

Abstract Mit dem Anhydrid (I) oder dem Amid (II) können die Amine (III) zu den Tri= "flamiden (IV) substituiert werden, aus denen dann mit Alkylierungsmitteln die Substitutionsprodukte (V) entstehen, die durch Red‐Al (XIII) oder Lithiumalanat reduktiv zu (VI) gespalten werden.
Superconductivity in the topological insulatorBi2Te3under hydrostatic pressure (2014)

We report the resistivity and ac susceptibility measurements of the topological insulator ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}$ single crystals at pressures up to 11 GPa. Under highly hydrostatic pressure conditions generated in a multi-anvil high-pressure apparatus, a pressure-induced superconductivity only appears above a critical pressure ${P}_{\mathrm{C}}\ensuremath{\sim}7 \mathrm{GPa}$, coinciding with a structural transition from a rhombohedral to a monoclinic structure. The absence of superconductivity in the rhombohedral phase at pressures below ${P}_{\mathrm{C}}$, which is contrary to previous studies using the high-pressure apparatus with a solid pressure medium, suggests that the occurrence of superconductivity in the rhombohedral phase is sensitive to pressure conditions such as pressure inhomogeneity or uniaxial stress.
Bill Lang’s many contributions to the Acoustical Society of America’s domestic standard’s program and to International Electrotechnical Commission (IEC) TC-29 (2005)

Over the last 50 years, Bill Lang has been a major force in both National and International Standards. He has been a leader and major contributor to both, which together constitute our ASA Standards program that ASA conducts under the American National Standards Institute (ANSI) umbrella. This paper concentrates on Bill’s contributions to the domestic portion of the Standards Program, contributions to our interactions with the International Electro-technical Commission (IEC) TC-29 (electro-acoustics), and Bill’s unique contributions to IEC TC-29.
Design of a Simultaneous Center-Fed X/Ka-Band SATCOM Reflector Antenna with Replacable C-Band Option (2007)

A 1.5m tri-band (C-, X- and Ka-band) center-fed SAT-COM terminal has been designed for shipboard applications. The terminal has two independent replaceable feeds; C-band and simultaneous X/Ka-band. Offset prime-focus and dual-reflector designs are optimum from a performance standpoint for a reflector of this electrical size, however the scarcity of real estate and other mechanical considerations on shipboard drives the design to a center-fed type. Of the available center-fed reflector types, a shaped ring-focus configuration was chosen since the ring-focus reflector has several advantages over Cassegrain/Gregorian types for reflectors in this electrical size range. The reflector antenna shape is derived numerically utilizing GO shaping techniques while the feeds are designed using the BOR MoM and PO methods. The resulting antenna has been constructed and tested, and results are presented.
Synthetic aperture confocal imaging (2004)

Confocal microscopy is a family of imaging techniques that employ focused patterned illumination and synchronized imaging to create cross-sectional views of 3D biological specimens. In this paper, we adapt confocal imaging to large-scale scenes by replacing the optical apertures used in microscopy with arrays of real or virtual video projectors and cameras. Our prototype implementation uses a video projector, a camera, and an array of mirrors. Using this implementation, we explore confocal imaging of partially occluded environments, such as foliage, and weakly scattering environments, such as murky water. We demonstrate the ability to selectively image any plane in a partially occluded environment, and to see further through murky water than is otherwise possible. By thresholding the confocal images, we extract mattes that can be used to selectively illuminate any plane in the scene.
Understanding the control of acyl flux through the lipid metabolic network of plant oil biosynthesis Molecular and cell biology of lipids (2016)

Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
Affinity Capture Using Vancomycin-Bound Magnetic Nanoparticles for the MALDI-MS Analysis of Bacteria (2005)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides a straightforward means to differentiate microorganism species based on mass spectral fingerprinting. The pathogen cell concentration in an infected sample, however, is generally lower than that capable of being detected directly by MALDI-MS. Furthermore, the presence of proteins or metabolites in biological fluids always causes unavoidable interference for the identification of microorganism species. Vancomycin, which binds to D-Ala-D-Ala moieties on the cell walls of Gram-positive bacteria and, therefore, inhibits peptidoglycan synthesis, is one of the most potent antibiotics. Thus, we have employed vancomycin-modified magnetic nanoparticles as affinity probes to selectively trap Gram-positive pathogens from sample solutions; i.e., these bacteria can be isolated from sample solutions by applying a magnetic field. The isolated cells could then be characterized by MALDI-MS. This approach effectively reduces the interference of protein and metabolite signals in the mass spectra of Gram-positive bacteria because vancomycin has such high specificity for the D-Ala-D-Ala units of the cell walls. The lowest cell concentration we detected for both Staphylococcus saprophyticus and Staphylococcus aureus in a urine sample (3 mL) was approximately 7 x 10(4) cfu/mL.
Contactless measurement method for HDD spindle motor parameters (2009)

Conventional method of measuring inductance involves using a R-L-C meter. Such measurement method has limitation on accuracy due to the interference of back EMF during rotation. Profiling of the inductance at various motor positions thus requires cumbersome mechanical locking of the rotor. In this paper, an elegant method is introduced to capture inductance profile of spindle motor without the need for mechanical locking. The method involves using a DC electrical locking signal super-positioned with a pulse measuring signal to perform the measurement. The DC locking signal is then made sweep to allow micro-stepping of the motor so that inductance profile could be captured at all rotor position. The proposed method is shown to be effective, supported by derivations and experimental results.
3D video compression with the H.264 codec (2012)

Advances in 3D scanning have enabled the real-time capture of high-resolution 3D video. With these advances comes the challenge of streaming and storing this 3D video in a manner that can be quickly and effectively used. To do this, different approaches have been taken, a popular one being image based encoding, which projects from 3D into 2D, uses 2D compression techniques, and then decodes from 2D back to 3D. One such technique that does this is the Holovideo technique, which has been shown to yield great compression ratios. However, the technique was originally designed for the RGB color space and until recently could not be used with codecs that use the YUV color space such as the H.264 codec. This paper addresses this issue, generalizing Holovideo to the YUV color space, allowing it to leverage the H.264 codec. Compression ratios of over 352 : 1 have been achieved when comparing it to the OBJ file format, with mean squared error as low as .204% making it a viable solution for 3D video compression.
Optogenetic studies of nicotinic contributions to cholinergic signaling in the central nervous system (2014)

Molecular manipulations and targeted pharmacological studies provide a compelling picture of which nicotinic receptor subtypes are where in the central nervous system (CNS) and what happens if one activates or deletes them. However, understanding the physiological contribution of nicotinic receptors to endogenous acetylcholine (ACh) signaling in the CNS has proven a more difficult problem to solve. In this review, we provide a synopsis of the literature on the use of optogenetic approaches to control the excitability of cholinergic neurons and to examine the role of CNS nicotinic ACh receptors (nAChRs). As is often the case, this relatively new technology has answered some questions and raised others. Overall, we believe that optogenetic manipulation of cholinergic excitability in combination with some rigorous pharmacology will ultimately advance our understanding of the many functions of nAChRs in the brain.
Supplementary Figure 3 from Inflammation-Induced NFATc1–STAT3 Transcription Complex Promotes Pancreatic Cancer Initiation by <i>Kras</i><sup>G12D</sup> (2023)

&lt;p&gt;PDF file 788K, Supplementary Figure 3 refers to Figure 3 and shows STAT3 and NFATc1 expression levels in human and murine pancreatic cancer cell lines as well as NFATc1-dependent STAT3 expression&lt;/p&gt;