gebhart/patrepeval huggingface dataset:
A comparison of transform and iterative reconstruction techniques for a volume-imaging PET scanner with a large axial acceptance angle (1995)

The authors present the results of comparing 3-D transform and iterative reconstruction methods with measured PET data from the HEAD PENN-PET scanner, which has a very large axial acceptance angle of 27/spl deg/. The algorithms compared are the 3-D-reprojection (3DRP) method, the iterative algebraic reconstruction technique (ART), and the maximum likelihood (ML-EM) algorithm. For the iterative methods, alternatives to the cubic voxel basis functions are also implemented. The comparisons are based on a series of figures of merit, including the point-spread function, the contrast recovery coefficient, and signal-to-noise ratios (SNR). The results show that the ART method implemented with the new basis functions requires only one cycle through the data to produce images with measured SNR values comparable to or better than the 3DRP method. The ML-EM method was run for 10 iterations and produced images with lower SNR values for the test phantom used. With the exception of the ML-EM results, these are in agreement with the authors' previous simulation studies.
Host B7x Promotes Pulmonary Metastasis of Breast Cancer (2013)

B7x (B7-H4 or B7S1) is an inhibitory member of the B7 family of T cell costimulation. It is expressed in low levels in healthy peripheral tissues, such as the lung epithelium, but is overexpressed in a variety of human cancers with negative clinical associations, including metastasis. However, the function of B7x in the context of cancer, whether expressed on cancer cells or on surrounding "host" tissues, has not been elucidated in vivo. We used the 4T1 metastatic breast cancer model and B7x knockout (B7x (-/-)) mice to investigate the effect of host tissue-expressed B7x on cancer. We found that 4T1 cells were B7x negative in vitro and in vivo, and B7x(-/-) mice had significantly fewer lung 4T1 tumor nodules than did wild-type mice. Furthermore, B7x(-/-) mice showed significantly enhanced survival and a memory response to tumor rechallenge. Mechanistic studies revealed that the presence of B7x correlated with reduced general and tumor-specific T cell cytokine responses, as well as with an increased infiltration of immunosuppressive cells, including tumor-associated neutrophils, macrophages, and regulatory T cells, into tumor-bearing lungs. Importantly, tumor-associated neutrophils strongly bound B7x protein and inhibited the proliferation of both CD4 and CD8 T cells. These results suggest that host B7x may enable metastasizing cancer cells to escape local antitumor immune responses through interactions with the innate and adaptive immune systems. Thus, targeting the B7x pathway holds much promise for improving the efficacy of immunotherapy for metastatic cancer.
Thermal Atomic Layer Etching of SiO2 by a “Conversion-Etch” Mechanism Using Sequential Reactions of Trimethylaluminum and Hydrogen Fluoride (2017)

The thermal atomic layer etching (ALE) of SiO<sub>2</sub> was performed using sequential reactions of trimethylaluminum (TMA) and hydrogen fluoride (HF) at 300 °C. Ex situ X-ray reflectivity (XRR) measurements revealed that the etch rate during SiO<sub>2</sub> ALE was dependent on reactant pressure. SiO<sub>2</sub> etch rates of 0.027, 0.15, 0.20, and 0.31 Å/cycle were observed at static reactant pressures of 0.1, 0.5, 1.0, and 4.0 Torr, respectively. Ex situ spectroscopic ellipsometry (SE) measurements were in agreement with these etch rates versus reactant pressure. In situ Fourier transform infrared (FTIR) spectroscopy investigations also observed SiO<sub>2</sub> etching that was dependent on the static reactant pressures. The FTIR studies showed that the TMA and HF reactions displayed self-limiting behavior at the various reactant pressures. In addition, the FTIR spectra revealed that an Al<sub>2</sub>O<sub>3</sub>/aluminosilicate intermediate was present after the TMA exposures. The Al<sub>2</sub>O<sub>3</sub>/aluminosilicate intermediate is consistent with a "conversion-etch" mechanism where SiO<sub>2</sub> is converted by TMA to Al<sub>2</sub>O<sub>3</sub>, aluminosilicates, and reduced silicon species following a family of reactions represented by 3SiO<sub>2</sub> + 4Al(CH<sub>3</sub>)<sub>3</sub> → 2Al<sub>2</sub>O<sub>3</sub> + 3Si(CH<sub>3</sub>)<sub>4</sub>. Ex situ X-ray photoelectron spectroscopy (XPS) studies confirmed the reduction of silicon species after TMA exposures. Following the conversion reactions, HF can fluorinate the Al<sub>2</sub>O<sub>3</sub> and aluminosilicates to species such as AlF<sub>3</sub> and SiO<sub>x</sub>F<sub>y</sub>. Subsequently, TMA can remove the AlF<sub>3</sub> and SiO<sub>x</sub>F<sub>y</sub> species by ligand-exchange transmetalation reactions and then convert additional SiO<sub>2</sub> to Al<sub>2</sub>O<sub>3</sub>. The pressure-dependent conversion reaction of SiO<sub>2</sub> to Al<sub>2</sub>O<sub>3</sub> and aluminosilicates by TMA is critical for thermal SiO<sub>2</sub> ALE. The "conversion-etch" mechanism may also provide pathways for additional materials to be etched using thermal ALE.
Hydrolytically stable polyurethanes (2014)

Polyisobutylene-based polyurethanes (PU) exhibit outstanding hydrolytic stability. PU samples were immersed in PBS at pH 7.4 and aqueous buffers at pH 1 and 11, and then heated at 85 °C for 10 weeks. According to SEC analysis, Mn, Mw, Mw/Mn did not change (within experimental variation) in the course of the test. In contrast, a PDMS-based PU severely degraded after one week under the same conditions.
A novel ALD SiBCN low-k spacer for parasitic capacitance reduction in FinFETs (2015)

FinFET has become the mainstream logic device architecture in recent technology nodes due to its superior electrostatic and leakage control [1,2,3,4]. However, parasitic capacitance has been a key performance detractor in 3D FinFETs. In this work, a novel low temperature ALD-based SiBCN material has been identified, with an optimized spacer RIE process developed to preserve the low-k value and provide compatibility with the down-stream processes. The material has been integrated into a manufacturable 14nm replacement-metal-gate (RMG) FinFET baseline with a demonstrated ~8% performance improvement in the RO delay with reliability meeting the technology requirement [4]. A guideline for spacer design consideration for 10nm node and beyond is also provided based on the comprehensive material properties and reliability evaluations.
Monitoring and Optimization of Industrial Batch Crystallization Processes using NIR and ATR UV-vis Spectroscopy (2010)

In the pharmaceutical industry, batch crystallization processes at production scale are not always well understood. Several factors have a significant impact on the process of crystallization, such as the physicochemical properties (solubility curve and super-saturation level), the crystal seeding (amount, purity and specific area), the engineering design (crystallizer and propeller), and the control (heating, cooling and stirring rates) [1]. When these factors are poorly understood or insufficiently controlled, they may produce batch-to-batch inconsistencies in terms of size distribution or polymorphic structure of crystals, and lead to pharmaceutical products that may be out of specifications. Online spectroscopic techniques are widely used in industry as they allow to acquire data in real-time, without any sampling, quenching or dilution procedure. Near-infrared (NIR) and attenuated total reflectance (ATR) ultraviolet visible (UV-vis) spectroscopy are two of these online spectroscopic techniques that are routinely used in industry to test, validate and monitor batch crystallization processes [2,3]. &lt;br&gt;&lt;br&gt; [1] Billot et al, "A Review of the use of process analytical technology for the understanding and optimization of production batch crystallization processes" Org. Process Res. Dev., 2010, 14, 511-523 &lt;br&gt; [2] Fevotte et al, "Applications of NIR spectroscopy to monitoring and analyzing the solid state during industrial crystallization processes" Int. J. Pharm., 2004, 273, 159-169 &lt;br&gt; [3] Barrett et al, "Application of ATR-UV spectroscopy for monitoring the crystallization of UV absorbing and non-absorbing molecules" Org. Process Res. Dev., 2005, 9, 348-355
Supplemental Table S1 from Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages (2023)

&lt;p&gt;TaqMan gene expression assays used for qPCR.&lt;/p&gt;
Chemical Mechanisms in Toxicology (2010)

Abstract Pharmaceutical scientists working in drug metabolism and toxicology today consider reactive metabolites of drugs or drug candidates an important potential toxicological issue. There is a critical demand for increased research on the mechanisms of immune‐mediated toxicities at the molecular level. This article deals with the mechanisms involved in the biotransformation of drugs to chemically reactive metabolites, current experimental techniques used to identify reactive metabolites, and the potential consequences of reactive metabolite formation.
An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron–sulfur cluster proteins (2014)

Metalloproteins represent a ubiquitous group of molecules which are crucial to the survival of all living organisms. While several metal-binding motifs have been defined, it remains challenging to confidently identify metalloproteins from primary protein sequences using computational approaches alone. Here, we describe a comprehensive strategy based on a machine learning approach to design and assess a penalized generalized linear model. We used this strategy to detect members of the iron-sulfur cluster protein family. A new category of descriptors, whose profile is based on profile hidden Markov models, encoding structural information was combined with public descriptors into a linear model. The model was trained and tested on distinct datasets composed of well-characterized iron-sulfur protein sequences, and the resulting model provided higher sensitivity compared to a motif-based approach, while maintaining a good level of specificity. Analysis of this linear model allows us to detect and quantify the contribution of each descriptor, providing us with a better understanding of this complex protein family along with valuable indications for further experimental characterization. Two newly-identified proteins, YhcC and YdiJ, were functionally validated as genuine iron-sulfur proteins, confirming the prediction. The computational model was then applied to over 550 prokaryotic genomes to screen for iron-sulfur proteomes; the results are publicly available at: . This study represents a proof-of-concept for the application of a penalized linear model to identify metalloprotein superfamilies on a large-scale. The application employed here, screening for iron-sulfur proteomes, provides new candidates for further biochemical and structural analysis as well as new resources for an extensive exploration of iron-sulfuromes in the microbial world.
Next-Generation Sequencing of a Single Domain Antibody Repertoire Reveals Quality of Phage Display Selected Candidates (2016)

Next-Generation Sequencing and bioinformatics are powerful tools for analyzing the large number of DNA sequences present in an immune library. In this work, we constructed a cDNA library of single domain antibodies from a llama immunized with staphylococcal enterotoxin B. The resulting library was sequenced, resulting in approximately 8.5 million sequences with 5.4 million representing intact, useful sequences. The sequenced library was interrogated using sequences of known SEB-binding single domain antibodies from the library obtained through phage display panning methods in a previous study. New antibodies were identified, produced, and characterized, and were shown to have affinities and melting temperatures comparable to those obtained by traditional panning methods. This demonstrates the utility of using NGS as a complementary tool to phage-displayed biopanning as a means for rapidly obtaining additional antibodies from an immune library. It also shows that phage display, using a library of high diversity, is able to select high quality antibodies even when they are low in frequency.
Coded-excitation Raman spectroscopy for Raman signal estimation in highly fluorescent media (2007)

Raman signal estimation in highly fluorescent media is investigated using multiple excitation lasers and an iterative EM spectral reconstruction algorithm. Results from an 8-laser system show estimation performance increases with the number of excitation lasers.
ALPSCore: Version 0.5.3 (2016)

The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. This release: Accumulators: Terse and verbose printing. Bugfixes. Python interface: separated out to an independent repository, ALPSCore-Python Dependency on boost::mpi is eliminated. Miscellaneous bugfixes and enhancements. For copyright see COPYRIGHT.TXT. For licensing see LICENSE.TXT. For acknowledgment in scientific publications see ACKNOWLEDGE.TXT.
Manufacturing implementation of deep-UV lithography for 500-nm devices (1992)

Lithographers have steadily reduced exposure wavelength and increased numerical aperture (NA) to maintain process window and simplicity. The G-line systems of the 1970s gave way to the I-line systems of the late 80s, and then to the deep ultraviolet (DUV) systems of today. This paper describes our characterization of a DUV lithography system for the manufacture of 16-Mb DRAM chips at 500-nm ground rules. The process consists of a positive-tone, aqueous-base developable photoresist with an overcoat for sensitivity control, and an anti- reflective coating (ARC) on selected levels. The exposure tools used are step-and-scan systems with a 0.36 NA and expose bandpass of 240 - 255 nm. Apply and develop processes are clustered with the expose tool to minimize defects, reduce cycle time, and eliminate process variables.
Rotationally-Consistent Novel View Synthesis for Humans (2020)

Human novel view synthesis aims to synthesize target views of a human subject given input images taken from one or more reference viewpoints. Despite significant advances in model-free novel view synthesis, existing methods present two major limitations when applied to complex shapes like humans. First, these methods mainly focus on simple and symmetric objects, e.g., cars and chairs, limiting their performances to fine-grained and asymmetric shapes. Second, existing methods cannot guarantee visual consistency across different adjacent views of the same object. To solve these problems, we present in this paper a learning framework for the novel view synthesis of human subjects, which explicitly enforces consistency across different generated views of the subject. Specifically, we introduce a novel multi-view supervision and an explicit rotational loss during the learning process, enabling the model to preserve detailed body parts and to achieve consistency between adjacent synthesized views. To show the superior performance of our approach, we present qualitative and quantitative results on the Multi-View Human Action (MVHA) dataset we collected (consisting of 3D human models animated with different Mocap sequences and captured from 54 different viewpoints), the Pose-Varying Human Model (PVHM) dataset, and ShapeNet. The qualitative and quantitative results demonstrate that our approach outperforms the state-of-the-art baselines in both per-view synthesis quality, and in preserving rotational consistency and complex shapes (e.g. fine-grained details, challenging poses) across multiple adjacent views in a variety of scenarios, for both humans and rigid objects.
The state of the art for artificial intelligence in lung digital pathology (2022)

Lung diseases carry a significant burden of morbidity and mortality worldwide. The advent of digital pathology (DP) and an increase in computational power have led to the development of artificial intelligence (AI)-based tools that can assist pathologists and pulmonologists in improving clinical workflow and patient management. While previous works have explored the advances in computational approaches for breast, prostate, and head and neck cancers, there has been a growing interest in applying these technologies to lung diseases as well. The application of AI tools on radiology images for better characterization of indeterminate lung nodules, fibrotic lung disease, and lung cancer risk stratification has been well documented. In this article, we discuss methodologies used to build AI tools in lung DP, describing the various hand-crafted and deep learning-based unsupervised feature approaches. Next, we review AI tools across a wide spectrum of lung diseases including cancer, tuberculosis, idiopathic pulmonary fibrosis, and COVID-19. We discuss the utility of novel imaging biomarkers for different types of clinical problems including quantification of biomarkers like PD-L1, lung disease diagnosis, risk stratification, and prediction of response to treatments such as immune checkpoint inhibitors. We also look briefly at some emerging applications of AI tools in lung DP such as multimodal data analysis, 3D pathology, and transplant rejection. Lastly, we discuss the future of DP-based AI tools, describing the challenges with regulatory approval, developing reimbursement models, planning clinical deployment, and addressing AI biases. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
P.144: Late‐News Poster : Synthesis and Electroluminescence Properties of Highly Efficient Blue Fluorescence Emitters Using Dual Core Chromophores (2013)

Abstract We propose new dual core chromophore materials with blue emission. One of these derivatives, TP‐AP‐TP, exhibits a high luminance EQE value of 7.51% and twice the lifetime of a commercialized material, MADN. The dual core chromophore materials have narrower PL and EL spectra and better thermal properties than the single core chromophore materials.
Influence of Additives in Electrolytic Solution on Mass Change of Zinc Electrodeposited Films. Investigation by Quartz Crystal Microbalance Measurement. (1997)

Natural additive agents such as glue and gelatin have been used for preventing impurities from precipitating during deposition and for surface leveling of deposited films in the electrowinning industry. The mechanism behind the effect of their agents on electrochemical deposition is not yet well understood.We studied the effect of various additives on electrodeposition process in a zinc sulfate electrolytic bath.We used polyethylene glycol (PEG M W 20000, 6000, 2000), polyacrylic acid (PAA M W 240000, 5000, 2000) and polyvinyl pyrrolidon (PVP M. W 360000, 40000, 10000), and their monomers as synthetic additives. We also used another eight types of additives including glycin, alanin, and proline as amino acid additives. Mass changes of deposits were monitored by quartz crystal microbalance (QCM) method. The surface morphology of zinc films was observed by FE-SEM.Results are as follows:1) Zinc deposition was inhibited in the presence of gelatin and polymer additives.2) Amino acid and monomer additives did not inhibit the deposition. Corresponding surface morphology was similar to that in the absence of additives.3) The inhibition effect of PAA was the highest of all tested additives.4) Characteristic mass change was detected during the deposition in the presence of PEG, PAA and PVP.5) From mass change measurements, inhibition by additives could be classified into four different modes(A) The inhibition effect increases with deposition time. (PEG)(B) The inhibition effect decreases with deposition time. (PAA)(C) The inhibition effect was constant during deposition. (Gelatin)(D) No inhibition. (Amino acid, Monomer)
Formoterol Delivered via a New Multi-Dose Dry Powder Inhaler (Certihaler ™ ) Is as Effective and Well Tolerated as the Formoterol Dry Powder Inhaler (Aerolizer ® ) in Children with Persistent Asthma (2005)

The Certihaler is a new multi-dose dry powder inhaler for the delivery of formoterol (Foradil), a long-acting beta(2)-agonist. This dose-ranging study compared the efficacy and safety of formoterol 5, 10, 15 and 30 microg and placebo administered via the Certihaler or formoterol 12 microg via a single-dose dry powder inhaler (Aerolizer) in children with persistent asthma. This was a randomized, placebo-controlled, double-blind, double-dummy, incomplete block crossover, dose-finding and pharmacokinetic study. Children (5-12 years, n = 77) received four of the active treatments twice weekly (BID) for 1 week separated by 1-week single-blind washouts. The primary efficacy variable was 12-h AUC of FEV(1) after 1 week's treatment. Secondary variables included serial 12-h FEV(1). A subset of patients (n = 37) participated in a pharmacokinetic analysis. All formoterol doses resulted in significant increases in 12-h AUC of FEV(1) compared with placebo, and there was no difference between active treatments. The onset of action of formoterol was <3 min for all active treatments. Doses of formoterol > or =10 microg via the Certihaler increased FEV(1) significantly for up to 12 h compared with placebo. The 5 microcg dose via the Certihaler and 12 microg dose via the Aerolizer had a significant effect up to 8 and 7 h post-dose, respectively. Urinary excretion of formoterol via the Certihaler increased in a dose-proportional manner. All formoterol doses were well tolerated, but some patients experienced tremor at the 15 and 30 microg doses. Despite the lack of significant differences between the active doses in the overall bronchodilation, formoterol 10 microg BID via the Certihaler was the dose that provided the best balance between efficacy and tolerability: its duration of action was sustained over 12 h, contrary to that the lower dose (5 microg BID), whereas its tolerability, especially with regard to tremor, was better than the higher doses (15 and 30 microg BID). Overall, Certihaler 10 microg BID was not significantly different from formoterol 12 microg BID via Aerolizer.
High mobility SiMOSFETs fabricated in a full 300mm CMOS process (2021)

The quality of the semiconductor-barrier interface plays a pivotal role in the demonstration of high quality reproducible quantum dots for quantum information processing. In this work, we have measured SiMOSFET Hall bars on undoped Si substrates in order to investigate the quality of the devices fabricated in a full CMOS process. We report a record mobility of 17'500 cm2/Vs with a sub-10 nm oxide thickness indicating a high quality interface, suitable for future qubit applications. We also study the influence of gate materials on the mobilities and discuss the underlying mechanisms, giving insight into further material optimization for large scale quantum processors.
Supplementary Figure 4 from Epidermal Growth Factor Receptors with Tyrosine Kinase Domain Mutations Exhibit Reduced Cbl Association, Poor Ubiquitylation, and Down-regulation but Are Efficiently Internalized (2023)

Supplementary Figure 4 from Epidermal Growth Factor Receptors with Tyrosine Kinase Domain Mutations Exhibit Reduced Cbl Association, Poor Ubiquitylation, and Down-regulation but Are Efficiently Internalized