gebhart/patrepeval huggingface dataset:
Microarray analysis of survival pathways in human PC-3 prostate cancer cells. (2007)

The overall analyses reveal an overrepresentation of differentially expressed genes related to cellular processes such as cell cycle regulation, lipid metabolism and steroid biosynthesis.
Cryptococcus neoformans Cells in Biofilms Are Less Susceptible than Planktonic Cells to Antimicrobial Molecules Produced by the Innate Immune System (2006)

The human pathogenic fungus Cryptococcus neoformans can form biofilms on polystyrene plates and medical devices in a process that requires capsular polysaccharide release. Although biofilms are known to be less susceptible to antimicrobial drugs, little is known about their susceptibility to antimicrobial molecules produced by the innate immune system. In this study, we investigated the susceptibility of C. neoformans cells in biofilm and planktonic states to oxidative and nonoxidative antimicrobial molecules produced by phagocytic cells. The effects of various immune effector molecules on the fungal mass, metabolic activity, and architecture of C. neoformans biofilms were measured by colony counts, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide reduction, and confocal microscopy, respectively. Biofilms were more resistant than planktonic cells to oxidative stress but remained vulnerable to cationic antimicrobial peptides. However, melanized biofilms were significantly less susceptible to antimicrobial peptides than nonmelanized biofilms. These results suggest that the biofilm phenotype increases resistance against host immune mechanisms, a phenomenon that could contribute to the ability of biofilm-forming microbes to establish persistent infections.
IDDF2023-ABS-0050 Longitudinal outcomes associated with non-alcoholic fatty liver disease. a meta-analysis of 129 studies (2023)

<h3>Background</h3> Non-alcoholic fatty liver disease (NAFLD) has risen significantly in global incidence and is widely considered a multisystem disease linked to numerous extrahepatic manifestations. We aim to investigate the associated longitudinal outcomes of NAFLD. <h3>Methods</h3> We performed a systematic review and meta-analysis of observational studies assessing longitudinal clinical outcomes of NAFLD from Medline and Embase electronic databases. Primary outcomes were incident cardiovascular-related, metabolic-related, cancer-related, and other outcomes associated with NAFLD. DerSimonian Laird random effects meta-analysis was performed. Pooled effect estimates with 95% confidence intervals were calculated. Heterogeneity among studies was evaluated using Cochran’s Q test and I<sup>2</sup> metrics, with two-tailed P values. <h3>Results</h3> 398 studies were retrieved for full-text sieve and assessed for eligibility. 129 studies were included. NAFLD patients had significant increases in risks of cardiovascular outcomes (n=44, HR: 1.43, 95%Cl: 1.27 to 1.60, p&lt;0.01, I<sup>2</sup>=97.50%), incident hypertension (n=9, HR: 1.75, 95%Cl: 1.46 to 2.08, p&lt;0.01, I<sup>2</sup>=74.00%), diabetes (n=37, HR: 2.56, 95%Cl: 2.10 to 3.13, p&lt;0.01, I<sup>2</sup>=98.90%), pre-diabetes (n=4, HR: 1.69, 95%Cl: 1.22 to 2.35, p&lt;0.01, I<sup>2</sup>=54.80%), metabolic syndrome (n=5, HR: 2.57, 95%Cl: 1.13 to 5.85, p=0.02, I<sup>2</sup>=96.10%), chronic kidney disease (n=14, HR: 1.38, 95%Cl: 1.27 to 1.50, p&lt;0.01, I<sup>2</sup>=80.20%), all cancers (n=15, HR: 1.54, 95%Cl: 1.35 to 1.76, p&lt;0.01, I<sup>2</sup>=97.30%) (specifically, hepatocellular carcinoma, colorectal, biliary tract, esophageal, stomach, thyroid and female genital cancers) and liver-related outcomes (n=14, HR: 3.92, 95%Cl: 2.05 to 7.49, p&lt;0.01, I<sup>2</sup>=98.50%) compared to non-NAFLD. NAFLD patients with advanced liver disease were associated with significantly greater risks (p=0.02) of incident diabetes than less severe NAFLD, compared to non-NAFLD. <h3>Conclusions</h3> This study emphasizes associations between NAFLD and cardiovascular, metabolic, oncological, and other outcomes. The multisystemic nature and increasing prevalence of NAFLD call for treatment targets, reducing systemic events and end-organ complications.
Measurement of Two-phase Flow using Multi-wave Ultrasound (Measurement of Bubble Rising Velocity using Correlation Method) (2006)

In this paper, two types of ultrasonic measurement techniques are attempted to obtain liquid and gas velocity distributions in bubbly flow. The first attempt is that the both of liquid and gas velocity distributions are obtained using an ultrasonic basic frequency and its echo signals. In order to separate the signals reflected on liquid-gas interfaces and particles, thresholding based on the ultrasonic echo intensity is applied. However, it is difficult to extract completely the echo signals reflected on the tracer particles. In order to overcome the difficulty, a multi-wave ultranonic transducer (TDX) is applied. The TDX consisted of two piezoelectric elements that have different basic frequency. The liquid velocity distribution is obtained using an ultrasonic velocity profiles (UVP) monitor at 8 MHz ultrasonic frequency, and the rising velocity of bubbles is measured using cross-correlation method at 2 MHz ultrasonic frequency. Using the technique, both of the liquid and gas velocity distributions are obtained accurately using the TDX.
Discovery of a Potent Small-Molecule Antagonist of Inhibitor of Apoptosis (IAP) Proteins and Clinical Candidate for the Treatment of Cancer (GDC-0152) (2012)

A series of compounds were designed and synthesized as antagonists of cIAP1/2, ML-IAP, and XIAP based on the N-terminus, AVPI, of mature Smac. Compound 1 (GDC-0152) has the best profile of these compounds; it binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domains of cIAP1 and cIAP2 with K(i) values of 28, 14, 17, and 43 nM, respectively. These compounds promote degradation of cIAP1, induce activation of caspase-3/7, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Compound 1 inhibits tumor growth when dosed orally in the MDA-MB-231 breast cancer xenograft model. Compound 1 was advanced to human clinical trials, and it exhibited linear pharmacokinetics over the dose range (0.049 to 1.48 mg/kg) tested. Mean plasma clearance in humans was 9 ± 3 mL/min/kg, and the volume of distribution was 0.6 ± 0.2 L/kg.
Japanese nationwide observational multicenter study of tumor BRCA1/2 variant testing in advanced ovarian cancer (2022)

The association between germline BRCA1 and BRCA2 pathogenic variants (mutations: gBRCAm) and ovarian cancer risk is well established. Germline testing alone cannot detect somatic BRCA1/2 pathogenic variants (sBRCAm), which is calculated based on the proportion of tumor BRCAm (tBRCAm) from tumor samples and gBRCAm. Homologous recombination deficiency (HRD) results mainly from genetic/epigenetic alterations in homologous recombination repair-related genes and can be evaluated by genomic instability status. In Japan, the prevalence of tBRCAm, sBRCAm, and HRD remains unclear. This multicenter, cross-sectional, observational study, CHaRacterIzing the croSs-secTional approach to invEstigate the prevaLence of tissue BRCA1/2 mutations in newLy diagnosEd advanced ovarian cancer patients (CHRISTELLE), evaluated the prevalence of tBRCAm, sBRCAm, and HRD in tumor specimens from newly diagnosed patients with ovarian cancer who underwent gBRCA testing. Of the 205 patients analyzed, 26.8% had a tBRCAm, including tBRCA1m (17.6%) and tBRCA2m (9.3%). The overall prevalence of tBRCAm, gBRCAm, sBRCAm, and HRD-positive status was 26.8%, 21.5%, 6.3%, and 60.0%, respectively. The calculated sBRCAm/tBRCAm ratio was 23.6% (13/55), and the prevalence of gBRCA variant of uncertain significance was 3.9%. These results suggest gBRCA testing alone cannot clearly identify the best course of treatment, highlighting the importance of sBRCA testing in Japan. The present results also suggest that testing for tBRCA and HRD should be encouraged in advanced ovarian cancer patients to drive precision medicine.
Longitudinal EEG model detects antisense oligonucleotide treatment effect and increased UBE3A in Angelman syndrome (2022)

Angelman syndrome is a neurodevelopmental disorder caused by deficiency of the maternally inherited <i>UBE3A</i> gene in neurons. Antisense oligonucleotide therapies are under development to reinstate UBE3A protein production. Non-invasive biomarkers to detect target engagement and treatment response are needed to support clinical trials. Delta power measured in the scalp EEG is a reliable biomarker for Angelman syndrome but varies widely across individuals and throughout development, making detection of a treatment effect using single measurements challenging. We utilized a longitudinal dataset of 204 EEG recordings from 56 subjects with Angelman syndrome to develop a natural history model of delta (2-4 Hz) power, with predictors of age, elapsed time, and relative delta power at an initial recording. Using this model, we computed the sample and effect sizes needed to detect a treatment effect in a human clinical trial with 80% power. We applied the same model structure to a mouse model of Angelman syndrome (<i>n</i> = 41) to detect antisense oligonucleotide-mediated treatment effects on absolute delta activity and <i>Ube3a</i> expression. In humans, delta power at a second time point can be reliably predicted using the natural history model. In mice, a treatment effect can be detected after antisense oligonucleotide treatment targeting the <i>Ube3a-</i>antisense transcript through at least 8 weeks post-treatment (<i>P</i> < 1e-15). Deviations in delta power from the expected natural history correlated with <i>Ube3a</i> expression in the mouse model (<i>P</i> < 0.001). Deviations in delta power from a human natural history model in Angelman syndrome can detect antisense oligonucleotide-mediated improvement in <i>Ube3a</i> expression in Angelman syndrome mice and may be relevant for human clinical trials.
Influence of implant diameter on surrounding bone (2007)

BIC was 71% and 73%, whereas ABD was 65% and 52%, for standard and wide implants, respectively. These differences were not statistically different (P>0.05). Correlation with IBD was then investigated. BIC was not correlated with IBD. ABD was not correlated to IBD for standard implants (r2=0.126), but it was correlated with wide implants (r2=0.82). In addition, a 1 : 1 ratio between IBD and ABD was found for wide implants. It can be concluded, within the limits of this study, that ABD may be influenced by implant diameter, perhaps due to differences in force dissipation.
Antagonism of delta(2)-opioid receptors by naltrindole-5'-isothiocyanate attenuates heroin self-administration but not antinociception in rats. (2000)

delta-Opioid receptors have been implicated in reinforcement processes and antagonists are available that produce long-lasting and selective antagonism of delta-opioid receptors in vivo. This experiment assessed the contribution of delta-opioid receptors to the antinociceptive and reinforcing properties of heroin. The effects of the irreversible delta-antagonist naltrindole-5'-isothiocyanate (5'-NTII) were evaluated on heroin self-administration and hot-plate antinociception in rats. 5'-NTII (10 nmol i.c.v.) shifted the dose-response curve for heroin self-administration downward, increasing the A(50) values on the ascending and descending limbs by approximately 0.5 log units and decreasing the maximum by 33%. 5'-NTII (40 nmol i.c.v.) shifted both limbs of the heroin self-administration dose-effect curve 1.2 log units to the right and decreased the maximum by 90%. Heroin self-administration gradually returned to baseline levels over 7 or 17 days after administration of 10 or 40 nmol 5'-NTII, respectively. 5'-NTII (40 nmol i.c.v.) decreased the self-administration of 0.17 mg/infusion cocaine by 40% while having no effect on responding maintained by 0.33 or 0.67 mg/infusion. 5'-NTII attenuated the antinociceptive effects of deltorphin (delta(2)) in a dose-dependent manner while having no effect on antinociception elicited after i.c. v. administration of [D-Pen(2),D-Pen(5)]-enkephalin (delta(1)) or [D-Ala(2),N-Me-Phe(4),Gly(5)-ol]-enkephalin (mu). In addition, the antinociceptive effects of heroin were not significantly affected by 5'-NTII (40 nmol i.c.v.). Therefore, 5'-NTII can attenuate the reinforcing effects of heroin at doses that do not affect its antinociceptive effects. Long-acting delta(2)-opioid antagonists may be beneficial in the treatment of heroin dependence or as adjuncts to reduce the abuse liability of opioid analgesics.
Suppression of 1∕f Noise in Accumulation Mode FD-SOI MOSFETs on Si(100) and (110) Surfaces (2009)

In this paper, a new approach to reduce the 1/f noise levels in the MOSFETs on varied silicon orientations, such as Si(100) and (110) surfaces, has been carried out. We focus on the Accumulation‐mode (AM) FD‐SOI device structure and demonstrate that the 1/f noise levels in this AM FD‐SOI MOSFETs are obviously reduced on both the Si(100) and (110) surfaces.
Abnormalities of phosphoprotein gene expression in three osteopetrotic rat mutations: Elevated mrna transcripts, protein synthesis, and accumulation in bone of mutant animals (1994)

Osteoclast abnormalities that characterize osteopetrosis, a disorder of bone resorption, may derive from aberrant signals from the osteoblast or the bone matrix. In the present studies, both synthesis and the bone matrix content of the major bone phosphoprotein component, osteopontin, were found to be elevated in three osteopetrotic rat mutations (ia, op, and tl). In whole bone, a twofold increase in the content of the characteristic amino acid O-phosphoserine for osteopontin occurred in op and tl mutant long bone, but a smaller (15%) and more variable increase was observed in ia mutant rat long bone. Extraction of the bone matrix components and partial purification by reverse phase chromatography showed a twofold increase in a phosphoprotein fraction relative to other noncollagenous components. Amino acid analysis and staining characteristics of SDS-PAGE fractionated proteins indicated this to be osteopontin. Organ cultures of calvarial bone from 4 day ia osteopetrotic mutant and normal rats in the presence of 3H-proline showed increased synthesis of this 60 kD protein, which was stimulated by vitamin D. Preparation of total cellular RNA from bone of 2- and 6-week-old mutants and normal rats supported increased synthesis of osteopontin as reflected by hybridization with osteopontin cDNA probe, showing significantly higher levels of mRNA transcripts in ia (3-5 fold), tl (1.4-2 fold), and op (6-25 fold) mutant bone compared to normal littermates. The changes in osteopontin mRNA levels in mutant bone were also examined in relation to other growth and phenotype-expressed genes. The findings of increased accumulation of osteopontin in osteopetrotic bone and increased synthesis by osteoblasts are interesting in light of the previously reported decrease in bone osteocalcin content (Endocrinology, 126:966, 1990), confirmed here by decreased osteocalcin mRNA transcripts. Such aberrations in the composition of skeletal extracellular matrix could be a reflection of or a contributing factor to the osteoclast abnormalities of some of these osteopetrotic disorders.
Anomalously Slow Conformational Change Dynamics of Polar Groups Anchored to Hydrophobic Surfaces in Aqueous Media (2020)

Water molecules within a thin hydration layer, spontaneously generated on hydrophobic protein surfaces, are reported to form a poorly dynamic network structure. However, how such a water network affects the conformational change dynamics of polar groups has never been explored, although such polar groups play a critical role in protein-protein and protein-ligand interactions. In the present work, we utilized as model protein surfaces a series of self-assembled monolayers (SAMs) appended with polar (Fmoc) or ionic (FITC) fluorescent head groups that were tethered via a 1.5-nm-long flexible oligoether chain to a hydrophobic silicon wafer surface, which was densely covered with paraffinic chains. We found that, not only in deionized water but also in aqueous buffer, these oligoether-appended head groups at ambient temperatures both displayed an anomalously slow conformational change, which required ∼10 h to reach a thermodynamically equilibrated state. We suppose that these behaviors reflect the poorly dynamic and low-permittivity natures of the thin hydration layer.
Mucus matters: Ferrets demonstrate sustained fibrosis and mucociliary decrement following bleomycin-induced pulmonary fibrosis (2018)

<b>Intro:</b> A gain-of-function promoter variant for MUC5B is the strongest risk factor for the development of idiopathic pulmonary fibrosis (IPF); yet, the role of MUC5B in IPF pathogenesis is unknown. Ferrets and humans have a similar distribution of MUC5B production in the lung. <b>Obj:</b> Determine if bleomycin(BL)-exposed ferrets develop features resembling IPF and elucidate the role of mucociliary clearance (MCC). <b>Methods:</b> BL (5U/kg) or saline control (SCt) was administered IT to ferrets. Fibrosis was assessed with μCT, hydroxyproline (Hyp), and SHG histology. Muc5B, a-SMA, acetylated tubulin and CCSP expression were assessed by IHC and IF. MC transport (MCT) and ciliary beat frequency (CBF) was assessed <i>ex-vivo</i> using μOCT. MCC was assessed <i>in vivo</i> by SPECT/CT imaging of Tc99-DTPA. <b>Results:</b> Apparent at 2wks, ground-glass opacities persisted through 6wks on μCT. Volumetric μCT analysis revealed increased fibrosis in BL lungs (increased 18.1±2.2% vs -0.8±0.8% in SCt, P&lt;0.001). At 6 wks, Hyp was elevated (8.1±1.4 μg/mg BL vs. 4.3±0.7μg/mg SCt, P&lt;0.04). SHG and IF revealed collagen-rich matrixes, scattered myofibroblasts, and a-SMA+ fibroblastic foci (FF). Abnormal expression of mucin-rich proximal airway markers was noted in cystic distal airspaces. μOCT demonstrated reduced CBF in the bronchi at 3wks and 6wks post-BL exposure (mean decrement -2.4 and -1.8 Hz vs. SCt, P&lt;0.01). Pilot data suggest <i>in vivo</i> MCC was reduced in BL ferrets (0.72% min<sup>-1</sup> BL vs. 2.16% min<sup>-1</sup> SCt, N=3). <b>Conclusion:</b> BL-exposed ferrets exhibit features of IPF not seen in rodents: FF, mucin-rich honeycomb cysts, bronchiolized distal airspaces, and sustained fibrosis associated with aberrant MCT.
Robust and Scalable Power System State Estimation via Composite Optimization (2017)

In today's cyber-enabled smart grids, high penetration of uncertain renewables, purposeful manipulation of meter readings, and the need for wide-area situational awareness, call for fast, accurate, and robust power system state estimation. The least-absolute-value (LAV) estimator is known for its robustness relative to the weighted least-squares (WLS) one. However, due to nonconvexity and nonsmoothness, existing LAV solvers based on linear programming are typically slow, hence inadequate for real-time system monitoring. This paper develops two novel algorithms for efficient LAV estimation, which draw from recent advances in composite optimization. The first is a deterministic linear proximal scheme that handles a sequence of convex quadratic problems, each efficiently solvable either via off-the-shelf algorithms or through the alternating direction method of multipliers. Leveraging the sparse connectivity inherent to power networks, the second scheme is stochastic, and updates only \emph{a few} entries of the complex voltage state vector per iteration. In particular, when voltage magnitude and (re)active power flow measurements are used only, this number reduces to one or two, \emph{regardless of} the number of buses in the network. This computational complexity evidently scales well to large-size power systems. Furthermore, by carefully \emph{mini-batching} the voltage and power flow measurements, accelerated implementation of the stochastic iterations becomes possible. The developed algorithms are numerically evaluated using a variety of benchmark power networks. Simulated tests corroborate that improved robustness can be attained at comparable or markedly reduced computation times for medium- or large-size networks relative to the "workhorse" WLS-based Gauss-Newton iterations.
54.4: 4.1 inch Top‐Emission AMOLED on Flexible Metal Foil (2005)

Abstract We have developed a 4.1 inch AMOLED display with top emission structure on stainless steel foil. The p‐channel TFTs on metal foil exhibited the field‐effect mobility of 75.1 cm 2 /Vs, threshold voltage of −3.9V, and subthreshold swing of 0.9V/dec. Active‐matrix back planes were fabricated with the poly‐Si TFT with a conventional pixel circuit consisting of 2 TFTs and 1 cap. The scan driver circuits with PMOS were integrated on the metal foil.
Phenotyping wheat under salt stress conditions using a 3D laser scanner (2016)

High-throughput phenotyping is a rapidly evolving field, with new technologies being developed that need to be tested under different experimental conditions. In this study, the PlantEye, a high-resolution three-dimensional (3D) laser scanner was used to phenotype wheat plants grown under control and salt stress in controlled environment conditions. The PlantEye scans plants from overhead, creating a data cloud from which the system computes traits such as 3D leaf area, plant height and leaf number. Moderately high correlations were observed between automatically calculated trait; 3D leaf area, and the manually measured traits leaf area, fresh biomass and dry biomass, although correlations were lower than those reported in previous studies in different crop species. As expected, salt stress caused significant reduction in plant growth, particularly leaf area and biomass production, which resulted in significantly reduced grain number and yield. The results here suggest that PlantEye was effective in phenotyping wheat, although improvements in the system setup, data processing and customer support would make this phenotyping tool suitable to be widely adopted for a range of plant species under diverse environmental conditions.
Right ventricular-vascular coupling in heart failure with preserved ejection fraction and pre- vs. post-capillary pulmonary hypertension (2017)

Abnormal right ventricular-vascular coupling identifies patients with HFpEF and additional pre-capillary PH, and predicts poor outcome in HFpEF.
Plant Cellular and Molecular Biotechnology: Following Mariotti’s Steps (2019)

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species.
In Situ Targeting of Antigen Presenting Cells Within Secondary Lymphoid Organs As A Means to Control Immune Responses (2005)

s: Abstracts for the 20th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer (Primary Authors are Italicized): TURNING IMMUNIZATION INTO TUMOR REGRESSION: OBSTACLES AND STRATEGIES