gebhart/patrepeval huggingface dataset:
Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2 (2011)

RBFOX1 and RBFOX2 are alternative splicing factors that are predominantly expressed in the brain and skeletal muscle. They specifically bind the RNA element UGCAUG, and regulate alternative splicing positively or negatively in a position-dependent manner. The molecular basis for the position dependence of these and other splicing factors on alternative splicing of their targets is not known. We explored the mechanisms of RBFOX splicing activation and repression using an MS2-tethering assay. We found that the Ala/Tyr/Gly-rich C-terminal domain is sufficient for exon activation when tethered to the downstream intron, whereas both the C-terminal domain and the central RRM are required for exon repression when tethered to the upstream intron. Using immunoprecipitation and mass spectrometry, we identified hnRNP H1, RALY, and TFG as proteins that specifically interact with the C-terminal domain of RBFOX1 and RBFOX2. RNA interference experiments showed that hnRNP H1 and TFG modulate the splicing activity of RBFOX1/2, whereas RALY had no effect. However, TFG is localized in the cytoplasm, and likely modulates alternative splicing indirectly.
Perpendicular write-head remanence characterization using a contact scanning recording tester (2005)

In this study, an experimental method for characterizing perpendicular write-head pole-tip remanence using a contact scanning recording tester is presented. The head remanence is characterized by imaging the written patterns generated by perpendicular write heads on dc-saturated perpendicular media. Write-head footprints are recorded with pulsed unidirectional currents while the head is stationary, followed by scanning the head in various directions at current-off state. Sufficient head remanent field yields written traces during the current-off scan. Projection of traces in multiple scanning directions enables pinpointing of the pole-tip remanence locations. It is found that the traces written by the remanent field appear only when pulse current amplitudes exceed a certain threshold value. The strength of remanent field also shows a dependence on current pulse polarity. The “stiffness” of the remanence is characterized by the amplitude of the opposite write current needed to eliminate the remanent field.
FTS3‐01‐01: HISTORY OF AMYLOID PET (2018)

After several false starts, the era of amyloid-beta positron emission tomography (PET) imaging began in earnest with the presentation of the first Pittsburgh Compound-B (PiB) data at the 2002 International Conference on Alzheimer's Disease in Stockholm. Review of the literature with personal reflections. The use of PiB spread rapidly to PET facilities capable of producing carbon-11, and efforts were already underway to develop fluorine-18-labeled amyloid tracers that would enable greater access to PET scanners without cyclotron facilities and enable widespread clinical use. Early findings documented a frequent presence of amyloid deposition in cognitively normal elderly – a finding that would later have implications on the clinical indications for amyloid imaging. It also became clear that a sizeable fraction of subjects with mild cognitive impairment (MCI) were amyloid-negative – a finding that would help mold subsequent appropriate use criteria. Amyloid tracers were first being employed in clinical trials of anti-amyloid therapies at about the same time that the FDA considered the path to approval for amyloid tracers in clinical use. After ground-breaking trials in terminally ill volunteers, three F-18 tracers were approved for clinical use with an indication to rule out Alzheimer's disease in the absence of amyloid. This was followed by a hearing by the Center for Medicaid and Medicare Services to consider the approval of payment for amyloid imaging scans for Medicare beneficiaries. Possibly related to the absence of a disease modifying anti-amyloid drug, approval was denied, but an option was included for coverage with evidence development – leading to the ongoing study “Imaging Dementia - Evidence for Amyloid Scanning” (IDEAS). Now, in 2018, amyloid imaging: 1) remains a critical element of many studies of aging and Alzheimer's disease; 2) is a basic component for both inclusion in clinical trials and is a primary or secondary outcome of anti-amyloid therapeutic trials; and 3) forms the foundation of new guidelines/frameworks on the clinical and research diagnosis/definition of preclinical, prodromal and probable Alzheimer's disease. However, lack of reimbursement has prevented the widespread clinical use of this technology that was met with so much excitement 15 years before.
Hydrothermal synthesis of strontium titanate: thermodynamic considerations, morphology control and crystallisation mechanisms (2017)

The hydrothermal/solvothermal method is one of the most versatile synthetic routes for producing a large number of compounds. The thermodynamic aspects, the control of morphology and the crystallisation mechanisms are reviewed and discussed in this highlight, with special emphasis on the synthesis of SrTiO<sub>3</sub>, as a model system.
Preparation of gold nanoparticles using reactive species produced in room-temperature ionic liquids by accelerated electron beam irradiation (2012)

Au nanoparticles that are expected to be a key material for supporting future technologies were produced with brief accelerated electron beam irradiation to various 1-alkyl-3-methylimidazolium cation ([R1MeIm]+)-based room-temperature ionic liquids (RTILs) with aurate. The resulting Au nanoparticles were able to remain in a nearly-monodispersed state in the RTILs for several weeks at least although the surface was not covered with a stabilizing agent, which is usually employed so as to prevent aggregation behaviour. The particle size increased with increasing the irradiation dose as well as decreasing the alkyl chain length of the [R1MeIm]+ if the RTIL consisted of the same anion species. The shapes of the Au nanoparticles obviously altered with the anionic species in the RTILs used for the preparation.
Endogenous expression and localization of myostatin and its relation to myosin heavy chain distribution in C2C12 skeletal muscle cells (2002)

Myostatin is a negative regulator of skeletal muscle growth. We have previously reported that recombinant myostatin protein inhibits DNA and protein synthesis in C2C12 cells. Our objective was to assess if C2C12 cells express myostatin, determine its sub-cellular localization and the developmental stage of C2C12 cells in which myostatin mRNA and protein are expressed. To study the endogenous expression of myostatin, C2C12 myoblasts were allowed to progress to myotubes, and changes in the levels of endogenous myostatin mRNA expression were determined by RT-PCR. The myostatin protein and the two major myosin heavy chain (MHC) isoforms (MHC-I and -II) were determined by Western blot. Confirmation of the relative MHC expression patterns was obtained by a modified polyacrylamide gel electropheretic (PAGE) procedure. Imunofluorescence staining was employed to localize the site of myostatin expression and the relative distribution of the MHC isoforms. Co-expression of these proteins was studied using a dual staining approach. Expression of myostatin mRNA was found in myotubes but not in myoblasts. Myostatin protein was seen in most but not all, of the nuclei of polynucleated fibers expressing MHC-II, and myostatin was detected in the cytoplasm of myotube. The localization of myostatin protein in myotube nuclei was confirmed by Western blot of isolated nuclear and cytoplasmic fractions. Incubation of C2C12 myotubes with graded doses of dexamethasone dose-dependently increased the intensity of nuclear myostatin immunostaining and also resulted in the appearance of cytoplasmic expression. In conclusion, myostatin was expressed mostly in C2C12 myotubes nuclei expressing MHC-II. Its predominant nuclear localization suggests that it may play a role in transcriptional regulation.
First Place—Resident Basic Science Award 1998: Role of Membrane Type 1‐Matrix Metalloproteinase and Gelatinase a in Head and Neck Squamous Cell Carcinoma Invasion in Vitro (1999)

The proteolytic activity of gelatinase A, a member of the matrix metalloproteinase (MMP) family, is considered to be a critical factor in tumor cell penetration of the extracellular matrix. To express catalytic activity, however, gelatinase A requires activation by another MMP, membrane type 1-matrix metalloproteinase (MT1-MMP). The head and neck squamous cell carcinoma cell line, UM-SCC-1, forms a quiescent monolayer atop collagen unless stimulated with epidermal growth factor (EGF; 3.5 nmol/L), which induces single cell invasion within 48 hours. To determine the role of the MT1-MMP/gelatinase A protease system in an in vitro stromal invasion model, expression vectors for MT1-MMP and gelatinase A were transfected into UM-SCC-1 (SCC-1/MT and SCC-1/gelA, respectively). SCC-1/MT tumor cells were found to invade in the absence of growth factor stimulation. Additionally, these cells displayed shorter onset to invasion and penetrated deeper into the collagen gel with EGF stimulation than did control vector transfectants. SCC-1/gelA cells similarly demonstrated invasion in the absence of EGF and a heightened invasive potential under EGF-stimulated conditions. These results suggest that the MT1-MMP/gelatinase A protease system participates in squamous cell carcinoma invasion of collagenous matrices.
Role of Dot1-Dependent Histone H3 Methylation in G1 and S Phase DNA Damage Checkpoint Functions of Rad9 (2005)

We screened radiation-sensitive yeast mutants for DNA damage checkpoint defects and identified Dot1, the conserved histone H3 Lys 79 methyltransferase. DOT1 deletion mutants (dot1Delta) are G1 and intra-S phase checkpoint defective after ionizing radiation but remain competent for G2/M arrest. Mutations that affect Dot1 function such as Rad6-Bre1/Paf1 pathway gene deletions or mutation of H2B Lys 123 or H3 Lys 79 share dot1Delta checkpoint defects. Whereas dot1Delta alone confers minimal DNA damage sensitivity, combining dot1Delta with histone methyltransferase mutations set1Delta and set2Delta markedly enhances lethality. Interestingly, set1Delta and set2Delta mutants remain G1 checkpoint competent, but set1Delta displays a mild S phase checkpoint defect. In human cells, H3 Lys 79 methylation by hDOT1L likely mediates recruitment of the signaling protein 53BP1 via its paired tudor domains to double-strand breaks (DSBs). Consistent with this paradigm, loss of Dot1 prevents activation of the yeast 53BP1 ortholog Rad9 or Chk2 homolog Rad53 and decreases binding of Rad9 to DSBs after DNA damage. Mutation of Rad9 to alter tudor domain binding to methylated Lys 79 phenocopies the dot1Delta checkpoint defect and blocks Rad53 phosphorylation. These results indicate a key role for chromatin and methylation of histone H3 Lys 79 in yeast DNA damage signaling.
Central Corneal Thickness Measured by Noncontact Specular Microscopy, Dual Rotating Scheimpflug Camera and Ultrasound Pachymetry (2015)

??: ????????, ?????????? ??? ? ??? ???????? ???? ??????? ???? ????? ???.&#13;\n??? ??: ??? 70? 70?? ???? ????????, ?????????? ??? ??? ??? ???????? ??? ??????? ???? ????? ?????.&#13;\n??: ????????, ?????????? ??? ? ??? ???????? ???? ??? ??????? ?? 567.70&amp;plusmn; 31.21 &amp;mu;m, 557.84 &amp;plusmn; 26.29 &amp;mu;m, 553.31 &amp;plusmn; 29.69 &amp;mu;m? ????????? ?? ??? ????? ??? ???????? ?? ?? ??????, ? ??? ??? ????? ??? ??? ???(p?0.05). ? ? ????????? ??? ??????? ?? ???? ??? ?????(p?0.05). ? ??? ?? ?? ????? ???(r?0.900, p?0.001).&#13;\n??: ????????? ?? ??? ??????? ??????????? ?? ??? ???????? ???? ??? ???? ?? ?? ? ?? ?? ??? ??? ??? ????. ?? ?????????? ???? ??? ??????? ??? ???????? ??? ?? ? ? ??? ?? ???? ???? ?????? ??? ?????????? ???? ?????????? ??? ???????? ??? ? ?? ? ? ??? ???? ????. Purpose&#13;\nTo compare central corneal thickness (CCT) as measured using noncontact specular microscopy (NCSM), dual rotating Scheimpflug camera (Galilei&amp;reg;), and ultrasound pachymetry (USP).&#13;\n&#13;\nMethods&#13;\nThe measurements of CCT using NCSM, dual rotating Scheimpflug camera and USP in 70 eyes of 70 healthy subjects were compared.&#13;\n&#13;\nResults&#13;\nThe average measurements of CCT using NCSM, dual rotating Scheimpflug camera, and USP were 567.70 &amp;plusmn; 31.21 &amp;micro;m, 557.84 &amp;plusmn; 26.29 &amp;micro;m, and 553.31 &amp;plusmn; 29.69 &amp;micro;m, respectively. The CCT measurement using NCSM was statistically significantly thicker than when measured using USP (p &amp;lt; 0.05). There was no significant difference between the NCSM and dual rotating Scheimpflug camera (p = 0.138). Additionally, there was no significant difference between the dual rotating Scheimpflug camera and USP (p = 0.656). A significant linear correlation was observed among the NCSM, dual rotating Scheimpflug camera, and USP (r &amp;gt; 0.900, p &amp;lt; 0.001).&#13;\n&#13;\nConclusions&#13;\nThe results of the 3 methods were significantly correlated but the measurement using NCSM was significantly thicker than when using USP. CCT measurements of healthy eyes using dual rotating Scheimpflug camera were more correlated with USP than NCSM. The CCT measurements using dual rotating Scheimpflug camera is a better alternative for USP than NCSM.
Allelochemics (2020)

Allelochemics comprise a vast number of known compounds, and hundreds more yet to be discovered, that mediate behavioral or physiological interactions between organisms of different species. They may benefit the emitter, the receiver, or both. Most are still mainly of scientific interest, but a few (principally attractants or repellents for insect pests) have been incorporated into operational pest management protocols.
Instantaneous topical drug quantification using a 3D printed microfluidic device and coherent Raman imaging (2023)

Cutaneous drug concentration quantification after topical application remains an active, yet challenging research area for topical drug development. Macroscale approaches quantify cutaneous pharmacokinetics 30 min to hours after application and miss rapid temporal and spatial dynamics that are vital to comprehend drug disposition. We have developed a 3D-printed applicator coupled with an inverted microscope and a rapidly-tunable fiber optic laser to quantify active pharmaceutical ingredients via sparse spectral sampling stimulated Raman scattering. The 3D-printed applicator is cost-effective (< $0.70/applicator) and utilizes a small formulation volume (20 µL). Ruxolitinib was formulated in two known permeation enhancers (propylene glycol and diethylene glycol monoethyl ether) that are known to display different permeation profiles to validate device capabilities. Results indicated that the applicator enabled relative-concentration monitoring immediately following drug product application. This approach has significant potential for investigating novel excipients, active pharmaceutical ingredients, and formulations to understand the permeation and biodistribution of these compounds.
Suppression of Density Waves in Clarifiers (1982)

Experiments on a 4-ft (1.2-m) diameter model circular clarifier operating at overflow rates and suspension concentrations corresponding to municipal treatment practice show that baffles designed to function as wave traps suppress low-frequency, large-amplitude density waves observed in these units. Simultaneous measurements of solids removal show substantial improvement. This work establishes the relationship between density waves and the deviation from ideal clarifier performance that earlier papers on internal waves by our research group suggested. The power spectrum of the internal waves and the effect of operating variables such as overflow rate, scraper speed, and suspended solid on the spectrum and solids removal are discussed.
Nanostructure Analysis Using Spatially Modulated Illumination Microscopy (2003)

For an improved understanding of cellular processes, it is highly desirable to develop light optical methods for the analysis of biological nanostructures and their dynamics in the interior of three-dimensionally (3D) conserved cells. Here, important structural parameters to be considered are the topology, i.e. the mutual positions and distances, as well as the sizes of the constituting subunits. This has become possible by the development of a novel method of far-field light fluorescence microscopy, spatially modulated illumination (SMI) microscopy. Using this approach, axial distances between fluorescence-labeled targets can be measured with an accuracy close to 1 nm; their sizes can be determined down to a few tens of nanometers. This approach can be extended to the determination of 3D positions and mutual 3D distances and sizes of any number of small objects/subunits that can be discriminated due to their spectral signatures. Consequently, the new approach allows an ‘in situ nanostructure elucidation, until now regarded to be beyond the possibilities of far-field light microscopy. Application examples discussed are: colocalization/nanosizing and topological analysis of large protein-protein complexes, of nucleic acid-protein complexes (such as transcription factories), or of the highly complex DNA-protein nanostructures of which active/ inactive gene regions in the eukaryotic cell nucleus are constituted.
A cache-based bandwidth optimized motion compensation architecture for video decoder (2017)

In video decoder applications, motion compensation (MC) is bandwidth consuming because of the non-regular memory access. Especially with the popularity of UHD video and the development of new coding standard (HEVC), external memory bandwidth becomes a crucial bottleneck. In this paper, we propose an area efficiency cache-based bandwidth optimization strategy to minimize the memory bandwidth. First a four-way parallel cache architecture is described. Then partially replacement strategy is proposed to further reduce memory bandwidth and power consumption. At last a column based storage scheme is provided to reduce the precharge/active frequency. We realize this idea using high level synthesis, which allow multiple iterations with quick turnaround time for micro architecture changes, and the results show that the averagely bandwidth reduction is up to 79.9% with moderate resource utilization, which outperforms the state-of-the-art works.
Retinal blood flow analysis using joint spectral and time domain optical coherence tomography (2008)

We propose a new technique of measuring and analysis of OCT signals: joint Spectral and Time domain Optical Coherence Tomography (STdOCT). This technique is based on a multiple spectral interferogram registration in time increments. The analysis of a single spectral interferogram provides an axial structure of a sample. The analysis of signals registered in time enables velocity estimation of moving sample. The method is applied to biomedical imaging, in particular to in vivo measurements of retinal blood circulation. The velocity estimations obtained with joint STdOCT are compared with the ones obtained by known, phase-resolved OCT. In contrast to the phase-resolved technique, STdOCT correctly reproduces parabolic shape of the flow velocity distribution despite decreasing signal-to-noise ratio (SNR).
Predictive Genomic Biomarkers of Hormonal Therapy Versus Chemotherapy Benefit in Metastatic Castration-resistant Prostate Cancer (2021)

Specific alterations in the DNA of tumors may assist in choosing between novel oral hormonal therapies and standard chemotherapy in advanced prostate cancer patients.
A High-Accuracy, Low-Order Thermal Model of SiC MOSFET Power Modules Extracted from Finite Element Analysis via Model Order Reduction (2019)

Silicon carbide (SiC) MOSFET power modules are being used for high power applications because of their superior thermal characteristics and high blocking voltage capabilities over traditional silicon power modules. This paper explores modeling the thermal process of a SiC MOSFET power module through a high-order finite element analysis (FEA) based thermal model and then reducing the order of the FEA thermal model using a Krylov subspace method. The low-order thermal model has a significantly reduced computation cost compared to the FEA model while preserving the accuracy of the model. The proposed method is applied to generate low-order thermal models for a SiC MOSFET, which are validated by computer simulations with respect to the FEA thermal model.
Assessing the Influence of OCT-A Device and Scan Size on Retinal Vascular Metrics (2020)

A better characterization of the confounds surrounding OCT-A retinal vasculature metrics can lead to improved application of these metrics as biomarkers for retinal and systemic diseases.
Odour Detection Methods: Olfactometry and Chemical Sensors (2011)

The complexity of the odours issue arises from the sensory nature of smell. From the evolutionary point of view olfaction is one of the oldest senses, allowing for seeking food, recognizing danger or communication: human olfaction is a protective sense as it allows the detection of potential illnesses or infections by taking into account the odour pleasantness/unpleasantness. Odours are mixtures of light and small molecules that, coming in contact with various human sensory systems, also at very low concentrations in the inhaled air, are able to stimulate an anatomical response: the experienced perception is the odour. Odour assessment is a key point in some industrial production processes (i.e., food, beverages, etc.) and it is acquiring steady importance in unusual technological fields (i.e., indoor air quality); this issue mainly concerns the environmental impact of various industrial activities (i.e., tanneries, refineries, slaughterhouses, distilleries, civil and industrial wastewater treatment plants, landfills and composting plants) as sources of olfactory nuisances, the top air pollution complaint. Although the human olfactory system is still regarded as the most important and effective "analytical instrument" for odour evaluation, the demand for more objective analytical methods, along with the discovery of materials with chemo-electronic properties, has boosted the development of sensor-based machine olfaction potentially imitating the biological system. This review examines the state of the art of both human and instrumental sensing currently used for the detection of odours. The olfactometric techniques employing a panel of trained experts are discussed and the strong and weak points of odour assessment through human detection are highlighted. The main features and the working principles of modern electronic noses (E-Noses) are then described, focusing on their better performances for environmental analysis. Odour emission monitoring carried out through both the techniques is finally reviewed in order to show the complementary responses of human and instrumental sensing.