gebhart/patrepeval huggingface dataset:
Simplified kinetic study of the reaction between perfluoro-methyl-hypofluorite and perfluoro-olefins (2008)

In the reaction between perfluoroolefins and perfluoroalkylhypofluorites [1] the existence of two different free radical reaction mechanisms is demonstrated by the presence of characteristic by-products. &#13;\nIn particular in the reaction between trifluoromethyl hypofluorite and highly reactive perfluoroolefins like CF2=CFOCF3 and CF2=CF2, the free radical oligomerization and dimerization products can be suppressed by utilizing the opportune experimental conditions.&#13;\nThese experimental conditions are characterized by the presence of hypofluorite during the addition reaction and can be performed by adding the olefin to the hypofluorite, these conditions herein referred as “Reverse hypofluorite addition”. are different from the standard methodologies described in the literature where generally the hypofluorite is added to the olefin. &#13;\nThe main products of the addition of CF3OF to CF2=CFOCF3 are perfluoro-2,2-bis-(methoxy)-ethane and perfluoro-1,3-bis-(methoxy)-ethane [2] in the molar ratio of 20% and 80% respectively.&#13;\nWe found experimental evidence for the termination products peroxide CF3OOCF3 and perfluoroethers C8F18O4 respectively. The first termination product CF3OOCF3 was present at high amount in the reaction where the CF3OF concentration was maintained always above zero and substantially constant, on the contrary the termination products C8F18O4 were completely absent. In this conditions the oligomerization and polymerization of the perfluoroolefins were also suppressed, as well as in the case of the very reactive TFE.&#13;\n&#13;\n[1] W. Navarrini, V. Tortelli, A. Russo, S. Corti, J. Fluorine Chem. 95(2),(1999)27-39&#13;\n[2] W. Navarrini, G. Resnati, P. Metrangolo, M. Cantini, F. Venturini, IT Patent app. MI2007A001384 (2007).
Innovative lateral field plates by gate fingers on STI regions in deep submicron CMOS (2008)

This paper demonstrates experimentally a novel design of medium voltage MOSFETs in 65nm baseline low-voltage CMOS with state-of-the-art Ron performance. The HV capability is achieved through layout innovation independently from the available process. We demonstrate that gate fingers on STI regions interleaving the drain extension can be used as field plates enhancing the reverse voltage capability of EDMOS transistors. In this layout definition of lateral field plates, the effective field plate capacitance is determined by the lateral distance between the gate finger and the drain extension. Such an implementation allows process-less field plate capacitors graded along the drain extension enabling more flexible electrical field shaping as compared to classical field plates in the dielectric stack. A substantial (~1.65x) improvement of Ron vs. BVds is demonstrated with such gate finger field plates.
Characterization of Tumor-immune Microenvironment by High-throughput Image Analysis of CD8 Immunohistochemistry Combined With Modified Masson’s Trichrome (2021)

With the advent of checkpoint inhibitors, there is increasing need to study the dynamics of CD8+ T-cells in the tumor microenviroment. In this article, we describe a semi-automated method to quantify and interrogate spatial relationships between T-cells and collagenous stroma in human and mouse tissue samples. The assay combines CD8 immunohistochemistry with modified Masson's trichrome. Slides are scanned and digital images are analyzed using an adjustable MATLAB algorithm, allowing for high-throughput quantification of cytotoxic T-cells and collagen. This method provides a flexible tool for unbiased quantification of T-cells and their interactions with tumor cells and tumor microenvironment in tissue samples.
TNF-α mediates obstruction-induced renal tubular cell apoptosis and proapoptotic signaling (2004)

Obstruction of the upper urinary tract induces a progressive loss in renal mass through apoptotic renal cell death. Although TNF-alpha has been implicated in ischemia-reperfusion-induced apoptotic renal cell death, its role in obstructive renal cell apoptosis remains unknown. To study this, male Sprague-Dawley rats were subjected to left unilateral ureteral obstruction vs. sham operation. Twenty-four hours before surgery and every 84 h thereafter, rats received either vehicle or a pegylated form of soluble TNF receptor type 1 (PEG-sTNFR1). The kidneys were harvested 1, 3, or 7 days postoperatively, and tissue samples were subsequently analyzed for TNF-alpha (ELISA, RT-PCR), Fas ligand (RT-PCR), apoptosis (TUNEL, ELISA), and caspase 8 and 3 activity (Western blot). Renal obstruction induced increased tissue TNF-alpha and Fas ligand mRNA levels, TNF-alpha protein production, apoptotic renal tubular cell death, and elevated caspase 8 and 3 activity, whereas treatment with PEG-sTNFR1 significantly reduced obstruction-induced TNF-alpha production, renal tubular cell apoptosis, and caspase activity. PEG-sTNFR1 did not significantly alter Fas ligand expression. These results demonstrate that TNF-alpha mediates obstruction-induced renal tubular cell apoptosis and proapoptotic signaling and identify TNF-alpha neutralization as a potential therapeutic option for the amelioration of obstruction-induced renal injury.
Analysis of an algorithm for irregular LDPC code construction (2004)

This work presents a rigorous analysis of an algorithm proposed by Tian et al. (2003) for the construction of irregular LDPC codes with reduced stopping sets and low error floors. Computation of the expected number of stopping sets of a given size proves that the algorithm significantly outperforms a random construction. We show that the algorithm provably reduces the expected number of stopping sets up to a certain size (based on the input parameters). The expected number of cycles of a given size is computed for both constructions.
Pharmacokinetic and Pharmacodynamic Modeling of a Copper‐Selective Chelator (TETA) in Healthy Adults (2009)

The population pharmacokinetics (PK) and pharmacodynamics (PD) of triethylenetetramine (TETA) dihydrochloride (trientine, GC811007) administered orally as 100-, 300-, 600-, or 1800-mg twice-daily doses were assessed in healthy adult male and female volunteers. This study was a randomized, double-blind, placebo-controlled, group-sequential, dose-escalating design. Forty participants, 10 per dose level (8 receiving TETA, 2 receiving placebo), received twice-daily doses for 14 consecutive days. A 2-compartment model for the PK and a linear direct effect model for drug-induced copper excretion (PD) were employed. The population PK/PD model was applied using the NONMEM software. Covariates tested were glomerular filtration rate (GFR), body weight, and gender. Multiple daily doses of TETA were safe and generally well tolerated. The linear 2-compartment model with first-order absorption well characterized the serum concentration data. Although its role was small, GFR had a statistically significant (P < .05) influence on systemic clearance (CL/F). The augmentation of copper excretion was well described by a direct linear model in which the slope was related to GFR and gender (P < .001). The intersubject coefficient of variation was 22.2% for slope (SL) and 82.5% for intercept (ER0). TETA has consistent single/multiple-dose pharmacokinetics and dose-proportional and serum concentration-proportional effects on enhancing copper excretion.
Efficacy of Upadacitinib in a Randomized Trial of Patients With Active Ulcerative Colitis (2020)

In a phase 2b trial, 8 weeks of treatment with upadacitinib was more effective than placebo for inducing remission in patients with moderately to severely active UC. (ClinicalTrials.gov, Number: NCT02819635).
A new single-layer plasma-developable photoresist using the catalysed crosslinking of poly(4-hydroxystyrene)via photogenerated acid (1994)

A new single-layer, dry developable chemically amplified resist is described. The resist consists of poly(4-hydroxystyrene), 1,2,4,5-tetra(acetoxymethyl)benzene and triphenylsulfonium hexafluoroantimonate, and functions via crosslinking as a result of an acid-catalysed electrophilic aromatic substitution reaction. In contrast to the normal wet resist development process that leads to a negative-tone image, a gas-phase modification of the exposed polymer film, followed by reactive oxygen etching, leads to a positive-tone image. The post-exposure modification is accomplished using gaseous 1,1,1,3,3,3-hexamethyldisilazane, a reagent that is able to diffuse selectively into the non-exposed, non-crosslinked regions of the polymer film to react with the poly(4-hydroxystyrene) and form silyl ethers. Dry-development of the treated film in an O2 plasma removes those areas of the film that have remained unsilylated, producing a positive-tone relief image.
Regulation of Casein Kinase-2 (CK2) Activity by Inositol Phosphates (2004)

Casein kinase 2 (CK2) was one of the first protein kinases to be discovered and has been suggested to be responsible for as much as one-fifth of the eukaryotic phosphoproteome. Despite being responsible for the phosphorylation of a vast array of proteins central to numerous dynamic cellular processes, the activity of CK2 appears to be unregulated. In the current study, we identified a protein kinase activity in rat liver supernatant that is up-regulated by inositol 1,3,4,5-tetrakisphosphate (IP4) and inositol hexakisphosphate (IP6). The substrate for the inositol phosphate-regulated protein kinase was identified as a phosphatidylcholine transfer protein-like protein. Using the phosphorylation of this substrate in an assay, we purified the inositol phosphate-regulated protein kinase and determined it to be CK2. Bacterially expressed recombinant CK2, however, showed very high basal activity and was only modestly activated by IP6 and not regulated by IP. We found that an endogenous component present in rat liver supernatant was able to inhibit both recombinant and liver-purified CK2 basal activity. Under these conditions, recombinant CK2 catalytic activity could be increased substantially by IP4, inositol 1,3,4,5,6-pentakisphosphate (IP5), and IP6. We concluded that, contrary to the previously held view, CK2 can exist in a state of low constitutive activity allowing for its regulation by inositol phosphates. The ability of the higher inositol phosphates to directly stimulate CK2 catalytic activity provides the first evidence that these signaling molecules can operate via a direct control of protein phosphorylation.
Intermediate CAG Repeat Expansion in the ATXN2 Gene Is a Unique Genetic Risk Factor for ALS−A Systematic Review and Meta-Analysis of Observational Studies (2014)

Amyotrophic lateral sclerosis (ALS) is a rare degenerative condition of the motor neurons. Over 10% of ALS cases are linked to monogenic mutations, with the remainder thought to be due to other risk factors, including environmental factors, genetic polymorphisms, and possibly gene-environmental interactions. We examined the association between ALS and an intermediate CAG repeat expansion in the ATXN2 gene using a meta-analytic approach. Observational studies were searched with relevant disease and gene terms from MEDLINE, EMBASE, and PsycINFO from January 2010 through to January 2014. All identified articles were screened using disease terms, gene terms, population information, and CAG repeat information according to PRISMA guidelines. The final list of 17 articles was further evaluated based on the study location, time period, and authors to exclude multiple usage of the same study populations: 13 relevant articles were retained for this study. The range 30-33 CAG repeats in the ATXN2 gene was most strongly associated with ALS. The meta-analysis revealed that the presence of an intermediate CAG repeat (30-33) in the ATXN2 gene was associated with an increased risk of ALS [odds ratio (OR) = 4.44, 95%CI: 2.91-6.76)] in Caucasian ALS patients. There was no significant difference in the association of this CAG intermediate repeat expansion in the ATXN2 gene between familial ALS cases (OR = 3.59, 1.58-8.17) and sporadic ALS cases (OR = 3.16, 1.88-5.32). These results indicate that the presence of intermediate CAG repeat expansion in the ATXN2 gene is a specific genetic risk factor for ALS, unlike monogenic mutations with an autosomal dominant transmission mode, which cause a more severe phenotype of ALS, with a higher prevalence in familial ALS.
Utilizing flip angle/TR equivalence to reduce breath hold duration in hyperpolarized 129Xe 1‐point Dixon gas exchange imaging (2021)

Using flip angle/TR equivalence, hyperpolarized <sup>129</sup> Xe gas exchange images can be acquired via the 1-point Dixon technique in as little as 6 s, compared to ~15 s for previously reported parameter settings. The resulting images from this accelerated scan have no significant differences from the standard method in qualitative appearance or quantitative metrics.
Identification of the Phosphorylation Sites of Cytosolic Phospholipase A2 in Agonist-stimulated Human Platelets and HeLa Cells (1998)

cPLA 2 , cytosolic phospholipase A 2 ; MAPK, mitogen-activated protein kinase; Sf9 cell, Spodoptera frugiperda cell; HPLC, high performance liquid chromatography; p38 mapk , 38-kDa stress-activated protein kinase; SB 203580, 4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)imidazole; PAGE, polyacrylamide gel electrophoresis; mbHPLC, microbore HPLC; MAPKAP-K2, MAPK-activated protein kinase 2; SB 202190, 4-(4-fluorophenyl)-2-(4hydroxyphenyl)-5-(4-pyridyl) imidazole; S437-PP, serine 437-containing phosphopeptide;
Correlating AFM Probe Morphology to Image Resolution for Single-Wall Carbon Nanotube Tips (2004)

Scanning and transmission electron microscopy were used to image hundreds of single-wall carbon nanotube probes and to correlate probe morphology with AFM image resolution. Several methods for fabricating such probes were evaluated, resulting in a procedure that produces image-quality single-wall nanotube probes at a rate compatible with their routine use. Surprisingly, about one-third of the tips image with resolution better than the nanotube probe diameter and, in exceptional cases, with resolution better than 1 nm. This represents the highest lateral resolution reported to date for a SWNT probe.
Design and Characterization of a Burst Mode 20 Mfps Low Noise CMOS Image Sensor (2023)

This paper presents a novel ultra-high speed, high conversion-gain, low noise CMOS image sensor (CIS) based on charge-sweep transfer gates implemented in a standard 180 nm CIS process. Through the optimization of the photodiode geometry and the utilization of charge-sweep transfer gates, the proposed pixels achieve a charge transfer time of less than 10 ns without requiring any process modifications. Moreover, the gate structure significantly reduces the floating diffusion capacitance, resulting in an increased conversion gain of 183 µV/<i>e</i>-. This advancement enables the image sensor to achieve the lowest reported noise of 5.1 <i>e</i>- rms. To demonstrate the effectiveness of both optimizations, a proof-of-concept CMOS image sensor is designed, taped-out and characterized.
Sustainable Throughput of Wireless LANs with Multipacket Reception Capability under Bounded Delay-Moment Requirements (2010)

With the rapid proliferation of broadband wireless services, it is of paramount importance to understand how fast data can be sent through a wireless local area network (WLAN). Thanks to a large body of research following the seminal work of Bianchi, WLAN throughput under saturated traffic condition has been well understood. By contrast, prior investigations on throughput performance under unsaturated traffic condition was largely based on phenomenological observations, which lead to a common misconception that WLAN can support a traffic load as high as saturation throughput, if not higher, under nonsaturation condition. In this paper, we show through rigorous analysis that this misconception may result in unacceptable quality of service: mean packet delay and delay jitter may approach infinity even when the traffic load is far below the saturation throughput. Hence, saturation throughput is not a sound measure of WLAN capacity under nonsaturation condition. To bridge the gap, we define safe-bounded-mean-delay (SBMD) throughput and safe-bounded-delay-jitter (SBDJ) throughput that reflect the actual network capacity users can enjoy when they require finite mean delay and delay jitter, respectively. Our earlier work proved that in a WLAN with multi-packet reception (MPR) capability, saturation throughput scales superlinearly with the MPR capability of the network. This paper extends the investigation to the nonsaturation case and shows that superlinear scaling also holds for SBMD and SBDJ throughputs. Our results here complete the demonstration of MPR as a powerful capacity-enhancement technique for WLAN under both saturation and nonsaturation conditions.
From PtCl2‐ and Acid‐Catalyzed to Uncatalyzed Cycloisomerization of 2‐Propargyl Anilines: Access to Functionalized Indoles (2007)

On the move: PtCl2-catalyzed electrophilic activation of an alkyne moiety triggers a heterocyclization accompanied by migrations of both an allyl group and an acetate group to produce an indole (see scheme). Variation of the reaction conditions (particularly the temperature) as well as substituents at the propargylic position and on the nitrogen atom allows easy and versatile access to a myriad of indole substrates.
Use of C. elegans as pluricellular model to study resistance/sensitivity mechanisms associated to cisplatin-based chemotherapy (2015)

Trabajo presentado en la V Spanish Worm Meeting, celebrada en Salamanca el 5 y 6 de marzo de 2015.
Crystal Growth and Luminescence Properties of Pr-Doped LiYF4and LiCaAlF6 (2009)

Pr-doped LiYF4 (YLF) and LiCaAlF6 (LiCAF) single crystals were grown by the micro-pulling-down (µ-PD) method. The crystals were transparent, 2.0 mm in diameter, and 40–50 mm in length. Neither visible inclusions nor cracks were observed. Transmittance, reflectance, and X-ray-excited emission spectra of Pr-doped YLF and LiCAF were measured. For both crystals, approximately 80% transmittance and 3% reflectance were achieved at visible wavelengths. Emission peaks due to Pr3+ 5d–4f transitions at approximately 220–250, 270, 330, and 410 nm were observed for both crystals.
Controlling Crystal Microstructure To Minimize Loss in Polymer Dielectrics (2017)

A model semicrystalline polymer, poly(ethylene naphthalate) (PEN), was used to examine how morphological factors inhibit chain segment relaxations that contribute to dielectric loss. This was achieved by manipulating the extent of crystallization and the crystalline microstructure through a combination of annealing and uniaxial drawing and investigating the effects on dielectric performance. Varying crystallization conditions influenced the dynamic Tg and extent of rigid amorphous fraction formation but had only a moderate effect on loss magnitude. Film orientation, however, greatly reduced loss through strain-induced crystallization and the development of oriented amorphous mesophasic regions. Postdrawing annealing conditions were capable of further refining the crystal microstructure and, in turn, the dielectric properties. These findings demonstrate that the semicrystalline polymer morphology can have a very significant influence on amorphous chain relaxations that contribute to dielectric loss, and understanding how processing conditions affect morphology is critical to the rational design of polymer dielectrics.
GTF3A mutations predispose to herpes simplex encephalitis by disrupting biogenesis of the host-derived RIG-I ligand RNA5SP141 (2022)

Herpes simplex virus 1 (HSV-1) infects several billion people worldwide and can cause life-threatening herpes simplex encephalitis (HSE) in some patients. Monogenic defects in components of the type I interferon system have been identified in patients with HSE, emphasizing the role of inborn errors of immunity underlying HSE pathogenesis. Here, we identify compound heterozygous loss-of-function mutations in the gene <i>GTF3A</i> encoding for transcription factor IIIA (TFIIIA), a component of the RNA polymerase III complex, in a patient with common variable immunodeficiency and HSE. Patient fibroblasts and <i>GTF3A</i> gene-edited cells displayed impaired HSV-1-induced innate immune responses and enhanced HSV-1 replication. Chromatin immunoprecipitation sequencing analysis identified the 5<i>S</i> ribosomal RNA pseudogene 141 (<i>RNA5SP141</i>), an endogenous ligand of the RNA sensor RIG-I, as a transcriptional target of TFIIIA. <i>GTF3A</i> mutant cells exhibited diminished <i>RNA5SP141</i> expression and abrogated RIG-I activation upon HSV-1 infection. Our work unveils a crucial role for TFIIIA in transcriptional regulation of a cellular RIG-I agonist and shows that <i>GTF3A</i> genetic defects lead to impaired cell-intrinsic anti-HSV-1 responses and can predispose to HSE.
Identifying Capacity Limitations in the Li/Oxygen Battery Using Experiments and Modeling (2011)

The Li/oxygen battery may achieve a high practical specific energy as its theoretical specific energy is Li assuming is the product. To help understand the physics of the Li/oxygen battery we present the first physics-based model that incorporates the major thermodynamic, transport, and kinetic processes. We obtain a good match between porous-electrode experiments and simulations by using an empirical fit to the resistance of the discharge products (which include carbonates and oxides when using carbonate solvents) as a function of thickness that is obtained from flat-electrode experiments. The experiments and model indicate that the discharge products are electronically resistive, limiting their thickness to tens of nanometers and their volume fraction in one of our discharged porous electrodes to a few percent. Flat-electrode experiments, where pore clogging is impossible, show passivation similar to porous-electrode experiments and allow us to conclude that electrical passivation is the dominant capacity-limiting mechanism in our cells. Although in carbonate solvents is not the dominant discharge product, we argue that the implications of this model, (i.e., electrical passivation by the discharge products limits the capacity) also apply if is the discharge product, as it is an intrinsic electronic insulator.
Microbioreactor arrays with integrated mixers and fluid injectors for high-throughput experimentation with pH and dissolved oxygen control (2006)

We have developed an integrated array of microbioreactors, with 100 microL working volume, comprising a peristaltic oxygenating mixer and microfluidic injectors. These integrated devices were fabricated in a single chip and can provide a high oxygen transfer rate (k(L)a approximately 0.1 s(-1)) without introducing bubbles, and closed loop control over dissolved oxygen and pH (+/-0.1). The system was capable of supporting eight simultaneous Escherichia coli fermentations to cell densities greater than 13 g-dcw L(-1) (1 cm OD(650 nm) > 40). This cell density was comparable to that achieved in a 4 litre reference fermentation, conducted with the same strain, in a bench scale stirred tank bioreactor and is more than four times higher than cell densities previously achieved in microbioreactors. Bubble free oxygenation permitted near real time optical density measurements which could be used to observe subtle changes in the growth rate and infer changes in the state of microbial genetic networks. Our system provides a platform for the study of the interaction of microbial populations with different environmental conditions, which has applications in basic science and industrial bioprocess development. We leverage the advantages of microfluidic integration to deliver a disposable, parallel bioreactor in a single chip, rather than robotically multiplexing independent bioreactors, which opens a new avenue for scaling small scale bioreactor arrays with the capabilities of bench scale stirred tank reactors.