gebhart/patrepeval huggingface dataset:
Supplemental Figures 1-6 from New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice (2023)

&lt;p&gt;Supplemental Figures 1-6. Supplemental Figure 1. A typical KRAS Sanger dye termination sequencing trace for a pancreatic cancer sample. The arrow indicates the mutation site; the black peak represents a wild-type allele and the red peak represents the mutant allele. Supplemental Figure 2. (A) Copy numbers per sample of methylated KCNK12 assayed form pancreatic juice of patients with normal pancreas (NP), chronic pancreatitis (CP), high grade dysplastic main-duct intraductal pancreatic mucinous neoplasm (IPMN), and pancreatic cancer (PC) were used to calculate (B) receiver operating characteristics curves of methylated KCNK12 for the detection of PC in comparison to NP (black) and CP (grey). Supplemental Figure 3. (A) Copy numbers per sample of methylated CLEC11A assayed form pancreatic juice of patients with normal pancreas (NP), chronic pancreatitis (CP), high grade dysplastic main-duct intraductal pancreatic mucinous neoplasm (IPMN), and pancreatic cancer (PC) were used to calculate (B) receiver operating characteristics curves of methylated CLEC11A for the detection of PC in comparison to NP (black) and CP (grey). Supplemental Figure 4. (A) Copy numbers per sample of methylated NDRG4 assayed form pancreatic juice of patients with normal pancreas (NP), chronic pancreatitis (CP), high grade dysplastic main-duct intraductal pancreatic mucinous neoplasm (IPMN), and pancreatic cancer (PC) were used to calculate (B) receiver operating characteristics curves of methylated NDRG4 for the detection of PC in comparison to NP (black) and CP (grey). Supplemental Figure 5. (A) Genomic copy numbers of methylated IKZF1 in normal pancreas (NP), chronic pancreatitis (CP), high grade dysplastic main-duct intraductal pancreatic mucinous neoplasm (IPMN), and pancreatic cancer (PC) were used to calculate (B) receiver operating characteristics curves of methylated IKZF1 for the detection of PC in comparison to NP (black) and CP (grey). Supplemental Figure 6. (A) Genomic copy numbers of methylated PKRCB in normal pancreas (NP), chronic pancreatitis (CP), high grade dysplastic main-duct intraductal pancreatic mucinous neoplasm (IPMN), and pancreatic cancer (PC) were used to calculate (B) receiver operating characteristics curves of methylated PKRCB for the detection of PC in comparison to NP (black) and CP (grey).&lt;/p&gt;
Web Service Security (2010)

Service Oriented Architecture is now the de facto standard that allows companies to open their services to others. Nowadays customers can build their own architectures and provide services by selecting the required interfaces from different business partners. Services can be combined in a loosely-coupled fashion over the network. But this new way of providing services across geographically dislocated organizations have significantly changed the security models. This new paradigm has forced security models to evolve from point-to-point to end-to-end security. However, this evolution is not straightforward and naive usage of the new models, such as WS-Security, can lead to security flaws. Our work addresses several security properties at different layers of the Web Service stack. In this context, we have proposed three complementary contributions. First, we proposed an approach named business process security view that is similar to view materialization in relational databases. This concept enhances security in cross-organizational business processes by ensuring the need-to-know principle on workflows. To achieve this we formalized business processes by regular expressions called flow control rules. In combination with a security specification, that expresses conditional accessibility based on the actual data flowing across business process, we presented an algorithm for the automatic derivation of such views. Second, we tackled security at the message layer, namely SOAP messages. These messages are prone to attacks that can lead to code injection, unauthorized accesses, identity theft, and more. This type of attacks, classified in literature as XML rewriting attacks, are all based on unauthorized, yet possible, modifications of SOAP messages. We proposed a formal solution to XML rewriting attacks on SOAP messages using regular tree grammar. The formal solution proposed here is a context-sensitive XML signature. To address the additional requirements of end-to-end security, where a SOAP message can pass through several intermediaries before reaching the final receiver, an adaptive variant of context-sensitive signature is also proposed. The solution addresses all known forms of XML rewriting attacks. Finally, we assess security properties by the mean of passive testing. This methodology relies on the execution trace of a system to validate security properties. We made an initial demonstration of this methodology by applying it to an industrial case study, SAP R/3. Then we adapted this methodology for SOA environment. It involved the development of a non-intrusive trace collection module dedicated to SOA, integrated to our case study prototype. This flexible methodology allowed us to validate properties like SoD that we addressed at business process level. All this research work has been implemented around an e-business case study.
Biosynthesis of Cyclic Monoterpenes (1986)

Cyclization of an allylic pyrophosphate is a key step in the biosynthesis of most monoterpenes. Early hypotheses concerning the nature of the acyclic precursor and the cyclization process are first described, and chemical models for the cyclization presented. Following a review of several representative cyclase enzymes and the reactions that they catalyze, a series of stereochemical and mechanistic experiments with partially purified cyclases are reported. The results of these studies have allowed a detailed description of events at the active site and the formulation of a unified stereochemical scheme for the multistep isomerization-cyclization reaction by which the universal precursor geranyl pyrophosphate is transformed to cyclic monoterpenes.
Plasmon–Interband Coupling in Nickel Nanoantennas (2014)

Plasmonic excitations are usually attributed to the free electron response at visible frequencies in the classic plasmonic metals Au and Ag. However, the vast majority of metals exhibit spectrally localized interband transitions or broad interband transition backgrounds in the energy range of interest for nanoplasmonics. Nevertheless, the interaction of interband transitions with localized plasmons in optical nanoantennas has hitherto received relatively little attention, probably because interband transitions are regarded as highly unwanted due to their strong damping effect on the localized plasmons. However, with an increasing number of metals (beyond Au and Ag) being considered for nanoplasmonic applications such as hydrogen sensing (Pd), UV-SERS (Al), or magnetoplasmonics (Ni, Fe, Co), a deeper conceptual understanding of the interactions between a localized plasmon mode and an interband transition is very important. Here, as a generic example, we examine the interaction of a localized (in energy space) interband transition with spectrally tunable localized plasmonic excitations and unearth the underlying physics in a phenomenological approach for the case of Ni disk nanoantennas. We find that plasmon–interband interactions can be understood in the classical picture of two coupled harmonic oscillators, exhibiting the typical energy anticrossing fingerprint of a coupled system approaching the strong-coupling regime.
Underwater endoscopic mucosal resection of large colorectal lesions (2014)

In this prospective study, 11 consecutive patients with neoplastic colorectal lesions (median size 20 mm, range 15 - 25 mm) underwent endoscopic polyp removal by underwater endoscopic mucosal resection (EMR). Six lesions were removed en bloc and five lesions were removed by piecemeal resection. Pathological examination revealed seven R0 resections, and in four cases the pathology could not be determined. Two cases of procedure-related bleeding occurred but these were easily managed using hemostatic forceps and clip application. No perforations or delayed bleedings were observed. Underwater EMR is a relatively simple, safe, and useful method for the removal of large colorectal lesions.
Cylindrical CPW-fed and CPS-fed slot antennas (2009)

Cylindrical antennas are needed in applications which require mounting on curved surfaces. This article presents two new designs of antennas printed on cylindrical substrates. The first antenna is a dual frequency coplanar waveguide (CPW)-fed double folded slot antenna operating at 5 and 7 GHz. This antenna is matched to the feed line without external matching circuitry and exhibits a gain of about 3.2 dBi. It has a bidirectional pattern in the E-plane and a more omnidirectional pattern in the H-plane. The second antenna is a coplanar strips (CPS)-fed folded slot antenna operating at 7 GHz. Its gain is about 2.56 dBi. The experimental and numerical results are provided for the return loss and radiation patterns with good agreement.
A Nonparametric Super-Efficient Estimator of the Average Treatment Effect (2020)

Doubly robust estimators are a popular means of estimating causal effects. Such estimators combine an estimate of the conditional mean of the outcome given treatment and confounders (the so-called outcome regression) with an estimate of the conditional probability of treatment given confounders (the propensity score) to generate an estimate of the effect of interest. In addition to enjoying the double-robustness property, these estimators have additional benefits. First, flexible regression tools, such as those developed in the field of machine learning, can be utilized to estimate the relevant regressions, while the estimators of the treatment effects retain desirable statistical properties. Furthermore, these estimators are often statistically efficient, achieving the lower bound on the variance of regular, asymptotically linear estimators. However, in spite of their asymptotic optimality, in problems where causal estimands are weakly identifiable, these estimators may behave erratically. We propose new estimation techniques for use in these challenging settings. Our estimators build on two existing frameworks for efficient estimation: targeted minimum loss estimation and one-step estimation. However, rather than using an estimate of the propensity score in their construction, we instead opt for an alternative regression quantity when building our estimators: the conditional probability of treatment given the conditional mean outcome. We discuss the theoretical implications and demonstrate the estimators’ performance in simulated and real data.
Enhanced uptake of doxorubicin into bronchial carcinoma: beta-glucuronidase mediates release of doxorubicin from a glucuronide prodrug (HMR 1826) at the tumor site. (1997)

Lack of tumor selectivity is a severe limitation of cancer chemotherapy. Consequently, reducing dose-limiting organ toxicities such as the cardiac toxicity of doxorubicin (Dox) is of major clinical relevance. Approaches that would facilitate a more tumor-selective anticancer therapy by using nontoxic prodrugs that are converted to active anticancer agents at the tumor site have been the subject of intensive research. One potential method to overcome the cardiac toxicity of Dox is to apply a nontoxic, glucuronide prodrug (HMR 1826) from which Dox is released by the action of beta-glucuronidase, an enzyme present at high levels in many tumors. Using a recently developed, isolated, perfused human lung model, we compared the uptake of Dox into normal lung and lung tumors after a 2.5-h lung perfusion with doxorubicin (n = 8) and with the novel doxorubicin glucuronide prodrug (n = 8). Dox showed a poor uptake into lung tumors as compared with normal lung [mean Dox concentration at the end of perfusion, 1.78 +/- 3.11 (median, 0.66) microg/g versus 22.03 +/- 10.4 (median, 18.5) microg/g; P < 0.001]. However, after perfusion with HMR 1826, the level of Dox in tumor tissue was about 7-fold higher than after perfusion with Dox itself [14.04 +/- 12.9 (median, 12.9) microg/g versus 1.78 +/- 3.11 (median, 0.66) microg/g, P < 0.05, n = 8]. In vitro experiments showed a significantly higher beta-glucuronidase expression and activity in the tumors. The extent of in vitro cleavage of HMR 1826 by homogenized lung tissue was closely related to the content of beta-glucuronidase (r = 0.9834, P < 0.0001). When D-saccharolactone, a specific inhibitor of beta-glucuronidase, was added to the perfusate containing HMR 1826, no accumulation of Dox in lung tissue was seen. These data indicate that the high Dox levels achieved in the tumors with HMR 1826 resulted from cleavage of the prodrug by beta-glucuronidase at the tumor site. Thus, the problem of poor Dox uptake into lung tumors could be circumvented by applying the doxorubicin glucuronide prodrug. Several lines of evidence based on both ex vivo and in vitro results indicate that the approach described using a glucuronide prodrug may be useful in facilitating more selective delivery of chemotherapy to tumors in humans.
Nanoparticle Flow in Polymer Grafted Channels (2019)

A better understanding of the specifics of nanoparticle transport through channels with polymer coated walls is of great importance for various biological, technological, and analytical processes. Here, we study flow of bare and ligand-functionalized nanoparticles in channels grafted with polymer brushes using dissipative particle dynamics. A dimensionless relationship is established between the ratio of the particle and solvent mean velocities and the scaling factor that equals the ratio of the particle size to the channel width reduced by the hydrodynamic thickness of a polymer brush. The simulated particle velocity profiles are found to be in agreement with experiments on the flow of polystyrene beads in hard-wall channels with the same scaling factor. The fact that the dimensions of particles and channels in simulations and experiments differed by 3 orders of magnitude confirms that the simulation results can be used to model experimental systems of larger size, in particular, nanoparticle separation on polymer grafted chromatographic columns.
A multirate digital controller for a 1.5-kW electric vehicle battery charger (1997)

This paper describes a power electronic system that, among other possibilities, can be used to charge electric vehicle batteries. A large-signal linear multirate digital controller for the charging current permits the charger to track and deliver a desired current trajectory for a wide range of loads. This controller simultaneously ensures that the charger draws power from the electric utility with unity power factor. The analytical development of the controller and experimental results from a prototype charger are presented.
N-heterocyclic carbene Pt(ii) complexes from caffeine: synthesis, structures and photoluminescent properties (2011)

The caffeine-derived N-heterocyclic carbene (NHC) complex [Pt(II)(C^N)(NHC)Cl] (C^N = 2-phenylpyridine), 4 has the opposite stereochemistry and a shorter Pt-C(carbene) bond compared to that of an analogous benzimidazole-derived N,N-heterocyclic carbene (NNHC) Pt complex 2. These suggest a lower trans influence of pyridyl N compared to cyclometallated carbon and an increased Pt-NHC π-backbonding because of decreased π-donation resulting from conjugation to the electron deficient pyrimidine of caffeine. Complex 4 has a lower emission quantum yield (Φ) and is blue-shifted into the green region of the visible spectrum relative to non-carbene Pt(II) cyclometalated complex 5.
Supplemental Tables S1-S4 from An Effective Immuno-PET Imaging Method to Monitor CD8-Dependent Responses to Immunotherapy (2023)

&lt;p&gt;Supplemental Tables S1-S4: Ex vivo biodistribution of 89Zr-malDFO-169 cDb in wt and CD8-blocked ARK mice (S1); Ex vivo biodistribution of 89Zr-malDFO-169 cDb in the adoptive T cell transfer model (S2); Ex vivo biodistribution of 89Zr-malDFO-169 cDb in the anti-CD137/CT26 immunotherapy model (S3); 89Zr-malDFO-169 cDb ex vivo biodistribution analysis at 22 h post-injection of anti-PD-L1 partial responding (S4).&lt;/p&gt;
Activated Phosphatidylinositol 3-Kinase Is Sufficient to Mediate Actin Rearrangement and GLUT4 Translocation in 3T3-L1 Adipocytes (1996)

Insulin stimulation of 3T3-L1 adipocytes causes rapid translocation of actin and the GLUT4 glucose transporter to the plasma membrane. Both processes depend on the activity of phosphatidylinositol 3-kinase. Using single cell microinjection, we have transiently expressed a constitutively activated mutant of phosphatidylinositol 3-kinase, p110*, in 3T3-L1 adipocytes. Fluorescent detection of GLUT4 protein and actin within these cells demonstrates that expression of p110* is sufficient to cause translocation of GLUT4 to the plasma membrane and the formation of actin membrane ruffles. These effects are inhibited by wortmannin in the p110*-expressing cells, indicating that the phosphatidylinositol 3-kinase activity of the protein is required. Overexpression of an identical protein containing a point mutation in the kinase domain, p110*Deltakin, was incapable of mediating either action, confirming that neither the microinjection process nor a nonspecific effect of the protein was responsible for the observed effects. These data suggest that although insulin is capable of inducing numerous signaling pathways, the isolated activation of phosphatidylinositol 3-kinase can initiate the signaling cascade leading to both actin rearrangement and GLUT4 translocation in the absence of insulin stimulation.
Permanent Reversal of Diabetes in NOD Mice (2007)

We disagree with how J. Nishio et al. ([1][1]) represent our published data on the permanent reversal of type 1 diabetes in NOD mice ([2][2]). Nishio et al. state ([1][1]) that “a FCA alone control was not included in the report by Kodama et al. ” ([3][3]). Further, in their response to our
Biodegradable Dextran Nanogels for RNA Interference: Focusing on Endosomal Escape and Intracellular siRNA Delivery (2009)

Abstract The successful therapeutic application of small interfering RNA (siRNA) largely relies on the development of safe and effective delivery systems that are able to guide the siRNA therapeutics to the cytoplasm of the target cell. In this report, biodegradable cationic dextran nanogels are engineered by inverse emulsion photopolymerization and their potential as siRNA carriers is evaluated. The nanogels are able to entrap siRNA with a high loading capacity, based on electrostatic interaction. Confocal microscopy and flow cytometry analysis reveal that large amounts of siRNA‐loaded nanogels can be internalized by HuH‐7 human hepatoma cells without significant cytotoxicity. Following their cellular uptake, it is found that the nanogels are mainly trafficked towards the endolysosomes. The influence of two different strategies to enhance endosomal escape on the extent of gene silencing is investigated. It is found that both the application of photochemical internalization (PCI) and the use of an influenza‐derived fusogenic peptide (diINF‐7) can significantly improve the silencing efficiency of siRNA‐loaded nanogels. Furthermore, it is shown that an efficient gene silencing requires the degradation of the nanogels. As the degradation kinetics of the nanogels can easily be tailored, these particles show potential for intracellular controlled release of short interfering RNA.
Candidal Brain Abscess Associated with Vascular Invasion: A Devastating Complication of Vascular Catheter-Related Candidemia (1995)

We describe a patient who developed Candida albicans brain abscess associated with prominent vascular invasion following an episode of central venous catheter-related fungemia. The increasing population of immunosuppressed patients and the frequent use of broad-spectrum antimicrobials, corticosteroids, chemotherapeutics, organ transplantation, and prolonged supportive measures are responsible for an increasing incidence of candidal infections. Brain abscess is a rare complication of candidemia but may be expected to become more common as venous catheter-related fungemia is encountered more frequently.
Association of Extreme Heat Events With Hospital Admission or Mortality Among Patients With End-Stage Renal Disease (2019)

In this study, extreme heat events were associated with increased risk of hospital admission or mortality among patients with ESRD, and the association was potentially affected by geographic region and race/ethnicity. Future studies with larger populations and broader geographic coverage are needed to better characterize this variability in risk and inform ESRD management guidelines and differential risk variables, given the projected increases in the frequency, duration, and intensity of EHEs.
Phase II study of nivolumab and salvage nivolumab/ipilimumab in treatment-naïve patients with advanced non-clear cell renal cell carcinoma (HCRN GU16-260-Cohort B) (2023)

NCT03117309.
Inhaled antibodies: Quality and performance considerations (2021)

The use of antibodies in the treatment of lung diseases is of increasing interest especially as the search for COVID-19 therapies has unfolded. Historically, the use of antibody therapy was based on multiple targets including receptors involved in local hyper-reactivity in asthma, viruses and micro-organisms involved in a variety of pulmonary infectious disease. Generally, protein therapeutics pose challenges with respect to formulation and delivery to retain activity and assure therapy. The specificity of antibodies amplifies the need for attention to molecular integrity not only in formulation but also during aerosol delivery for pulmonary administration. Drug product development can be viewed from considerations of route of administration, dosage form, quality, and performance measures. Nebulizers and dry powder inhalers have been used to deliver protein therapeutics and each has its advantages that should be matched to the needs of the drug and the disease. This review offers insight into quality and performance barriers and the opportunities that arise from meeting them effectively.
Hybrid Multiscale Formulation for Coupled Flow and Geomechanics (2016)

We devise a hybrid MultiScale Finite Element-Finite Volume (h-MSFE-FV) framework to simulate single-phase flow through elastic deformable porous media. The coupled problem is solved based on a two-field fine-scale mixed finite element-finite volume formulation of the governing equations, namely conservation laws of linear momentum and mass, in which the primary unknowns are the displacement vector and pressure. For the MSFE displacement stage, we develop sets of local basis functions for the displacement vector over coarse cells, subject to reduced boundary condition. This MSFE stage is then coupled with the MSFV method for flow, where coarse and dual-coarse grids are imposed to obtain approximate but conservative multiscale solutions. Numerical experiments are presented to demonstrate accuracy and robustness of the proposed h-MSFE-FV method---both as an approximate, non-iterative solver, and a preconditioner.