gebhart/patrepeval huggingface dataset:
Diclofenac Prevents an Early Event of Macular Thickening After Cataract Surgery in Patients with Diabetes (2007)

Postoperative macular thickening following cataract surgery in patients with non- or mild nonproliferative-diabetic retinopathy cannot be fully suppressed by either topical diclofenac or betamethasone. Nonetheless, diclofenac protected against an early event of postoperative CME and also a decrease of IOP.
Fast Neutron Multiplicity Counter Based on Stilbene and EJ-309 Detectors (2017)

See uploaded file
Supplementary Table 5 from Multilevel Whole-Genome Analysis Reveals Candidate Biomarkers in Clear Cell Renal Cell Carcinoma (2023)

&lt;p&gt;PDF file - 107K, Significantly expressed genes in regions that are cytogenetically associated with copy-number aberrations in aberrant versus diploid tumors as based by GSEA and integration of protein data&lt;/p&gt;
Application of the Magnetoresistive Tensor Model to the Hard Axis Behavior of 81/19 Permalloy Magnetoresistive Sensor Elements (2006)

Hard axis (HA) behavioral models for magnetoresistive sensors (from highly ordered thin films) often are developed in such a fashion as to concentrate on the HA behavior only. This work uses a tensor based approach and a single domain concept to demonstrate how to calculate the magnetoresistance (AMR) for a given resistor and concentrates on the in-plane AMR only.
Nonlinear wavelet transforms for image coding (2002)

We examine the central issues of invertibility, stability, artifacts, and frequency-domain characteristics in the construction of nonlinear analogs of the wavelet transform. The lifting framework for wavelet construction motivates our analysis and provides new insight into the problem. We describe a new type of nonlinearity for use in constructing nonlinear transforms: a set of linear predictors that are chosen adaptively using a nonlinear selection function. We also describe how earlier families of nonlinear filter banks can be extended through the use of prediction functions operating on a causal neighborhood. We present preliminary results for a synthetic test image.
Prevalence-induced concept change in human judgment (2018)

Why do some social problems seem so intractable? In a series of experiments, we show that people often respond to decreases in the prevalence of a stimulus by expanding their concept of it. When blue dots became rare, participants began to see purple dots as blue; when threatening faces became rare, participants began to see neutral faces as threatening; and when unethical requests became rare, participants began to see innocuous requests as unethical. This "prevalence-induced concept change" occurred even when participants were forewarned about it and even when they were instructed and paid to resist it. Social problems may seem intractable in part because reductions in their prevalence lead people to see more of them.
Functional Imaging and Language (1994)

Positron emission tomography (PET) provides an unprecedented opportunity to study the organization of cognitive functions in the working brain of normal individuals. A number of PET experiments, based on well-established paradigms derived from cognitive psychology, have investigated several aspects of language processing. These studies show that word processing is carried out by a distributed network of cortical areas with functional specificity. Results of this research sometimes confirm--sometimes clearly contradict--classic axioms of language organization. This article illustrates some of the methodological issues in PET research, then provides an overview of the most relevant studies using PET. Integrated with other functional imaging methodologies and with behavioral data from cognitive psychology and lesion studies, PET will certainly continue to represent a precious tool to enhance our knowledge of the functional organization of language.
Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions (2021)

The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein.
Engineering Plant-Microbe Symbiosis for Rhizoremediation of Heavy Metals (2006)

The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium, Pseudomonas putida 06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing P. putida endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.
On-chip screening method for cell migration genes based on a transfection microarray (2008)

Cell migration plays a major role in a variety of biological processes and a detailed understanding of associated mechanisms should lead to advances in the medical sciences, for example, in drug discovery for cancer therapy. However, the traditional methods used for analysis of cell migration cannot easily be scaled up for high-throughput screening. In this study, we have attempted to develop a novel simple method for high-throughput phenotypic screening for the identification of genes that are required for cell migration. As the appropriate cell line for the method, we found NBT-L2b cells that would be suitable for screening of migration-related genes in our method without influence by other cellular processes. Moreover, the idea for printing both the labeled fibronectin, for identification of the starting region of a cell, and the green fluorescent protein (GFP) expression vector, for identification of cells that had been transfected with siRNA and of the end point of migration, brings a rapid and efficient high-throughput screening procedure. Our new method will lead to an enhanced understanding of cell migration.
European Society of Gastrointestinal Endoscopy (ESGE)Guideline: Prophylaxis of post-ERCP pancreatitis (2010)

Pancreatitis is the most common complication of endoscopic retrograde cholangiopancreatography (ERCP). Risk factors for post-ERCP pancreatitis (PEP) are both patient-related and procedure-related. Identification of patients at high risk for PEP is important in order to target prophylactic measures. Prevention of PEP includes administration of nonsteroidal inflammatory drugs (NSAIDs), use of specific cannulation techniques, and placement of temporary pancreatic stents. The aim of this guideline commissioned by the European Society of Gastrointestinal Endoscopy (ESGE) is to provide practical, graded, recommendations for the prevention of PEP.
Effect of image artifacts, organ motion, and poor segmentation on the reliability and accuracy of three-dimensional chamfer matching (1997)

Our objective was to investigate the influence of various image artifacts on three-dimensional chamfer matching. A number of artificial and natural artifacts (for instance, as a model for CT-MR matching) were introduced or suppressed in pairs of pelvic CT scans, and a perturbation study was used to determine reliability and accuracy in a well known ground truth situation. In general, chamfer matching is extremely robust against missing data, low resolution, and poor segmentation of the images. In the presence of artifacts, minimization of the average distance outperformed minimization of the root-mean-square distance. Outliers in the scan from which the point list is obtained must be avoided. For example, rotation of the femurs reduces CT-CT registration accuracy by 1-2 mm. The robustness of chamfer matching is confirmed by a limited perturbation study of CT-MR registration for the pelvic region. In conclusion, chamfer matching is extremely accurate and reliable if outliers are avoided in the scan from which the point list is derived, and the average distance is used as a cost function.
Rapid whole-brain quantitative MT imaging (2023)

The combination of rapid B<sub>1</sub>-T<sub>1</sub> mapping and MT-weighted imaging using a 2D multi-slice spiral SPGR research sequence offers excellent prospects for rapid whole-brain quantitative MT imaging in the clinical setting.
Prostate Cancer Progression Correlates with Increased Humoral Immune Response to a Human Endogenous Retrovirus GAG Protein (2013)

Preferential expression of GAG-HERV-K ch22q11.23 in prostate cancer tissue and increased frequency of autoantibodies observed in patients with advanced prostate cancer make this protein one of the first bona fide retroviral cancer antigens in humans, with potential as a biomarker for progression and biochemical recurrence rate of prostate cancer. Clin Cancer Res; 19(22); 6112-25. ©2013 AACR.
Coherence transfer by single-transition cross-polarization: Quantitation of cross-correlation effects in nuclear magnetic resonance (2000)

It is shown that selective single-transition cross-polarization (ST-CP) may be achieved in four-level systems such as encountered in NMR (nuclear magnetic resonance) of scalar-coupled two-spin systems (for example, N15–H1 groups in peptides), by employing two selective resonant fields applied to a pair of connected transitions with RF amplitudes much weaker than the separation of the parallel transitions (e.g., the scalar coupling constant JNH). The transfer benefits from differential line narrowing due to interference between the N15 chemical shift anisotropy and N15–H1 dipolar coupling, which is clearly observed in N15-labeled human ubiquitin at 600 MHz.
Estimation of the Bit Error Rate in a PRML Channel, Taking Account of Read/Write Nonlinearity (1998)

In MR heads, read-nonlinearity and write-nonlinearity, which is manifested in phenomena such as nonlinear transition shift (NLTS), degrade the bit error rate (BER) performance in a PRML read channel. We discuss a simple method of estimating these nonlinearity effects for a PRML read channel, and compare the calculated and experimental results. In a PRML read channel, the BER can be easily calculated from the noise deviation after the equalization, and the nonlinearities increase the noise deviation. The calculation and experimental results show a proportional relationship between the noise deviation due to read nonlinearity and the absolute value of the amplitude asymmetry. The deviation due to NLTS can be calculated by considering the first and second adjacent transition shifts and write precompensation. The total effects of the nonlinearities are easily calculated by adding the squares of all the noise deviations.
Assessing the molecular structure basis for biomass recalcitrance during dilute acid and hydrothermal pretreatments (2013)

The production of cellulosic ethanol from biomass is considered a promising alternative to reliance on diminishing supplies of fossil fuels, providing a sustainable option for fuels production in an environmentally compatible manner. The conversion of lignocellulosic biomass to biofuels through a biological route usually suffers from the intrinsic recalcitrance of biomass owing to the complicated structure of plant cell walls. Currently, a pretreatment step that can effectively reduce biomass recalcitrance is generally required to make the polysaccharide fractions locked in the intricacy of plant cell walls to become more accessible and amenable to enzymatic hydrolysis. Dilute acid and hydrothermal pretreatments are attractive and among the most promising pretreatment technologies that enhance sugar release performance. This review highlights our recent understanding on molecular structure basis for recalcitrance, with emphasis on structural transformation of major biomass biopolymers (i.e., cellulose, hemicellulose, and lignin) related to the reduction of recalcitrance during dilute acid and hydrothermal pretreatments. The effects of these two pretreatments on biomass porosity as well as its contribution on reduced recalcitrance are also discussed.
Synthesis, CP-MAS NMR Characterization, and Antibacterial Activities of Glycine and Histidine Complexes of Cd(SeCN)2and Hg(SeCN)2 (2013)

The synthesis and characterization of cadmium and mercury complexes of selenocyanate of the type [(L)M(SeCN)2] are described, where L is L-Histidine (His) or L-Glycine (Gly) and M is Cd(2+) or Hg(2+). These complexes are obtained by the reaction of 1 equivalent of respective amino acids with metal diselenocyanate precursor in a mixture of solvents (methanol : water = 1 : 1). These synthesized compounds are characterized by analytical and various spectroscopic techniques such as elemental analysis (EA), IR, H,1 and C13 NMR in solution and in the solid state for C13 and N15. The in vitro antibacterial activities of these complexes have been investigated with standard type cultures of Escherichia coli (MTCC 443), Klebsiella pneumoniae (MTCC 109), Pseudomonas aeruginosa (MTCC 1688), Salmonella typhi (MTCC 733), and Staphylococcus aureus (MTCC 737).
General Utilities (2016)

This section explains the functions move(), move_if_noexcept(), forward(), swap(), and exchange(). In passing, it also introduces the concepts of move semantics and perfect forwarding.
Phantom limb pain intensity is associated with generalized hyperalgesia (2019)

Abstract After limb amputation, most amputees suffer from phantom limb pain (PLP). The mechanisms underlying this condition are complex and insufficiently understood. Altered somatosensory sensitivity (either heightened or lowered) might contribute to PLP. Recent studies have tested this assumption but mainly focused on the residual limb. However, altered somatosensation in PLP might be generalized. In this study, we applied quantitative sensory testing to 37 unilateral upper-limb amputees (23 with PLP, 14 without PLP) and 19 healthy controls. We assessed thresholds to heat pain (HPT), pressure pain (PPT), warmth detection (WDT), and two-point discrimination (2PDT) at the residual limb, a homologous point and the thenar of the intact limb, and both corners of the mouth. We did not find significant differences in any of the thresholds between the groups. However, higher PLP intensity was significantly related to lower HPT at all measured body sites except for the residual limb. At the residual limb, lower HPT were observed in more distal amputations and in amputees showing a higher degree of prosthesis use. Although WDT did by itself not significantly correlate with PLP intensity at any of the body sites, multiple regression analysis showed the highest multiple correlations with PLP intensity for a combination of high WDT and low HPT at the corners of the mouth. In this model, the combination of HPT and WDT shared 58% of the variance with PLP intensity. Other factors of potential importance, especially residual limb pain, were not significantly associated to any sensory threshold. We conclude that the intensity, but not the presence of PLP is positively associated with higher heat pain sensitivity. Since this association was observed at various, distributed body sites, we suggest that central mechanisms might be underlying such generalized hyperalgesia.
Information-theoretic interpretation of Besov spaces (2000)

Besov spaces classify signals and images through the Besov norm, which is based on a deterministic smoothness measurement. Recently, we revealed the relationship between the Besov norm and the likelihood of an independent generalized Gaussian wavelet probabilistic model. In this paper, we extend this result by providing an information- theoretical interpretation of the Besov norm as the Shannon codelength for signal compression under this probabilistic mode. This perspective unites several seemingly disparate signal/image processing methods, including denoising by Besov norm regularization, complexity regularized denoising, minimum description length processing, and maximum smoothness interpolation. By extending the wavelet probabilistic model, we broaden the notion of smoothness space to more closely characterize real-world data. The locally Gaussian model leads directly to a powerful wavelet- domain. Wiener filtering algorithm for denoising.
Characterization of Phosphorylation-defective Mutants of Human P-glycoprotein Expressed in Mammalian Cells (1996)

To assess the role of phosphorylation of the human multidrug resistance MDR1 gene product P-glycoprotein for its drug transport activity, phosphorylation sites within its linker region were subjected to mutational analysis. We constructed a 5A mutant, in which serines at positions 661, 667, 671, 675, and 683 were replaced by nonphosphorylatable alanine residues, and a 5D mutant carrying aspartic acid residues at the respective positions to mimic permanently phosphorylated serine residues. Transfection studies revealed that both mutants were targeted properly to the cell surface and conferred multidrug resistance by diminishing drug accumulation. In contrast to wild-type P-glycoprotein, the overexpressed 5A and the 5D mutants exhibited no detectable levels of phosphorylation, either in vivo following metabolic labeling of cells with [32P]orthophosphate or in vitro in phosphorylation assays with protein kinase C, cAMP-dependent protein kinase, or a P-glyco-protein-specific protein kinase purified from multidrug-resistant KB-V1 cells. These results reconfirm that the major P-glycoprotein phosphorylation sites are located within the linker region. Furthermore, the first direct evidence is provided that phosphorylation/dephosphorylation mechanisms do not play an essential role in the establishment of the multidrug resistance phenotype mediated by human P-glycoprotein.
ZnO / TiO 2 nanonetwork as efficient photoanode in excitonic solar cells (2009)

An innovative nanonetwork composed of TiO2 nanoparticles and single-crystalline ZnO nanowires is demonstrated as efficient photoanode in excitonic solar cells. Such architecture benefits of the capability of high sensitizer loading offered by the nanoparticles and of the direct conduction path for electrons guaranteed by the nanowires. The combination of these features leads to improved light absorption, electron photogeneration, and charge collection. The nanonetwork was implemented in a dye-sensitized solar-cell architecture demonstrating threefold enhancement of the efficiency with respect to a nanowire photoanode of the same thickness. Cell efficiency of 1.6% was obtained in 1.5 μm thick nanonetwork.
Abstract 496: Inflammatory responses with infiltrating DC and functional cytotoxic T lymphocytes in the dermal vaccination sites of GVAX/ipilimumab treated prostate cancer patients. (2013)

Abstract We have been studying the safety and clinical efficacy of the Prostate GVAX vaccine (consisting of two allogeneic GM-CSF secreting tumor cell lines: LNCaP and PC3) and the CTLA-4 blocking antibody ipilimumab in prostate cancer patients in a phase I/II dose escalation/expansion trial. To assess immune reactivity against the GVAX vaccine, immune infiltrate analysis of the vaccination sites was performed. Punch biopsies of the vaccination site were taken 48 hours after the 1st, 5th, and 11th injections and analyzed by immunohistochemical staining. Injection of the GVAX vaccine evoked striking local reactions that were characterized by local erythema, induration and swelling in all patients. Analysis of the vaccination site biopsies revealed that the GVAX/ipilimumab combination resulted in an inflammatory response in the skin with intradermal infiltrates of CD1a+ dendritic cells (DC), DC-SIGN+/CD68+ immature DC/macrophages, CD14+ monocyte-like cells, eosinophils, and of CD4+, CD8+, and Granzyme-B+ T lymphocytes. Strikingly, CD56+ NK cells were completely absent. The inflammatory response significantly increased over the course of treatment and resulted in accelerated clearance of the vaccine in vivo. Moreover, analysis revealed that the PC3 vaccine was more immunogenic, and induced a more potent anti-vaccine T cell response. The latter was confirmed in an in vitro cytotoxicity assay. Upon multiple vaccinations T cell reactivity to PC3 was significantly enhanced in the PC3 but not in the LNCaP vaccination sites, whereas reactivity to LNCaP was not enhanced in either vaccination site. We conclude that the GVAX/ipilimumab combination elicits a local immune infiltrate that increases over time, consistent with an induced CD8+ effector T cell mediated cytolytic response, only in vaccination sites of the PC3 component of the vaccine. Citation Format: Saskia J. Santegoets, Leonieke JJ van Mens, Jeroen AM Beliën, Anita GM Stam, Sinead M. Lougheed, Rik J. Scheper, Shabnam Samiei, Helen Gall, Karin Jooss, Jean-Marie Cuillerot, Natalie Sacks, Kirsten Hege, Winald R. Gerritsen, Alfons JM van den Eertwegh, Tanja D. de Gruijl. Inflammatory responses with infiltrating DC and functional cytotoxic T lymphocytes in the dermal vaccination sites of GVAX/ipilimumab treated prostate cancer patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 496. doi:10.1158/1538-7445.AM2013-496
Novel BEM Simulation of Mixing in Polymer Flows Including Non-Linear Effects (2000)

When numerically analyzing mixing in polymer processes, there are several difficulties that the engineer will encounter; such as moving boundaries, complex geometries and non-linear material behavior. The Boundary Element Method (BEM), as a technique which requires only boundaries (surfaces) to be meshed, is ideal to simulate problems with moving boundaries and complex geometries. However, the introduction of non-linear material behavior requires domain information. This study applies the Monte Carlo technique to integrate the domain and keep the boundary-only discretization. Results show the influence of non-linear effects, such as shear-thinning viscosity, when characterizing mixing in polymer processing equipment.
Cover Picture: Production of Renewable Hexanols from Mechanocatalytically Depolymerized Cellulose by Using Ir‐ReOx/SiO2 catalyst (ChemSusChem 4/2015) (2015)

The Front Cover image shows that in a biphasic reaction system (n-decane+H2O), high yields of hexanols can be produced from mechanocatalytically depolymerized cellulose by using Ir–ReOx/SiO2 as catalyst, which was developed in our laboratory. Hexanols would be an attractive candidate for biofuels and chemicals that could contribute to the solution of the energy crisis to some extent, such as the stars light up the night sky. In addition, the treatment of cellulose is put into the red tornado. More details can be found in the Full Paper by Liu et al. on page 628 (DOI: 10.1002/cssc.201403010).