gebhart/patrepeval huggingface dataset:
RMG nMOS 1<sup>st</sup> process enabling 10x lower gate resistivity in N7 bulk FinFETs (2015)

A novel RMG process in which the n-type work function metal (nWFM) is deposited first and then selectively removed from the pMOS devices is presented for the first time. The key benefit of this nMOS 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> process lies in increased gate-fill space which results in about 10× improvement in the pMOS effective gate resistivity at gate lengths (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) around 22 nm, an improvement which is predicted by modeling to extend down to L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> <;14 nm. The complete removal of the nWFM in the pMOS devices is evidenced by restored p-type effective work function (eWF) values in large area capacitors and matched pMOS threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) values in bulk FinFET devices with L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> down to 22 nm. Furthermore, selective removal of the nWFM is confirmed physically down to L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ~16 nm providing further evidence that the process is scalable towards N7 dimensions.
Dentate gyrus-specific knockdown of adult neurogenesis impairs spatial and object recognition memory in adult rats (2009)

New granule cells are born throughout life in the dentate gyrus of the hippocampal formation. Given the fundamental role of the hippocampus in processes underlying certain forms of learning and memory, it has been speculated that newborn granule cells contribute to cognition. However, previous strategies aiming to causally link newborn neurons with hippocampal function used ablation strategies that were not exclusive to the hippocampus or that were associated with substantial side effects, such as inflammation. We here used a lentiviral approach to specifically block neurogenesis in the dentate gyrus of adult male rats by inhibiting WNT signaling, which is critically involved in the generation of newborn neurons, using a dominant-negative WNT (dnWNT). We found a level-dependent effect of adult neurogenesis on the long-term retention of spatial memory in the water maze task, as rats with substantially reduced levels of newborn neurons showed less preference for the target zone in probe trials >2 wk after acquisition compared with control rats. Furthermore, animals with strongly reduced levels of neurogenesis were impaired in a hippocampus-dependent object recognition task. Social transmission of food preference, a behavioral test that also depends on hippocampal function, was not affected by knockdown of neurogenesis. Here we identified a role for newborn neurons in distinct aspects of hippocampal function that will set the ground to further elucidate, using experimental and computational strategies, the mechanism by which newborn neurons contribute to behavior.
Supplementary Table S5 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map (2023)

&lt;p&gt;Supplementary Table S5. Quantification of peptides identified bound to dasatinib by mass spectrometry.&lt;/p&gt;
Acceleration of computation of φ-polynomials (2013)

The benefits of making an effective use of impressive computational power offered by multi-core platforms are investigated for the computation of φ-polynomials used in the description of freeform surfaces. Specifically, we devise parallel algorithms based upon the recurrence relations of both Zernike polynomials and gradient orthogonal Q-polynomials and implement these parallel algorithms on Graphical Processing Units (GPUs) respectively. The results show that more than an order of magnitude improvement is achieved in computational time over a sequential implementation if these recurrence-based parallel algorithms are adopted in the computation of the φ-polynomials.
Carrier envelope phase noise in stabilized amplifier systems (2006)

Carrier envelope phase noise in femtosecond oscillators is analyzed with respect to the impact of high frequency phase fluctuations in such systems on chirped pulse amplifier phase stability.
Theory and computational techniques for analysis of discrete-time control systems with disturbances (2011)

Abstract Control problems with hard bounds on the control values, restrictions on the state trajectory over a finite time horizon, and guaranteed behaviour despite the disturbances, are difficult to solve using frequency-based design methods. Such problems have received much attention over the past decade. In order to address them one needs to study system evolution in the time domain. The central concept that emerges in such studies is that of the reach set. This paper is devoted to the formulation of the reachability problem for discrete-time dynamical systems with disturbances. The concept of maxmin and minmax forward and backward reach sets is addressed. Invariance of the backward reach set is discussed. The emphasis of the paper is on discrete-time linear systems, for which the ellipsoidal computational method is described. The synthesis of maxmin and minmax closed-loop control for steering the system to a given target set using ellipsoidal backward reach set approximations is explained. The ellipsoidal method covered in the paper is implemented in the Ellipsoidal Toolbox for MATLAB, a popular collection of ellipsoidal calculus routines freely available online. Keywords: discrete-time systems with disturbancesmaxmin/minmax closed-loop controlellipsoidal calculus Acknowledgements The authors thank Alexander B. Kurzhanski for his valuable advice and critical comments that helped shaping this article. Notes Parallelotope is a zonotope with 2 n vertices, where n is the state space dimension. Minkowski sum of sets is defined as . is nonempty if and only if both, 𝒲 and 𝒵 are nonempty. If 𝒲 and 𝒵 are convex, is convex. Hausdorff semidistance between compact sets is defined as where denotes inner product. Here we assume matrices A(·) to be nondegenerate. The Minkowski difference of sets is defined as . If 𝒲 and 𝒵 are convex, is convex if it is nonempty. Note that where is the closed convex hull and also the second Fenchel conjugate of g(l). See Citation36 for definitions. Note that for Equation(51) A(t) must be invertible. The symbol ‘≈’ means that and where ε>0, and its dependency on regularization coefficient α is described in Citation21. The target set may still be reached at time t 1, but only if the disturbance allows. T is given for the continuous-time system Equation(80). The general approach is to obtain internal ellipsoidal approximations for several values of l 1 and then select the one, for which the corresponding is the closest to x 0. For this particular example, the disturbance values were chosen randomly within their specified bounds. Additional informationNotes on contributorsPravin Varaiya Research supported by NSF Award DMS-0807771.
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease (2016)

Inflammatory bowel disease (IBD) is associated with risk variants in the human genome and dysbiosis of the gut microbiome, though unifying principles for these findings remain largely undescribed. The human commensal Bacteroides fragilis delivers immunomodulatory molecules to immune cells via secretion of outer membrane vesicles (OMVs). We reveal that OMVs require IBD-associated genes, ATG16L1 and NOD2, to activate a noncanonical autophagy pathway during protection from colitis. ATG16L1-deficient dendritic cells do not induce regulatory T cells (T(regs)) to suppress mucosal inflammation. Immune cells from human subjects with a major risk variant in ATG16L1 are defective in T(reg) responses to OMVs. We propose that polymorphisms in susceptibility genes promote disease through defects in "sensing" protective signals from the microbiome, defining a potentially critical gene-environment etiology for IBD.
Low kinetic-energy particle process for hillock-free pure aluminum metallization (2003)

Formation of hillock-free aluminum films has been realized by a low-kinetic-energy particle process. The process utilized the low-energy (a few tens of electron volts) Ar-ion bombardment of the growing film surface for modifying the thin-film properties. Completely
The Effects of Transcriptional Regulatory Sequences Introduced into a Retroviral Genome (1986)

Chimeric plasmids in which the herpes thymidine kinase (tk) gene replaced portions of the Rous sarcoma viral genome were used to assess the relationship between viral transcription and that of an exogenous gene located within the viral genome. The entire tk gene and portions of the gene were positioned in both orientations within the viral gag and pol genomic region (which serves as intron for viral env mRNA). Microinjection assays then determined the amount of viral genomic transcription by quantitation of the amount of viral env mRNA produced. Separate injections also assayed for the presence of tk mRNA. Both mRNAs were produced unless the 3' region of the tk gene was present within the viral genome and in the same transcriptional sense. In this case viral env mRNA production was nearly abolished.
Structural Stability and Prebiotic Properties of Resistant Starch Type 3 Increase Bile Acid Turnover and Lower Secondary Bile Acid Formation (2005)

Microbial metabolism is essential in maintaining a healthy mucosa in the large bowel, preferentially through butyrate specific mechanisms. This system depends on starch supply. Two structurally different resistant starches type 3 (RS3) have been investigated with respect to their resistance to digestion, fermentability, and their effects on the composition and turnover of bile acids in rats. RSA (a mixture of retrograded maltodextrins and branched high molecular weight polymers), which is more resistant than RSB (a retrograded potato starch), increased the rate of fermentation accompanied by a decrease of pH in cecum, colon, and feces. Because they were bound to RS3, less bile acids were reabsorbed, resulting in a higher turnover through the large bowel. Because of the rise of volume, the bile acid level was unchanged and the formation of secondary bile acids was partly suppressed. The results proved a strong relation between RS3, short chain fatty acid production, and microflora. However, butyrate specific benefits are only achieved by an intake of RS3 that result in good fermentation properties, which depend on the kind of the resistant starch structures.
Multiplexed Salivary Protein Profiling for Patients with Respiratory Diseases Using Fiber-Optic Bundles and Fluorescent Antibody-Based Microarrays (2013)

Over the past 40 years, the incidence and prevalence of respiratory diseases have increased significantly throughout the world, damaging economic productivity and challenging health care systems. Current diagnoses of different respiratory diseases generally involve invasive sampling methods such as induced sputum or bronchoalveolar lavage that are uncomfortable, or even painful, for the patient. In this paper, we present a platform incorporating fiber-optic bundles and antibody-based microarrays to perform multiplexed protein profiling of a panel of six salivary biomarkers for asthma and cystic fibrosis (CF) diagnosis. The platform utilizes an optical fiber bundle containing approximately 50,000 individual 4.5 μm diameter fibers that are chemically etched to create microwells in which modified microspheres decorated with monoclonal capture antibodies can be deposited. On the basis of a sandwich immunoassay format, the array quantifies human vascular endothelial growth factor (VEGF), interferon gamma-induced protein 10 (IP-10), interleukin-8 (IL-8), epidermal growth factor (EGF), matrix metalloproteinase 9 (MMP-9), and interleukin-1 beta (IL-1β) salivary biomarkers in the subpicomolar range. Saliva supernatants collected from 291 individuals (164 asthmatics, 71 CF patients, and 56 healthy controls (HC)) were analyzed on the platform to profile each group of patients using this six-analyte suite. It was found that four of the six proteins were observed to be significantly elevated (p < 0.01) in asthma and CF patients compared with HC. These results demonstrate the potential to use the multiplexed protein array platform for respiratory disease diagnosis.
The Effect of Granulocyte-colony Stimulating Factor on Rotator Cuff Healing After Injury and Repair (2015)

Postoperative stem cell mobilization agents may be an effective way to enhance rotator cuff repair. Future studies regarding the kinetics of mobilization, the homing capacity of mobilized cells to injured tissues, and the ability of homing cells to participate in regenerative pathways are necessary.
SkQ1 Ophthalmic Solution for Dry Eye Treatment: Results of a Phase 2 Safety and Efficacy Clinical Study in the Environment and During Challenge in the Controlled Adverse Environment Model (2016)

Miotech S.A.
High Precision Feedforward Tracking Control System for Next Generation Optical Disks (2011)

This paper proposes a new high-precision feedforward tracking control system in single-rate sampling. The experimental results confirm that the proposed system well suppresses the tracking error on condition of disk rotation speed 7200[rpm] DVD. Therefore, the proposed system realizes high-precision tracking control.
Machine Learning Guided Operational Intelligence from Synchrophasors (Final Report) (2021)

Schweitzer Engineering Laboratories (SEL) and Oregon State University (OSU) received over 27 terabytes of electrical power system phasor measurement unit (PMU) data for the Eastern, Western, and ERCOT interconnections. The dataset includes measurements spread across 446 PMUs from early 2016 to mid 2018 depending on the interconnect. The full dataset was split into a training and test (holdout) dataset by PNNL. All data was received in the Apache Parquet format. The overarching goal of this project is to develop and execute a strategy to mitigate data anomalies, perform analysis on the dataset, and detect anomalous events in the data.
Supplementary Figure 2 from Telomerase Peptide Vaccination in NSCLC: A Phase II Trial in Stage III Patients Vaccinated after Chemoradiotherapy and an 8-Year Update on a Phase I/II Trial (2023)

&lt;p&gt;PDF file - 2567KB&lt;/p&gt;
Simulation of liquid drop breakup behavior in a flow field using discrete element techniques (1992)

In this study, a discrete element technique was used to simulate drop breakup in two dimensions. A series of simulations in which the drop breakup occurred in the presence of a flow field was performed. The density ratio of the flow field to the drop in the simulations was comparable to many of the isothermal liquid/liquid drop breakup experiments performed to investigate hydrodynamic breakup during Fuel Coolant Interactions (FCIs). The randomly directed internal kinetic energy of the drop increased rapidly at the beginning of the interaction between the drop and the flow field due to momentum transfer from the flow field to the drop. After the initial increase in internal energy of the drop, the momentum transferred from the flow field to the drop in the form of translational kinetic energy of the center of mass of the drop. It was also observed that the drops simulated in the presence of a flow field required higher internal kinetic energies to fragment than did the drops observed in the simulations performed in the absence of a flow field.
Amphiphilic Glycoconjugated Porphyrin Heterodimers as Two‐Photon Excitable Photosensitizers: Design, Synthesis, Photophysical and Photobiological Studies (2018)

Abstract A new family of amphiphilic glycoconjugated porphyrin dimers usable in two‐photon photodynamic therapy was designed, prepared and characterized. The physicochemical and biological data were presented and discussed. Their two‐photon absorption cross section was determined, revealing quite good performances of the compounds (δ ≈ 300 GM at 880 nm for 2 and 3 and δ ≈ 1000 GM at 840 nm for 5 and 6 ). Despite their promising photophysical properties, porphyrin dimers are penalized by their low solubility and an insufficient penetration into tumour cells. Incorporation into nanocarriers such as lipid vesicles could be profitable, provided that the positioning and degree of freedom of the saccharide moieties are optimal to target the receptors of the cells of interest.
Functional analyses of lipocalin-type and hematopoietic prostaglandin D synthases. (2004)

Prostaglandin (PG) D synthase (PGDS) catalyzes the isomerization of PGH(2) to PGD(2), which acts as an endogenous somnogen and an allergic mediator. There are two distinct types of PGDS: one is lipocalin-type PGDS (L-PGDS) localized in the central nervous system, male genitals, and heart; and the other is hematopoietic PGDS (H-PGDS) in mast cells and Th2 lymphocytes. L-PGDS is the same as beta-trace, a major protein in human cerebrospinal fluid, and is also secreted into the seminal plasma and plasma. The L-PGDS concentration in various body fluids is useful as a marker for various diseases such as renal failure and coronary atherosclerosis. H-PGDS is a cytosolic enzyme and is a member of the Sigma class of glutathione S-transferase. We determined the X-ray crystallographic structures of H-PGDS and L-PGDS. We also generated the gene-knockout (KO) mice and the human enzyme-overexpressing transgenic mice for each PGDS. L-PGDS-KO mice lacked PGE(2)-induced tactile allodynia and rebound of non-rapid eye movement sleep after sleep deprivation. Human L-PGDS-overexpressing transgenic mice showed an increase in non-rapid eye movement sleep due to accumulation of PGD(2) in the brain after tail clipping. H-PGDS-KO mice showed an allergic reaction weaker than that of the wild-type mice.
Generation of the induced pluripotent stem cell line CSSi006-A (3681) from a patient affected by advanced-stage Juvenile Onset Huntington's Disease (2018)

Juvenile Onset Huntington's Disease (JOHD) is a rare variant of HD withage of onset ≤20 years, accounting for 3-10% of all HD patients. The rarity occurrence of JOHD cases, who severely progress towards mental and physical disability with atypical clinical manifestations compared to classical HD, are responsible of general lack of knowledge about this variant. We obtained a fully reprogrammed iPS cell line from fibroblasts of a JOHD patient carrying 65 CAG repeats and age at onset at age 15. At the biopsy time, the patient showed an advanced stage after 10 years of disease.
Medical Concept Embeddings for SNOMED-CT (Jan 2019 version) (2020)

This dataset contains the SNOMED-CT medical concept embeddings trained using the following text and graph embedding methods. Averaged Word Embedding (300) ELMo (1024) Universal Sentence Encoder (512) BERT (768) Deepwalk (128) Node2Vec (128) HARP (128) LINE (128) The tar file contains eight JSON files corresponding to the aforementioned embedding techniques. The number (in parenthesis) besides each embedding method represents the dimensionality of the embedding. Each JSON file contains a python dictionary of the form SNOMED concept ID (String): Embedding (List). If you find this resource useful in your research, please consider citing our paper: "Pattisapu, N., Patil, S., Palshikar, G. and Varma, V., Medical Concept Normalization by Encoding Target Knowledge, Proceedings of Machine Learning Research 116:246–259, 2020 Machine Learning for Health (ML4H) at NeurIPS 2019" Warning: The dataset size is large (~12 GB). Please ensure that you have sufficient network bandwidth and disk space before requesting a download.
Improved blind demixing methods for recovering dense neuronal morphology from barcode imaging data (2021)

Abstract Cellular barcoding methods offer the exciting possibility of ‘infinite-pseudocolor’ anatomical reconstruction — i.e., assigning each neuron its own random unique barcoded ‘pseudocolor,’ and then using these pseudocolors to trace the microanatomy of each neuron. Here we use simulations, based on densely-reconstructed electron microscopy microanatomy, with signal structure matched to real barcoding data, to quantify the feasibility of this procedure. We develop a new blind demixing approach to recover the barcodes that label each neuron. We also develop a neural network which uses these barcodes to reconstruct the neuronal morphology from the observed fluorescence imaging data, ‘connecting the dots’ between discontiguous amplicon signals. We find that accurate recovery should be feasible, provided that the barcode signal density is sufficiently high. This study suggests the possibility of mapping the morphology and projection pattern of many individual neurons simultaneously, at high resolution and at large scale, via conventional light microscopy.
Discovering Digital Tumor Signatures—Using Latent Code Representations to Manipulate and Classify Liver Lesions (2021)

Modern generative deep learning (DL) architectures allow for unsupervised learning of latent representations that can be exploited in several downstream tasks. Within the field of oncological medical imaging, we term these latent representations "digital tumor signatures" and hypothesize that they can be used, in analogy to radiomics features, to differentiate between lesions and normal liver tissue. Moreover, we conjecture that they can be used for the generation of synthetic data, specifically for the artificial insertion and removal of liver tumor lesions at user-defined spatial locations in CT images. Our approach utilizes an implicit autoencoder, an unsupervised model architecture that combines an autoencoder and two generative adversarial network (GAN)-like components. The model was trained on liver patches from 25 or 57 inhouse abdominal CT scans, depending on the experiment, demonstrating that only minimal data is required for synthetic image generation. The model was evaluated on a publicly available data set of 131 scans. We show that a PCA embedding of the latent representation captures the structure of the data, providing the foundation for the targeted insertion and removal of tumor lesions. To assess the quality of the synthetic images, we conducted two experiments with five radiologists. For experiment 1, only one rater and the ensemble-rater were marginally above the chance level in distinguishing real from synthetic data. For the second experiment, no rater was above the chance level. To illustrate that the "digital signatures" can also be used to differentiate lesion from normal tissue, we employed several machine learning methods. The best performing method, a LinearSVM, obtained 95% (97%) accuracy, 94% (95%) sensitivity, and 97% (99%) specificity, depending on if all data or only normal appearing patches were used for training of the implicit autoencoder. Overall, we demonstrate that the proposed unsupervised learning paradigm can be utilized for the removal and insertion of liver lesions at user defined spatial locations and that the digital signatures can be used to discriminate between lesions and normal liver tissue in abdominal CT scans.