gebhart/patrepeval huggingface dataset:
Toward controlled resist line-edge roughness: material origin of line-edge roughness in chemically amplified positive-tone resists (2000)

Material origin of resist line edge roughness (LER) in positive-tone chemically amplified resists has been investigated by designing experiments to mimic the composition and the morphology of the resists in the line edge regions where the resist consists of both the protected polymer and its de-protected counterparts. Blends of the protected and the de-protected base polymers for two silicon containing, positive-tone chemically amplified resists were prepared. Morphology and surface roughness of thin films of the polymer blends were probed with atomic force microscope (AFM). AFM results clearly showed that the protected polymer and its de- protected counterparts form distinct phase separated morphology after spin coating and baking. This phase separation leads to surface roughening of the blend films. Furthermore, the surface roughness of the blend films is enhanced after development with an aqueous TMAH developer. These results suggest that the material origin of resist LER in positive-tone chemically amplified resists stems from the compositional heterogeneity due to phase incompatibility of the protected base polymer and its de-protected counterparts in the line edge regions. The effects of blend composition, the extent of de-protection, and processing conditions on the morphology and surface roughness will be presented. The implications of these findings for high-resolution resist design will also be discussed.
Probabilistic Data Detection for Probe-Based Storage Channels in the Presence of Jitter (2009)

Probe-storage devices employ large arrays of probes to write/read data in parallel in some storage medium. Because of their inherent parallelism and the independence of data retrieved from different probes, these devices lend themselves naturally to low-density parity-check (LDPC) codes and associated soft/iterative decoding techniques. In this paper, a concatenated coding scheme for a particular probe-storage channel is presented that comprises an inner (d, k)-constrained code and an outer LDPC code, and the problem of probabilistic data retrieval for this channel is addressed. In particular, soft information is generated by explicitly accounting for the channel output statistics in the presence of jitter and additive noise, based on derived analytical expressions.
Supplementary Figure 5 from Targeting HER-2/<i>neu</i> in Early Breast Cancer Development Using Dendritic Cells with Staged Interleukin-12 Burst Secretion (2023)

Supplementary Figure 5 from Targeting HER-2/&lt;i&gt;neu&lt;/i&gt; in Early Breast Cancer Development Using Dendritic Cells with Staged Interleukin-12 Burst Secretion
The Phosphoinositide Kinase PIKfyve Promotes Cathepsin-S-Mediated Major Histocompatibility Complex Class II Antigen Presentation (2018)

Antigen presentation to T cells in major histocompatibility complex class II (MHC class II) requires the conversion of early endo/phagosomes into lysosomes by a process called maturation. Maturation is driven by the phosphoinositide kinase PIKfyve. Blocking PIKfyve activity by small molecule inhibitors caused a delay in the conversion of phagosomes into lysosomes and in phagosomal acidification, whereas production of reactive oxygen species (ROS) increased. Elevated ROS resulted in reduced activity of cathepsin S and B, but not X, causing a proteolytic defect of MHC class II chaperone invariant chain Ii processing. We developed a novel universal MHC class II presentation assay based on a bio-orthogonal "clickable" antigen and showed that MHC class II presentation was disrupted by the inhibition of PIKfyve, which in turn resulted in reduced activation of CD4<sup>+</sup> T cells. Our results demonstrate a key role of PIKfyve in the processing and presentation of antigens, which should be taken into consideration when targeting PIKfyve in autoimmune disease and cancer.
A new sixth-order Eigenmike® spherical microphone array for spatial sound field recording (2023)

A new spherical microphone array capable of up to 6-th order spatial sound field recording is described. Spherical microphone array beamforming is normally accomplished by judicially combining multiple acoustic pressure microphones appropriately mounted on the surface of a rigid sphere to form a set of orthonormal spherical harmonic modal beams or “Eigenbeams” (also referred to as Higher-Order-Ambisonics). Eigenbeamformer processing exploits the diffraction and scattering of the incident acoustic waves onto the rigid sphere. General beamformers are then created by properly combining the orthonormal Eigenbeams to form and steer a desired set of beampatterns up to the decomposition order limit. One advantage of using the modal decomposition approach to beamforming is that it is computationally compact, and results in an elegant scalable beamformer architecture. Steering beams formed by the spherical array is accomplished by a computationally simple matrix multiply. Another benefit is that beampatterns formed using spherical array processing maintain their design spatial responses independent of the steering direction. Beampatterns can also be frequency independent. In this talk, we will describe a new 64-element spherical microphone array and associated software capable of up to 6-th order performance, as well as present some real-world measurements.
Compressive Sampling in Spectral Imaging Systems (2006)

Optical prefilters shape the analog-digital interface in imaging systems to implement generalized spatio-spectral sampling. The Duke Imaging and Spectroscopy Program explores generalized sampling systems, this talk focuses specifically on spectral encoding for compressive spatial imaging.
Identification of an IgG CDR sequence contributing to co‐purification of the host cell protease cathepsin D (2016)

Recombinant therapeutic monoclonal antibodies (mAbs) must be purified from host cell proteins (HCPs), DNA, and other impurities present in Chinese hamster ovary (CHO) cell culture media. HCPs can potentially result in adverse clinical responses in patients and, in specific cases, have caused degradation of the final mAb product. As reported previously, residual traces of cathepsin D caused particle formation in the final product of mAb-1. The current work was focused on identification of a primary sequence in mAb-1 responsible for the binding and consequent co-purification of trace levels of CHO cathepsin D. Surface plasmon resonance (SPR) was used to detect binding between immobilized CHO cathepsin D and a panel of mAbs. Out of 13 mAbs tested, only mAb-1 and mAb-6 bound to cathepsin D. An LYY motif in the HC CDR2 was common, yet unique, to only these two mAbs. Mutation of LYY to AAA eliminated binding of mAb-1 to cathepsin D providing confirmation that this sequence motif was involved in the binding to CHO cathepsin D. Interestingly, the binding between mAb-1 and cathepsin D was weaker than that of mAb-6, which may be related to the fact that two aspartic acid residues near the LYY motif in mAb-1 are replaced with neutral serine residues in mAb-6. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:140-145, 2017.
The active metabolite of Clopidogrel disrupts P2Y12 receptor oligomers and partitions them out of lipid rafts (2006)

P2Y12, a G protein-coupled receptor that plays a central role in platelet activation has been recently identified as the receptor targeted by the antithrombotic drug, clopidogrel. In this study, we further deciphered the mechanism of action of clopidogrel and of its active metabolite (Act-Met) on P2Y12 receptors. Using biochemical approaches, we demonstrated the existence of homooligomeric complexes of P2Y12 receptors at the surface of mammalian cells and in freshly isolated platelets. In vitro treatment with Act-Met or in vivo oral administration to rats with clopidogrel induced the breakdown of these oligomers into dimeric and monomeric entities in P2Y12 expressing HEK293 and platelets respectively. In addition, we showed the predominant association of P2Y12 oligomers to cell membrane lipid rafts and the partitioning of P2Y12 out of rafts in response to clopidogrel and Act-Met. The raft-associated P2Y12 oligomers represented the functional form of the receptor, as demonstrated by binding and signal transduction studies. Finally, using a series of receptors individually mutated at each cysteine residue and a chimeric P2Y12/P2Y13 receptor, we pointed out the involvement of cysteine 97 within the first extracellular loop of P2Y12 in the mechanism of action of Act-Met.
A broad and potent neutralization epitope in SARS-related coronaviruses (2022)

Many neutralizing antibodies (nAbs) elicited to ancestral SARS-CoV-2 through natural infection and vaccination generally have reduced effectiveness to SARS-CoV-2 variants. Here we show therapeutic antibody ADG20 is able to neutralize all SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize all VOCs, albeit with reduced potency against Omicron. Thus, this highly conserved and vulnerable site can be exploited for design of universal vaccines and therapeutic antibodies.
Experimental and computational investigation of a centrifugal compressor stage (2005)

This paper presents experimental and computational investigations on a centrifugal compressor stage to study unsteady interaction flow and to verify the capability of computational fluid dynamics (CFD) codes. Detailed instantaneous flow has been measured at several different measuring positions using a hot-wire anemometer with the phase-locked ensemble-averaged technique. To describe quantitatively the unsteady effect induced from the impeller, an unsteady intensity is defined in this paper. Also, two computational investigations for the tested centrifugal compressor are performed and compared with corresponding experimental data: one is a steady method with the deterministic stress model and the other is an unsteady method with the sliding interface technique.
Phosphodiesterase-5 Inhibitor Use in Robot Assisted Radical Prostatectomy Patients Is Associated with Reduced Risk of Death: A Propensity Score Matched Analysis of 1,058 Patients (2023)

PDE5i administration after RARP were associated with overall survival of patients with prostate cancer. A further randomized control trial may reveal whether routine use of PDE5i after prostatectomy can improve survival of prostate cancer patient.
Scaling down of tunnel oxynitride in NAND flash memory: oxynitride selection and reliabilities (2002)

The selection of a manufacturable furnace-grown oxynitride process and reliability issues of the scaled tunnel oxide are examined. As the oxide thickness is scaled down, the cycling endurance, read life time and program disturb characteristics in a NAND flash memory with the tunnel oxynitride are improved compared to the conventional dry oxide.
Chemical methods to interrogate bacterial quorum sensing pathways (2012)

Bacteria frequently manifest distinct phenotypes as a function of cell density in a phenomenon known as quorum sensing (QS). This intercellular signalling process is mediated by "chemical languages" comprised of low-molecular weight signals, known as autoinducers, and their cognate receptor proteins. As many of the phenotypes regulated by QS can have a significant impact on the success of pathogenic or mutualistic prokaryotic-eukaryotic interactions, there is considerable interest in methods to probe and modulate QS pathways with temporal and spatial control. Such methods would be valuable for both basic research in bacterial ecology and in practical medicinal, agricultural, and industrial applications. Toward this goal, considerable recent research has been focused on the development of chemical approaches to study bacterial QS pathways. In this Perspective, we provide an overview of the use of chemical probes and techniques in QS research. Specifically, we focus on: (1) combinatorial approaches for the discovery of small molecule QS modulators, (2) affinity chromatography for the isolation of QS receptors, (3) reactive and fluorescent probes for QS receptors, (4) antibodies as quorum "quenchers," (5) abiotic polymeric "sinks" and "pools" for QS signals, and (6) the electrochemical sensing of QS signals. The application of such chemical methods can offer unique advantages for both elucidating and manipulating QS pathways in culture and under native conditions.
Health care utilization and outcomes in older adults after Traumatic Brain Injury: A CENTER-TBI study (2022)

The rate of impairment and disability following TBI in older adults is substantial, and poorer outcomes across domains are associated with worse preinjury health. Nonetheless, a considerable number of patients fully or partially returns to their preinjury functioning. There should not be pessimism about outcomes in older adults who survive.
A Review of Recent Progress in Diesel Engine Noise Reduction (1982)

&lt;div class="htmlview paragraph"&gt;The challenge presented and the progress made in engine noise reduction are reviewed. The excitation sources are examined together with approaches to their reduction. The importance of the engine structure is recognised and mathematically based modelling techniques are described. Recommendations are given for general engine noise reduction techniques.&lt;/div&gt;
Universal Semi-Supervised Semantic Segmentation (2019)

In recent years, the need for semantic segmentation has arisen across several different applications and environments. However, the expense and redundancy of annotation often limits the quantity of labels available for training in any domain, while deployment is easier if a single model works well across domains. In this paper, we pose the novel problem of universal semi-supervised semantic segmentation and propose a solution framework, to meet the dual needs of lower annotation and deployment costs. In contrast to counterpoints such as fine tuning, joint training or unsupervised domain adaptation, universal semi-supervised segmentation ensures that across all domains: (i) a single model is deployed, (ii) unlabeled data is used, (iii) performance is improved, (iv) only a few labels are needed and (v) label spaces may differ. To address this, we minimize supervised as well as within and cross-domain unsupervised losses, introducing a novel feature alignment objective based on pixel-aware entropy regularization for the latter. We demonstrate quantitative advantages over other approaches on several combinations of segmentation datasets across different geographies (Germany, England, India) and environments (outdoors, indoors), as well as qualitative insights on the aligned representations.
The Impact of Glycerol on an Affibody Conformation and Its Correlation to Chemical Degradation (2021)

The addition of glycerol to protein solutions is often used to hinder the aggregation and denaturation of proteins. However, it is not a generalised practice against chemical degradation reactions. The chemical degradation of proteins, such as deamidation and isomerisation, is an important deteriorative mechanism that leads to a loss of functionality of pharmaceutical proteins. Here, the influence of glycerol on the chemical degradation of a protein and its correlation to glycerol-induced conformational changes is presented. The time-dependent chemical degradation of a pharmaceutical protein, GA-Z, in the absence and presence of glycerol was investigated in a stability study. The effect of glycerol on protein conformation and oligomerisation was characterised using asymmetric field-flow fractionation and small-angle neutron scattering in a wide glycerol concentration range of 0-90% <i>v</i>/<i>v</i>. The results from the stability study were connected to the observed glycerol-induced conformational changes in the protein. A correlation between protein conformation and the protective effect of glycerol against the degradation reactions deamidation, isomerisation, and hydrolysis was found. The study reveals that glycerol induces conformational changes of the protein, which favour a more compact and chemically stable state. It is also shown that the conformation can be changed by other system properties, e.g., protein concentration, leading to increased chemical stability.
Note on the history effect in fluid mechanics (2019)

A freshman mechanics course often includes a theoretical discussion or demonstration of the motion of solid particles through fluids. The effect of viscosity is typically considered to provide a drag force on the particle which at each instant is proportional to the particle velocity. We present a brief discussion of the limitations of this approach and the importance of the so-called history effect first considered by Boussinesq and Basset in the late 19th century.
Superhydrophobic modification of gate dielectrics for densely packed pentacene thin film transistors (2007)

Pentacene organic thin film transistors (OTFTs) with low-k and high-k hybrid gate dielectrics by CF4 plasma treatment exhibited excellent device performance with field effect mobilities (maximum 1.41cm2∕Vs), a low threshold voltage of +1V, and on/off current ratios of 105 at −5V gate bias. After CF4 plasma treatment, fluorine atoms diffuse into the interior low-k polymer and eliminate ionic impurities which reduce the leakage current density and overall pentacene initial growth on the superhydrophobic surface is significantly improved. It seems apparent that proper surface treatment is desirable for higher quality pentacene film and improving the performance of OTFTs.
Memory for gist and detail information in Alzheimer's disease and mild cognitive impairment. (2006)

Two experiments examined different forms of gist and detail memory in people with Alzheimer's disease (AD) and those with amnestic mild cognitive impairment (MCI). In Experiment 1, 14 AD, 14 MCI, and 22 control participants were assessed with the Deese-Roediger-McDermott paradigm. Results indicated that false recognition of nonstudied critical lures (gist memory) was diminished in the AD compared with the MCI and control groups; the two latter cohorts performed similarly. In Experiment 2, 14 AD, 20 MCI, and 26 control participants were tested on a text memory task. Results revealed that recall of both macropropositions (gist information) and micropropositions (detail information) decreased significantly in AD and in MCI as compared with control participants. This experiment also revealed that the impairment was comparable between gist and detail memory. In summary, the results were consistent across experiments in the AD but not in the MCI participants. The discrepancy in MCI participants might be explained by differences in the degree of sensitivity of the experimental procedures and/or by the differences in the cognitive processes these procedures assessed.
Supplementary Figure 1 from Clusterin Inhibition Using OGX-011 Synergistically Enhances Hsp90 Inhibitor Activity by Suppressing the Heat Shock Response in Castrate-Resistant Prostate Cancer (2023)

&lt;p&gt;PDF file 150K&lt;/p&gt;
[Therapeutics of non-alcoholic fatty liver disease]. (2007)

非酒精性脂肪性肝病(NAFLD)及其主要类型-非酒精性脂肪性肝炎(NASH),不仅是肝酶持续异常的首要病因,而且可导致失代偿期肝硬化、肝细胞癌以及肝衰竭.随着亚洲地区肥胖症和糖尿病患者的不断增多,近期NAFLD或NASH的患病率仍将不断攀升并呈现出低年龄化的发病趋势[1].为此,亚太地区NAFLD工作组起草了NAFLD诊疗指南,无疑这将对本地区NAFLD的诊断和治疗起到重要指导作用[2-4]。
A proposal of an open PET geometry (2008)

The long patient port of a PET scanner tends to put stress on patients, especially patients with claustrophobia. It also prevents doctors and technicians from taking care of patients during scanning. In this paper, we proposed an 'open PET' geometry, which consists of two axially separated detector rings. A long and continuous field-of-view (FOV) including a 360 degrees opened gap between two detector rings can be imaged enabling a fully 3D image reconstruction of all the possible lines-of-response. The open PET will become practical if iterative image reconstruction methods are applied even though image reconstruction of the open PET is analytically an incomplete problem. First we implemented a 'masked' 3D ordered subset expectation maximization (OS-EM) in which the system matrix was obtained from a long 'gapless' scanner by applying a mask to detectors corresponding to the open space. Next, in order to evaluate imaging performance of the proposed open PET geometry, we simulated a dual HR+ scanner (ring diameter of D = 827 mm, axial length of W = 154 mm x 2) separated by a variable gap. The gap W was the maximum limit to have axially continuous FOV of 3W though the maximum diameter of FOV at the central slice was limited to D/2. Artifacts, observed on both sides of the open space when the gap exceeded W, were effectively reduced by inserting detectors partially into unnecessary open spaces. We also tested the open PET geometry using experimental data obtained by the jPET-D4. The jPET-D4 is a prototype brain scanner, which has 5 rings of 24 detector blocks. We simulated the open jPET-D4 with a gap of 66 mm by eliminating 1 block-ring from experimental data. Although some artifacts were seen at both ends of the opened gap, very similar images were obtained with and without the gap. The proposed open PET geometry is expected to lead to realization of in-beam PET, which is a method for an in situ monitoring of charged particle therapy, by letting the beams pass through the gap. The proposed open PET geometry will also allow simultaneous PET/CT measurements of the same PET FOV as the CT FOV, in contrast to the conventional PET/CT where each FOV is separated by several tens of centimeters.