gebhart/patrepeval huggingface dataset:
A Statistical Model for Quantification and Prediction of Cardiac Remodelling: Application to Tetralogy of Fallot (2011)

Cardiac remodelling plays a crucial role in heart diseases. Analyzing how the heart grows and remodels over time can provide precious insights into pathological mechanisms, eventually resulting in quantitative metrics for disease evaluation and therapy planning. This study aims to quantify the regional impacts of valve regurgitation and heart growth upon the end-diastolic right ventricle (RV) in patients with tetralogy of Fallot, a severe congenital heart defect. The ultimate goal is to determine, among clinical variables, predictors for the RV shape from which a statistical model that predicts RV remodelling is built. Our approach relies on a forward model based on currents and a diffeomorphic surface registration algorithm to estimate an unbiased template. Local effects of RV regurgitation upon the RV shape were assessed with Principal Component Analysis (PCA) and cross-sectional multivariate design. A generative 3-D model of RV growth was then estimated using partial least squares (PLS) and canonical correlation analysis (CCA). Applied on a retrospective population of 49 patients, cross-effects between growth and pathology could be identified. Qualitatively, the statistical findings were found realistic by cardiologists. 10-fold cross-validation demonstrated a promising generalization and stability of the growth model. Compared to PCA regression, PLS was more compact, more precise and provided better predictions.
Hydrogel to guide chondrogenesis versus osteogenesis of mesenchymal stem cells for fabrication of cartilaginous tissues (2019)

The ideal combination of hydrogel components for regeneration of cartilage and cartilaginous interfaces is a significant challenge because control over differentiation into multiple lineages is necessary. Stabilization of the phenotype of stem cell derived chondrocytes is needed to avoid undesired progression to terminal hypertrophy and tissue mineralization. A novel ternary blend hydrogel composed of methacrylated poly(ethylene glycol) (PEG), gelatin, and heparin (PGH) was designed to guide chondrogenesis by bone marrow derived mesenchymal stem cells (BMSCs) and maintenance of their cartilaginous phenotype. The hydrogel material effects on chondrogenic and osteogenic differentiation by BMSCs were evaluated in comparison to methacrylated gelatin hydrogel (GEL), a conventional bioink used for both chondrogenic and osteogenic applications. PGH and GEL hydrogels were loaded with goat BMSCs and cultured in chondrogenic and osteogenic mediums in vitro over six weeks. The PGH showed no sign of mineral deposition in an osteogenic environment in vitro. To further evaluate material effects, the hydrogels were loaded with adult human BMSCs (hBMSCs) and transforming growth factor β-3 and grown in subcutaneous pockets in mice over eight weeks. Consistent with the in vitro results, the PGH had greater potential to induce chondrogenesis by BMSCs in vivo compared to the GEL as evidenced by elevated gene expression of chondrogenic markers, supporting its potential for stable cartilage engineering. The PGH also showed a greater percentage of GAG positive cells compared to the GEL. Unlike the GEL, the PGH hydrogel exhibited anti-osteogenic effects in vivo as evidenced by negative Von Kossa staining and suppressed gene expression of hypertrophic and osteogenic markers. By nature of their polymer composition alone, the PGH and GEL regulated BMSC differentiation down different osteochondral lineages. Thus, the PGH and GEL are promising hydrogels to regenerate stratified cartilaginous interfacial tissues in situ, such as the mandibular condyle surface, using undifferentiated BMSCs and a stratified scaffold design.
All-optical packet-drop demonstration using 100-Gb/s words by integrating fiber-based components (1998)

Packet-drop function for a time-division multiplexing network using 100-Gb/s, 8-b words is experimentally demonstrated by integrating all-optical header processing and payload demultiplexing with electrooptic packet routing. The header processor consists of two levels of all-optical logic gates based on low birefringent nonlinear optical loop mirrors (NOLMs), and the payload demultiplexer is a two-wavelength NOLM. Both devices are driven by synchronized lasers with timing jitter under 1 ps. The contrast ratios for both header processor and demultiplexer are 10:1 and that of the packet router is 17 dB. The switching energies for header processing and payload reading are 10 and 1 pJ/pulse, respectively.
Catalogue des Ascomycètes récoltés dans la Loire – 2e addendum (2015)

Catalogue of Ascomycetes collected in the French department of Loire – 2nd addendum. This notice is the second addendum to the check-list of Ascomycetes collected in the French department of Loire. Some corrections are given to the initial catalogue and new data coming from collections made in 2013 are added.
Methylchloroisothiazolone‐induced growth inhibition and lethality in Escherichia coli (1995)

Exposure of log phase Escherichia coli cells to inhibitory levels of 5-chloro-2-methyl-isothiazolin-3-one (MCI) results in rapid bacteriostasis and a delayed onset of bactericidal activity. Inhibition of respiration occurs within the same time frame as bacteriostasis, and is followed by a decline in intracellular ATP levels. In vitro and in vivo experiments suggest that growth inhibition is the result of selective inhibition of particular targets, with succinate dehydrogenase being identified as a possible target. Such selectivity was not anticipated from this highly reactive molecule. MCI-induced lethality is positively correlated with a loss of reduced protein sulphydryls (r2 = 0.79). A greater than equimolar loss of reduced protein sulphydryls, compared with the number of MCI molecules added, and a reduction in killing by MCI after induction of the OxyR regulon suggest that free radical generation may have a role in the antibacterial activity of MCI. We present an examination of the in vivo effects of MCI exposure on bacterial cells, and evidence that the isothiazolones exhibit selectivity in their cellular targets and antimicrobial effects.
Recombinant bispecific antibodies (bsMAb) to carcinoembryonic antigen (CEA): Promising new agents for pretargeted radioimmunotherapy (RAIT) of solid tumors (2004)

3105 Background: Although radiolabeled antibodies are effective treatments for lymphoma, to be effective for solid tumors, the radiation dose needs to be increased. Streptavidin-biotin pretargeting methods have been reported to increase the radiation dose to tumors and improve therapeutic responses in lymphoma and solid tumor models. Because of the high immunogenicity of streptavidin, we have developed a pretargeting method that will use recombinant, humanized anti-CEA bsMAbs to localize either 90Y or 177Lu. Methods: Recombinant bsMAb monovalent (bispecific diabody; 40 kD) or divalent (trivalent bsMAb; 80 kD) to CEA and monovalent binding to a novel hapten, histamine-succinyl-glycine (HSG), were tested in nude mice bearing a human colon tumor xenograft, GW-39. Results: When the bsMAb dose and interval between the bsMAb and111In-DOTA-di-HSG peptide were properly adjusted, tumor targeting within 3 h after the 111In-peptide could achieve levels of nearly 30 percent injected dose per gram (% ID/g), which rivaled the maximum tumor uptake achieved with an 111In-labeled anti-CEA IgG 2 days after its injection. Tumor/blood ratios were as high 30:1 for the pretargeting at 3 h after the peptide injection. Analysis of time-activity curves over 5–7 days, comparing targeting of 90Y-radioactivity, using the trivalent bsMAb pretargeting method with a 90Y-peptide, to a 90Y-anti-CEA IgG, showed pretargeting had a 1.7-fold higher AUC with a 3-fold higher dose rate advantage than the IgG at equitoxic toxic injected activity. Preliminary studies using the 90Y-peptide pretargeting method have shown complete arrest of the growth of established (0.35 cm3) colonic cancer xenografts in nude mice over a 14-week period, whereas tumors in untreated or animals receiving the same dose of the 90Y-peptide progressed rapidly. Conclusions: These studies indicate that pretargeting using these recombinant bsMAb could potentially provide sufficient targeting enhancement to be an effective therapeutic in solid tumors. (Supported in part by the Office of Science (BER), U.S. Department of Energy grant DE-FG01–95ER62028.) Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration IBC Pharmaceuticals, Inc.; Immunomedics, Inc. IBC Pharmaceuticals, Inc.; Immunomedics, Inc.
Ultra-Thin SOI CMOS Using Laser Spike Anneal (2006)

We have investigated the impact of laser spike anneal (LSA) on the performance of ultra-thin SOI MOSFETs. LSA was found to significantly reduce the parasitic external resistance in UTSOI devices. Reduced external resistance in conjunction with improved gate activation resulted in a substantial improvement in nFET performance. A conventional spike RTA followed by LSA at 1300C enhances nFET drive current, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> , by 20% and the effective drive current, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> , by 30% (at I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> equiv 1 muA/mum). The RTA+LSA approach was found to have a smaller impact on pFET performance. This is attributed to boron loss due to segregation into the buried oxide (BOX) during the RTA. The RTA+LSA process also resulted in improved AC performance (~ 10% improvement in ring oscillator stage delay at fixed leakage current) compared to an RTA-only process. We have found that an LSA-only process significantly suppresses boron segregation and increases dopant activation, resulting in a 50% reduction in the p-type sheet resistance when compared to a conventional high temperature RTA-only process. The introduction of LSA provides a path for high performance UTSOI CMOS
Pre-treatment breast MRI and diffuse optical spectroscopic tomography can predict complete response to neoadjuvant chemotherapy (2016)

Analysis of breast DCE-MR and NIR tomography imaging of 17 patients undergoing NAC showed combined pre-TX contrast intensity and HbT were statistically significant in differentiating the patients with versus without complete pathological response (AUC=0.94).
Insulin Is a Superior Antidote for Cardiovascular Toxicity Induced by Verapamil in the Anesthetized Canine (1994)

KLINE, JEFFREY A.; TOMASZEWSKI, CHRISTIAN A.; SCHROEDER, J. DAVID; RAYMOND, RICHARD M.Author Information
Genotype × Environment Interaction for Grain Color in Hard White Spring Wheat (2003)

Improvement of grain color in hard white spring wheat ( Triticum aestivum L.) breeding programs depends on understanding the influences of genotype (G), environment (E), and their interaction (G × E). The objectives of this study were to quantify genetic variability for grain color and assess the nature of the G × E interaction in determining grain color in 79 spring wheat genotypes. Twelve check cultivars [seven hard red (HR), four hard white (HW), and one soft white (SW)] and 67 white‐seeded Australian (AUS) accessions were grown at two locations across 2 yr. Wheat genotypes differed significantly in agronomic traits, grain protein, and kernel hardness. Grain and meal color were quantified using Hunterlab colorimeter values. Whole grain color values without ( L = 40.9–50.4 units; a = 7.0–8.3; b = 13.6–19.1) and with NaOH treatment ( L = 22.7–38.1; a = 7.7–9.7; b = 9.2–17.9) varied among genotypes. Using ground meal, color values ( L = 80.1–84.9; a = 1.8–2.6; b = 8.9–11.8), yellow pigment content (2.5–4.8 μg g −1 ), and lutein content (1.8–3.7 μg g −1 ) varied among genotypes. Genotype × location (L) interactions were not significant for colorimetric and pigmentation variables. The Azallini and Cox test detected one crossover G × year (Y) interaction for grain a ‐value (without NaOH), one for grain b ‐value (without NaOH), and 12 for lutein content. Genetic variation exists for grain color among HW genotypes. The noncrossover nature of G × E interactions for grain color indicates that white‐seeded genotypes selected as superior in one environment will be superior in other environments.
The design and in vivo testing of a locally stiffness-matched porous scaffold (2019)

An increasing volume of work supports utilising the mechanobiology of bone for bone ingrowth into a porous scaffold. However, typically during in vivo testing of implants, the mechanical properties of the bone being replaced are not quantified. Consequently there remains inconsistencies in the literature regarding 'optimum' pore size and porosity for bone ingrowth. It is also difficult to compare ingrowth results between studies and to translate in vivo animal testing to human subjects without understanding the mechanical environment. This study presents a clinically applicable approach to determining local bone mechanical properties and design of a scaffold with similar properties. The performance of the scaffold was investigated in vivo in an ovine model. The density, modulus and strength of trabecular bone from the medial femoral condyle from ovine bones was characterised and power-law relationships were established. A porous titanium scaffold, intended to maintain bone mechanical homeostasis, was additively manufactured and implanted into the medial femoral condyle of 6 ewes. The stiffness of the scaffold varied throughout the heterogeneous structure and matched the stiffness variation of bone at the surgical site. Bone ingrowth into the scaffold was 10.73±2.97% after 6 weeks. Fine woven bone, in the interior of the scaffold, and intense formations of more developed woven bone overlaid with lamellar bone at the implant periphery were observed. The workflow presented will allow future in vivo testing to test specific bone strains on bone ingrowth in response to a scaffold and allow for better translation from in vivo testing to commercial implants.
Co-Silencing of Tissue Transglutaminase-2 and Interleukin-15 Genes in a Celiac Disease Mimetic Mouse Model Using a Nanoparticle-in-Microsphere Oral System (2021)

Celiac disease is a chronic inflammatory condition characterized by activation of the immune system in response to deamidation of gluten peptides brought about by tissue transglutaminase-2 (TG2). Overexpression of interleukin-15 (IL-15) in the intestinal epithelium and the lamina propria leads to the dysregulation of the immune system, leading to epithelial damage. The goal of this study was to develop an RNA interference therapeutic strategy for celiac disease using a combination of TG2 and IL-15 gene silencing in the inflamed intestine. TG2 and IL-15 silencing siRNA sequences, along with scrambled control, were encapsulated in a nanoparticle-in-microsphere oral system (NiMOS) and administered in a poly(I:C) mouse model of celiac disease. Single TG2 and IL-15 siRNA therapy and the combination showed effective gene silencing in vivo. Additionally, it was found that IL-15 gene silencing alone and combination in the NiMOS significantly reduced other proinflammatory cytokines. The tissue histopathology data also confirmed a reduction in immune cell infiltration and restoration of the mucosal architecture and barrier function in the intestine upon treatment. Overall, the results of this study show evidence that celiac disease can be potentially treated with an oral microsphere formulation using a combination of TG2 and IL-15 RNA interference therapeutic strategies.
Troubleshooting Transiently-Recurring Errors in Production Systems with Blame-Proportional Logging (2018)

Many problems in production systems are transiently recurring— they occur rarely, but when they do, they recur for a short period of time. Troubleshooting these problems is hard as they are rare enough to be missed by sampling techniques, and traditional postmortem analyses of runtime logs suffer either from low-fidelity of logging too little or from the overhead of logging too much. This paper proposes AUDIT, a system specifically designed for troubleshooting transiently-recurring problems in cloud-based production systems. The key idea is to use lightweight triggers to identify the first occurrence of a problem and then to use its recurrences to perform blame-proportional logging. When a problem occurs, AUDIT automatically assigns a blame rank to methods in the application based on their likelihood of being relevant to the root-cause of the problem. Then AUDIT enables heavy-weight logging on highly-ranked methods for a short period of time. Over a period of time, logs generated by a method is proportional to how often it is blamed for various misbehaviors, allowing developers to quickly find the root-cause of the problem. We have implemented AUDIT for cloud applications. We describe how to utilize system events to efficiently implement lightweight triggers and blame ranking algorithm, with negligible to
Association between markers of collagen turnover, arterial stiffness and left ventricular hypertrophy in chronic kidney disease (CKD): the Renal Research Institute (RRI)-CKD Study (2011)

Our results demonstrate the association of PIIINP (but not C1TP), a circulating biomarker of collagen synthesis with arterial stiffness (but not with LVMI) in a CKD cohort, independent of eGFR. This suggests that altered collagen turnover may play a role in the pathogenesis of arterial stiffness in CKD.
Scalable synthesis and polymerisation of a β-angelica lactone derived monomer (2020)

A new bio-based norbornene polymer was prepared starting from β-angelica lactone, prepared in a sustainable and scalable manner from the platform chemical levulinic acid. The new material displays transparency comparable to petrochemical-derived polynorbornene.
Effect of Graphite on the Mechanical and Petrophysical Properties of Class G Oil Well Cement (2023)

Casing cementing is one of the most crucial operations in the oil well drilling process since it determines the durability and stability of the well throughout its life. Different additives have been mixed into the oil well cement slurry to improve the properties of both the cement slurry and the solidified cement sheath. Graphite is a waste material with a huge potential to be utilized in cementing to improve the properties of the oil well cement and reduce the graphite waste content in the environment. This study intends to analyze the effect of graphite on alteration in properties of the cement compressive and tensile strength, Poisson's ratio, Young's modulus, porosity, and permeability for three days of curing. Based on the trend of the properties during the three days of curing, equations were established to describe the future change in cement properties with time. Two formulas of cement, the base (with no graphite) and graphite-based (with 0.2% by weight of cement graphite) were prepared in this study. The results showed that the graphite successfully increased the compressive strength, tensile strength, and Poisson's ratio of the cement sheath, throughout the curing process. Young's modulus was decreased after the incorporation of graphite which indicates an enhancement in cement resistance to shear forces. The porosity and permeability were also decreased indicating formation of a more densified cement sheath.
Genetic Incorporation of a Small, Environmentally Sensitive, Fluorescent Probe into Proteins in Saccharomyces cerevisiae (2009)

Here, we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), can be genetically incorporated into proteins in yeast with excellent selectivity and efficiency by means of an orthogonal tRNA/aminoacyl-tRNA synthetase pair. This small, environmentally sensitive fluorophore was site-specifically incorporated into Escherichia coli glutamine binding protein and used to directly probe local structural changes caused by ligand binding. The small size of Anap and the ability to introduce it by simple mutagenesis at defined sites in the proteome make it a useful local probe of protein structure, molecular interactions, protein folding, and localization.
High-speed and transoceanic distance transmission with hybrid Raman-EDFA and coded modulation (2015)

We review recent high-capacity ultra-long haul experiments using hybrid Raman-EDFAs with optimized nonlinear performance and coded modulation with variable spectral efficiency. We discuss techniques that enabled record capacity (54Tb/s over 9,150km) and record capacity-distance product 534Pb/s*km (52.2Tb/s over 10,230km) demonstrations.
Structural and Biochemical Evaluation of the Interaction of the Phosphatidylinositol 3-Kinase p85α Src Homology 2 Domains with Phosphoinositides and Inositol Polyphosphates (1999)

Src homology 2 (SH2) domains exist in many intracellular proteins and have well characterized roles in signal transduction. SH2 domains bind to phosphotyrosine (Tyr(P))-containing proteins. Although tyrosine phosphorylation is essential for protein-SH2 domain interactions, the binding specificity also derives from sequences C-terminal to the Tyr(P) residue. The high affinity and specificity of this interaction is critical for precluding aberrant cross-talk between signaling pathways. The p85alpha subunit of phosphoinositide 3-kinase (PI 3-kinase) contains two SH2 domains, and it has been proposed that in competition with Tyr(P) binding they may also mediate membrane attachment via interactions with phosphoinositide products of PI 3-kinase. We used nuclear magnetic resonance spectroscopy and biosensor experiments to investigate interactions between the p85alpha SH2 domains and phosphoinositides or inositol polyphosphates. We reported previously a similar approach when demonstrating that some pleckstrin homology domains show binding specificity for distinct phosphoinositides (Salim, K., Bottomley, M. J., Querfurth, E., Zvelebil, M. J., Gout, I., Scaife, R., Margolis, R. L., Gigg, R., Smith, C. I., Driscoll, P. C., Waterfield, M. D., and Panayotou, G. (1996) EMBO J. 15, 6241-6250). However, neither SH2 domain exhibited binding specificity for phosphoinositides in phospholipid bilayers. We show that the p85alpha SH2 domain Tyr(P) binding pockets indiscriminately accommodate phosphoinositides and inositol polyphosphates. Binding of the SH2 domains to Tyr(P) peptides was only poorly competed for by phosphoinositides or inositol polyphosphates. We conclude that these ligands do not bind p85alpha SH2 domains with high affinity or specificity. Moreover, we observed that although wortmannin blocks PI 3-kinase activity in vivo, it does not affect the ability of tyrosine-phosphorylated proteins to bind to p85alpha. Consequently phosphoinositide products of PI 3-kinase are unlikely to regulate signaling through p85alpha SH2 domains.
Sporiolides A and B, New Cytotoxic Twelve-Membered Macrolides from a Marine-Derived Fungus Cladosporium Species (2004)

Two new cytotoxic twelve-membered macrolides, sporiolides A (1) and B (2), were isolated from the cultured broth of a fungus Cladosporium sp., which was separated from an Okinawan marine brown alga Actinotrichia fragilis, and the structures were elucidated by spectroscopic data. Sporiolides A (1) and B (2) exhibited cytotoxicity against murine lymphoma L1210 cells. Spoliolide A (1) showed antifungal activity against Cryptococcus neoformans and Neurospora crassa.