gebhart/patrepeval huggingface dataset:
GH Action in Prostate Cancer Cells Promotes Proliferation, Limits Apoptosis, and Regulates Cancer-related Gene Expression (2022)

Previous studies investigating the effects of blocking the growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis in prostate cancer found no effects of the growth hormone receptor (GHR) antagonist, pegvisomant, on the growth of grafted human prostate cancer cells in vivo. However, human GHR is not activated by mouse GH, so direct actions of GH on prostate cancer cells were not evaluated in this context. The present study addresses the species specificity of GH-GHR activity by investigating GH actions in prostate cancer cell lines derived from a mouse Pten-deletion model. In vitro cell growth was stimulated by GH and reduced by pegvisomant. These in vitro GH effects were mediated at least in part by the activation of JAK2 and STAT5. When Pten-mutant cells were grown as xenografts in mice, pegvisomant treatment dramatically reduced xenograft size, and this was accompanied by decreased proliferation and increased apoptosis. RNA sequencing of xenografts identified 1765 genes upregulated and 953 genes downregulated in response to pegvisomant, including many genes previously implicated as cancer drivers. Further evaluation of a selected subset of these genes via quantitative reverse transcription-polymerase chain reaction determined that some genes exhibited similar regulation by pegvisomant in prostate cancer cells whether treatment was in vivo or in vitro, indicating direct regulation by GH via GHR activation in prostate cancer cells, whereas other genes responded to pegvisomant only in vivo, suggesting indirect regulation by pegvisomant effects on the host endocrine environment. Similar results were observed for a prostate cancer cell line derived from the mouse transgenic adenocarcinoma of the mouse prostate (TRAMP) model.
Immuno-PET in Inflammatory Bowel Disease: Imaging CD4-Positive T Cells in a Murine Model of Colitis (2018)

Inflammatory bowel diseases (IBDs) in humans are characterized in part by aberrant CD4-positive (CD4+) T-cell responses. Currently, identification of foci of inflammation within the gut requires invasive procedures such as colonoscopy and biopsy. Molecular imaging with antibody fragment probes could be used to noninvasively monitor cell subsets causing intestinal inflammation. Here, GK1.5 cys-diabody (cDb), an antimouse CD4 antibody fragment derived from the GK1.5 hybridoma, was used as a PET probe for CD4+ T cells in the dextran sulfate sodium (DSS) mouse model of IBD. <b>Methods:</b> The DSS mouse model of IBD was validated by assessing changes in CD4+ T cells in the spleen and mesenteric lymph nodes (MLNs) using flow cytometry. Furthermore, CD4+ T cell infiltration in the colons of colitic mice was evaluated using immunohistochemistry. <sup>89</sup>Zr-labeled GK1.5 cDb was used to image distribution of CD4+ T cells in the abdominal region and lymphoid organs of mice with DSS-induced colitis. Region-of-interest analysis was performed on specific regions of the gut to quantify probe uptake. Colons, ceca, and MLNs were removed and imaged ex vivo by PET. Imaging results were confirmed by ex vivo biodistribution analysis. <b>Results:</b> An increased number of CD4+ T cells in the colons of colitic mice was confirmed by anti-CD4 immunohistochemistry. Increased uptake of <sup>89</sup>Zr-maleimide-deferoxamine (malDFO)-GK1.5 cDb in the distal colon of colitic mice was visible in vivo in PET scans, and region-of-interest analysis of the distal colon confirmed increased activity in DSS mice. MLNs from colitic mice were enlarged and visible in PET images. Ex vivo scans and biodistribution confirmed higher uptake in DSS-treated colons (DSS, 1.8 ± 0.40; control, 0.45 ± 0.12 percentage injected dose [%ID] per organ, respectively), ceca (DSS, 1.1 ± 0.38; control, 0.35 ± 0.09 %ID per organ), and MLNs (DSS, 1.1 ± 0.58; control, 0.37 ± 0.25 %ID per organ). <b>Conclusion:</b><sup>89</sup>Zr-malDFO-GK1.5 cDb detected CD4+ T cells in the colons, ceca, and MLNs of colitic mice and may prove useful for further investigations of CD4+ T cells in preclinical models of IBD, with potential to guide development of antibody-based imaging in human IBD.
Occurrence and characterisation of intervening sequences (IVSs) within 16S rRNA genes from two atypical Campylobacter species, C. sputorum and C. curvus (2010)

A polymerase chain reaction (PCR) method was carried out on 21 isolates of atypical Campylobacter sputorum (n=14) and C. curvus (n=7) using a primer pair to amplify the helix 11 region within 16S ribosomal RNA (rRNA) gene sequences. Following sequencing and alignment analysis, 14 C. sputorum (100%) and six C. curvus (86%) isolates were shown to carry intervening sequences (IVSs) in this region. Interestingly, the nucleotide sequences of all the IVSs were identical among the 14 C. sputorum isolates (n=5 C. sputorum biovar [bv] paraureolyticus; n=5 by fecalis; n=4 by sputorum). In addition, two different nucleotide lengths and sequences of IVSs were identified among the six C. curvus isolates. On the first prediction of the secondary structure model of the IVSs in 16S rRNA genes, stem and loop structures were identified. In the purified RNA fractions from the 20 Campylobacter isolates carrying IVSs, no 16S rRNA was evident. Instead, other smaller RNA fragments were identified. Thus, the primary 16S rRNA transcripts may have been fragmented in the 20 isolates. This is the first demonstration of atypical C. sputorum and C. curvus isolates carrying IVSs in the helix 11 region in 16S rRNA genes.
Synthesis and Photophysical Properties of 1,1,4,4‐Tetracyanobutadienes Derived from Ynamides Bearing Fluorophores** (2022)

1,1,4,4-Tetracyanobutadienes (TCBDs) bearing a large diversity of fluorophores were prepared following a multi-step synthesis. In a crucial last step, all compounds were obtained from the corresponding ynamides, which were particularly suitable for the formation of the TCBDs in the presence of tetracyanoethylene via a [2+2] cycloaddition/retroelectrocyclization step (CA-RE). Several fluorenyl derivatives in addition to phenanthrenyl and terphenyl ones provided ynamide-based TCBDs affording remarkable emission properties covering a large range of wavelengths. Those compounds emit both in solid state and in solution from the visible region to the NIR range, depending on the molecular structures. Quantum yields in cyclohexane reached unforeseen values for such derivatives, up to 7.8 %. A huge sensitivity to the environment of the TCBDs has also been unraveled for most of the compounds since we observed a dramatic fall of the quantum yields when changing the solvent from cyclohexane to toluene, while they are almost non-emissive in dichloromethane.
Forecasting of Reservoir Inflow by the Combination of Deep Learning and Conventional Machine Learning (2021)

Recently, forecasting of inflow to a reservoir by employing machine learning techniques is getting attention for maximization of generation of hydroelectricity and prevention of disaster caused by flooding. In this context, forecasting of peak inflow caused by heavy rain or melting of snow is of utmost importance to properly utilize water for hydroelectricity, limit the damage to the reservoir/dam and issue flood advisory. The conventional methods of forecasting, which build a forecasting model by using the reservoir inflow data with observed and/or forecasted weather data by minimizing the overall forecasting errors, fail to predict the peak inflow because the number of peak inflows is very small compared to number of normal inflows. To forecast the peak inflow more accurately, we propose a method called Peak-oriented Forecasting by Model Switching (PForMS) which is a hybrid approach that utilizes the forecasting capabilities of both conventional machine learning and Deep Learning-based methods. To show the effectiveness of the proposed method, we perform experiments with five publicly available dam data sets from Japan and the USA and evaluate the proposed method and existing methods in term of AUC (Area under the ROC Curve) of forecasting peak inflow of various heights. Experimental results suggest that our proposed method is able to forecast the higher peaks of inflow more accurately than the existing methods of conventional machine learning and Deep Learning.
Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance (2012)

A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.
Deleterious systems effects due to polarization scrambling in the presence of polarization dependent loss (2003)

We experimentally verify that this low-frequency polarization scrambling at the transmitter will produce significant system performance degradation for a link with non-negligible values of instantaneous polarisation dependent loss (PDL). We also measure the system BER fluctuation using a recirculating loop testbed that can emulate distributed PDL along an 800-km NRZ transmission link at a 10-Gb/s data rate. We emphasize that network designers might determine that polarization scrambling will be necessary for polarisation mode dispersion (PMD) monitoring, but this could require either the reduction of PDL in all in-line components or the use of a PDL compensator.
Approaching a cluster of aluminium(III) selenide: [Al4Se5(H)2(NMe3)4] (1997)

The reaction of trans-[{Me3N(H)Al(µ-Se)}2] with N,N,N′,N″,N″-pentamethyldiethylenetriamine (pmdeta) in toluene affords the tetranuclear, alane selenide cluster [Al4Se5(H)2(NMe3)4] (structurally authenticated and ab initio modelled), and with PhTeTePh yields a mixed chalcogenide trans-[{Me3N(PhTe)Al(µ-Se)}2].
Reconstruction of insulin secretion by deconvolution: Domain of validity of a monoexponential impulse response model. (1996)

Insulin secretion rate (ISR) in vivo is reconstructed by deconvolution from plasma concentration of C-peptide (CP), a peptide with linear kinetics which is co-secreted with insulin but is not extracted by the liver. Deconvolution requires the knowledge of the CP impulse response. A two-exponential (2E) model is usually chosen to describe the CP impulse response but a one-exponential (1E) model is also used in the literature. The purpose here is to discuss the domain of validity of the 1E model in reconstructing the ISR by deconvolution. In particular, we show that the 1E model can be reliably used only if the ISR spectrum is concentrated in a narrow frequency band and a suitable input is designed for its identification.
Physiological Function of G Protein-Coupled Receptors (GPCRs) and Research Trends for Orphan GPCRs (2005)

G 단백질 연결 수용체 (G protein-coupled receptor, GPCR)는 세포막에 존재하는 단백질 중 가장 큰 대가족 (superfamily) 수용체 군으로 세포 바깥으로부터 오는 신호를 세 포 안으로 전달시켜주는 역할을 한다. 인간 유전체에는 현 재까지 약 800여종의 GPCR 유전자가 존재하는 것으로 알 려지고 있다. GPCR은 인간의 몸 안팎에 존재하는 다양한 리간드 (ligand)의 표적 단백질로, 크게 후각 및 미각 자극 에 반응하는 감각 수용체 그룹 (olfactory/gustatory GPCR) 과 신경전달물질, 호르몬 등 각종 신호전달물질에 반응하는 수용체 그룹 (transmitter GPCR)으로 분류할 수 있다. 인간 유전체에는 약 367종의 transmitter GPCR이 발견되고 있으 며, 이들은 인간의 생식, 대사, 면역, 운동, 소화, 호흡, 순환, 수면, 심리작용 등 대부분의 생리적 기능 조절에 중요한 역 할을 수행한다. GPCR 작용 리간드는 다양한 질병.질환과 관계되어 있어 GPCR은 제약 시장에서 가장 주목받는 약물 작용점으로 여겨지고 있다. Transmitter GPCR 중 그 리간 드와 기능이 밝혀지지 않은 것들을 고아 GPCR (orphan GPCR, oGPCR)이라 하며, 이들의 리간드를 찾는 deorphanization 연구는 신약개발의 핵심적인 위치에 있다. 본 리뷰 에서는 GPCR의 전반적인 생리활성 기전과 oGPCR 연구동 향에 대하여 논의하겠다.
Perceptual time-varying modelling of speech signals for ASR and compression application (2005)

Perceptual audio coders and Automatic Speech Recognition (ASR) systems are commonly based on short-time analysis. This paper presents a generalized model for time-varying coefficients based on psychoacoustic properties of the human ear. The proposed model is evaluated in the framework of speaker independent speech recognition using Hidden Markov Models (HMM). The generalized model is compared to the traditional most popular MFCC. The comparison is made with respect to the models baud rate and the total error rate measured in an extensive Speech recognition experiment. The recognition based on the well established speech recognition development environment, the HTK and using the TIDIGIT as the evaluation database. The time varying model achieves better recognition rate in comparison to MFCC, while the proposed model baud rate is about one third of the baud rate that is used in the case of MFCC. In addition, a preliminary evaluation of the model robustness to noise was carried out and is presented. 1.
Supplementary Data from Evaluation of d-Methionine as a Novel Oral Radiation Protector for Prevention of Mucositis (2023)

Supplementary Data from Evaluation of d-Methionine as a Novel Oral Radiation Protector for Prevention of Mucositis
Scalable virtual Ge templates for III-V integration on Si wafers (2012)

We demonstrate the scalability of a low temperature CVD approach to the fabrication of Sn doped Ge templates on Si wafers with 100 and 150 mm format. Successful demonstration of this Ge growth technique on 150 mm wafer format suggests the possibility of expanding this technology to even larger wafer sizes. Increase of Sn content in Ge-Sn alloy to 1% allows engineering of materials with lattice constant larger than Ge for better matched III-V multijunction PV stacks and leading to enhancement of the bottom PV junction performance. Additional alloying of Si with Ge-Sn system can increase the bandgap of the material and thus reach the desirable 1.0 eV range while lattice matching Ge/Si(100) at the same time.
Well-arranged novel InGaN hexagonal nanoplates at the tops of nitrogen-polarity GaN nanocolumn arrays (2012)

Periodically arranged novel InGaN hexagonal nanoplates were fabricated at the tops of square-lattice N-polarity GaN nanocolumn arrays. The key finding in this work is that the growth of InGaN on N-polarity GaN nanocolumns led to a peculiar nanoplate structure. The InGaN nanoplates with thicknesses of 50-100 nm extended outward from the narrow nanocolumns with diameters of 100-150 nm, to form larger hexagonal nanoplates with a typical side length of 250 nm.
Efficient Self-Ensemble Framework for Semantic Segmentation (2021)

Ensemble of predictions is known to perform better than individual predictions taken separately. However, for tasks that require heavy computational resources, \textit{e.g.} semantic segmentation, creating an ensemble of learners that needs to be trained separately is hardly tractable. In this work, we propose to leverage the performance boost offered by ensemble methods to enhance the semantic segmentation, while avoiding the traditional heavy training cost of the ensemble. Our self-ensemble framework takes advantage of the multi-scale features set produced by feature pyramid network methods to feed independent decoders, thus creating an ensemble within a single model. Similar to the ensemble, the final prediction is the aggregation of the prediction made by each learner. In contrast to previous works, our model can be trained end-to-end, alleviating the traditional cumbersome multi-stage training of ensembles. Our self-ensemble framework outperforms the current state-of-the-art on the benchmark datasets ADE20K, Pascal Context and COCO-Stuff-10K for semantic segmentation and is competitive on Cityscapes. Code will be available at github.com/WalBouss/SenFormer.
ESD on CHMOS Devices - Equivalent Circuits, Physical Models and Failure Mechanisms (1985)

Using new techniques it is possible to construct an EOS/ESD equivalent circuit of a product. Location of energy dissipation during an EOS/ESD event is determined by a pulsed near infrared technique. Rules for predicting location of ESD dissipation are defined. N+-P-N+ structures and n-channel transistors suffer from a current lock-on effect, which is apparently caused by a runaway oxide trapping mechanism. Different failure mechanisms are observed at narrow and wide pulse widths. Hot electron induced damage occurs under mechanical handling conditions. On CMOS outputs the n-channel device absorbs most of the ESD, and is very fragile.
An Attempt to Find a Suitable Biomass for Biochar-Based Polypropylene Biocomposites (2018)

Four biomass wastes (rice husk, coffee husk, coarse wool, and landfill wood) were added with biochar and polypropylene (PP) to manufacture biocomposites. Individual biomasses were tested for their combustion behavior using cone calorimeter. Biocomposites were analyzed for their fire/thermal, mechanical, and morphological properties. Wood had the most desirable comprehensive effect on both the mechanical and fire properties of composites. In particular, wood and biochar composite exhibited the highest values of tensile/flexural properties with a relatively low peak heat release rate. In general, application of waste derived biochar and biomasses drastically reduced the susceptibility of neat PP towards fire.
Exenatide induces carcinoembryonic antigen‐related cell adhesion molecule 1 expression to prevent hepatic steatosis (2017)

Exenatide, a glucagon-like peptide-1 receptor agonist, induces insulin secretion. Its role in insulin clearance has not been adequately examined. Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) promotes hepatic insulin clearance to maintain insulin sensitivity. Feeding C57BL/6J mice a high-fat diet down-regulates hepatic <i>Ceacam1</i> transcription to cause hyperinsulinemia, insulin resistance, and hepatic steatosis, as in <i>Ceacam1</i> null mice (<i>Cc1</i><sup><i>-/-</i></sup> ). Thus, we tested whether exenatide regulates <i>Ceacam1</i> expression in high-fat diet-fed mice and whether this contributes to its insulin sensitizing effect. Exenatide (100 nM) induced the transcriptional activity of wild-type <i>Ceacam1</i> promoter but not the constructs harboring block mutations of peroxisome proliferator-activated receptor response element and retinoid X receptor alpha, individually or collectively, in HepG2 human hepatoma cells. Chromatin immunoprecipitation analysis demonstrated binding of peroxisome proliferator-activated receptor gamma to <i>Ceacam1</i> promoter in response to rosiglitazone and exenatide. Consistently, exenatide induced <i>Ceacam1</i> messenger RNA expression within 12 hours in the absence but not in the presence of the glucagon-like peptide-1 receptor antagonist exendin 9-39. Exenatide (20 ng/g body weight once daily intraperitoneal injection in the last 30 days of feeding) restored hepatic <i>Ceacam1</i> expression and insulin clearance to curb diet-induced metabolic abnormalities and steatohepatitis in wild-type but not <i>Cc1</i><sup><i>-/-</i></sup> mice fed a high-fat diet for 2 months. <i>Conclusion</i>: Exenatide promotes insulin clearance in parallel with insulin secretion to prevent chronic hyperinsulinemia and the resulting hepatic steatosis, and this contributes to its insulin sensitizing effect. Our data further highlight the relevance of physiologic insulin metabolism in maintaining insulin sensitivity and normal lipid metabolism. (<i>Hepatology Communications</i> 2018;2:35-47).
Application of Regioselectively Substituted Methylcelluloses To Characterize the Reaction Mechanism of Cellulase (1996)

6-O-Methylcellulose (6MC) and 2,3-di-O-methylcellulose (23MC), having every structural unit of them regioselectivery substituted, and ununiformly 2,3-di-O-methylated cellulose (23MCU), having a trace amount of unsubstituted glucose units (U) in the same molecular chain, were used to investigate the structure of the scission point in enzymatic degradation with Trichoderma viride cellulase. For 6MC, the glycosidic bond between two adjacent substituted units could be cleaved to give oligomers with a degree of polymerization of ca. 8, while 23MC was not degraded. The characteristics of hydrolysis changed by substituted positions of substituents even though the same methyl groups were used. In addition, 23MC inhibited the hydrolysis of (carboxymethyl)cellulose. Interestingly, even in such unfavorable circumstances, 23MCU which was almost composed of 23MC was hydrolyzed, and further the initial velocity of this reaction was significantly high. Moreover, the amount of reducing ends produced corresponded to the amount of U, suggesting that only the linkages between U and 2,3-di-O-methylated units were cleaved because the cellulase could not cleave glycosidic bonds between two adjacent substituted 2,3-di-O-methylated units. By analyzing the kinetics of the cellulase reactions on the above cellulose model compounds, we were able to estimate the effect of the substituted regions on the hydrolysis in the cellulose derivatives. Especially, 2,3-di-O-methylated regions competitively inhibited the hydrolysis of U in other molecular chains. However, they activated the scission of U in the same molecular chain.
Methodology for optimalin situalignment and setting of bendable optics for nearly diffraction-limited focusing of soft x-rays (2013)

We demonstrate a comprehensive and broadly applicable methodology for the optimal in situ configuration of bendable soft x-ray Kirkpatrick-Baez mirrors. The mirrors used for this application are preset at the Advanced Light Source Optical Metrology Laboratory prior to beamline installation. The in situ methodology consists of a new technique for simultaneously setting the height and pitch angle of each mirror. The benders of both mirrors were then optimally tuned in order to minimize ray aberrations to a level below the diffraction-limited beam waist size of 200 nm (horizontal)×100 nm (vertical) . After applying this methodology, we measured a beam waist size of 290 nm (horizontal)×130 nm (vertical) with 1 nm light using the Foucault knife-edge test. We also discuss the utility of using a grating-based lateral shearing interferometer with quantitative wavefront feedback for further improvement of bendable optics.
A laser Doppler velocimeter for pulsatile water flow measurements in resonant hydraulic circuits (1979)

Abstract Described is a laser Doppler velocimeter designed to measure a small oscillatory velocity component superposed to the steady water flow of a resonant hydraulic circuit in fully developed turbulent conditions. A frequency tracker with lock-in analysis of the velocity output is used. The rms amplitude of the oscillatory velocity component is measured with an accuracy of 1.5 mm s-1, and the mean velocity is about 3 ms-1. The resonance behaviour of the velocity amplitude measured at a fixed point of the circuit is reported for the exciting frequency range 2–5 Hz.