gebhart/patrepeval huggingface dataset:
Association of polybromo-associated BAF (PBAF) complex mutations with overall survival (OS) in cancer patients (pts) treated with checkpoint inhibitors (ICIs). (2019)

103 Background: ICIs have shown benefit across several metastatic carcinomas, yet predictive biomarkers are still lacking. 20% of malignancies harbor alterations in ≥1gene that is part of PBAF complex. With recent data suggesting an association between PBRM1 mutations (mts) and outcomes in renal cell carcinoma (RCC) pts treated with ICIs (Miao, Science, 2018), we examined the association between PBAF mts and OS in ICI-treated patients across several solid cancer (ca) types. Methods: Of 6007 pts with different ca histologies and targeted exome sequencing (Oncopanel) at Dana Farber Cancer institute (DFCI), 138 pts had truncating mts in any PBAF gene (SMARCA4, PBRM1, and ARID2) or oncogenic missense mts in SMARCA4 and were treated with ICIs. 138 histology-matched DFCI pts had none. A publicly-available cohort (2:1 histology matched) from Memorial Sloan Kettering (MSKCC) (Samstein et al., Nature Genetics, 2019) of 621 ca pts (PBAF mutant [MT] = 207, PBAF wild type [WT] = 414) treated with ICIs was analyzed for association between PBAF mts and OS. OS was defined from time from ICI initiation. OS was compared by Cox regression between PBAF MT and PBAF WT. Hazard ratio (HR) was derived using univariable and multivariable analysis (MVA) adjusted for ICI regimen (single vs combination) and age. Results: Median (Md) follow-up for the combined cohort (n = 897) was 27 months (m). Major histologies were non-small cell lung ca (268; 29.9%), melanoma (220; 24.5%), RCC (181; 20.2%), and bladder ca (65; 7.2%). Results on univariable and MVA analyses from individual and combined cohorts are presented below. Conclusions: PBAF mts are associated with survival in ICI-treated ca pts. Work in progress with non-ICI treated pts will determine if this is prognostic or predictive of response. [Table: see text]
3D Support for Business Process Simulation (2009)

Simulation is a key technique for the design and redesign of business processes and is used to evaluate new business process models with respect to key performance indicators. The increasing complexity of todaypsilas business processes hampers a quick identification of weak points of a business process design that were uncovered during simulation. In this paper we add a third dimension into the description of process and data objects, which enables a compact 3D view of objects in process modeling as well as simulation. The benefits are statistical analysis of simulation results based on volume and size changes of 3D process and data objects as well as customized 3D simulation views. First evaluations indicate the effectiveness of our approach, which goes beyond conventional simulation tools for business processes.
Manipulation of Lignin Monomer Composition Combined with the Introduction of Monolignol Conjugate Biosynthesis Leads to Synergistic Changes in Lignin Structure (2022)

The complexity of lignin structure impedes efficient cell wall digestibility. Native lignin is composed of a mixture of three dominant monomers, coupled together through a variety of linkages. Work over the past few decades has demonstrated that lignin composition can be altered through a variety of mutational and transgenic approaches such that the polymer is derived almost entirely from a single monomer. In this study, we investigated changes to lignin structure and digestibility in Arabidopsis thaliana in near-single-monolignol transgenics and mutants and determined whether novel monolignol conjugates, produced by a FERULOYL-CoA MONOLIGNOL TRANSFERASE (FMT) or a p-COUMAROYL-CoA MONOLIGNOL TRANSFERASE (PMT), could be integrated into these novel polymers to further improve saccharification efficiency. Monolignol conjugates, including a new conjugate of interest, p-coumaryl p-coumarate, were successfully integrated into high-H, high-G and high-S lignins in A. thaliana. Regardless of lignin composition, FMT- and PMT-expressing plants produced monolignol ferulates and monolignol p-coumarates, respectively, and incorporated them into their lignin. Through the production and incorporation of monolignol conjugates into near-single-monolignol lignins, we demonstrated that substrate availability, rather than monolignol transferase substrate preference, is the most important determining factor in the production of monolignol conjugates, and lignin composition helps dictate cell wall digestibility.
RACE (2013)

A wide range of applications, including bioinformatics, time series, and log analysis, depend on the identification of repetitions in very long sequences. The problem of finding maximal pairs subsumes most important types of repetition-finding tasks. Existing solutions require both the input sequence and its index (typically an order of magnitude larger than the input) to fit in memory. Moreover, they are serial algorithms with long execution time. Therefore, they are limited to small datasets, despite the fact that modern applications demand orders of magnitude longer sequences. In this paper we present RACE, a parallel system for finding maximal pairs in very long sequences. RACE supports parallel execution on stand-alone multicore systems, in addition to scaling to thousands of nodes on clusters or supercomputers. RACE does not require the input or the index to fit in memory; therefore, it supports very long sequences with limited memory. Moreover, it uses a novel array representation that allows for cache-efficient implementation. RACE is particularly suitable for the cloud (e.g., Amazon EC2) because, based on availability, it can scale elastically to more or fewer machines during its execution. Since scaling out introduces overheads, mainly due to load imbalance, we propose a cost model to estimate the expected speedup, based on statistics gathered through sampling. The model allows the user to select the appropriate combination of cloud resources based on the provider's prices and the required deadline. We conducted extensive experimental evaluation with large real datasets and large computing infrastructures. In contrast to existing methods, RACE can handle the entire human genome on a typical desktop computer with 16GB RAM. Moreover, for a problem that takes 10 hours of serial execution, RACE finishes in 28 seconds using 2,048 nodes on an IBM BlueGene/P supercomputer.
Figure S3 from MCL1 and DEDD Promote Urothelial Carcinoma Progression (2023)

&lt;p&gt;DEDD overexpression confers resistance to TNFα mediated apoptosis.&lt;/p&gt;
Efficient 3D Fully Convolutional Networks for Pulmonary Lobe Segmentation in CT Images (2019)

The human lung is a complex respiratory organ, consisting of five distinct anatomic compartments called lobes. Accurate and automatic segmentation of these pulmonary lobes from computed tomography (CT) images is of clinical importance for lung disease assessment and treatment planning. However, this task is challenging due to ambiguous lobar boundaries, anatomical variations and pathological deformations. In this paper, we propose a high-resolution and efficient 3D fully convolutional network to automatically segment the lobes. We refer to the network as Pulmonary Lobe Segmentation Network (PLS-Net), which is designed to efficiently exploit 3D spatial and contextual information from high-resolution volumetric CT images for effective volume-to-volume learning and inference. The PLS-Net is based on an asymmetric encoder-decoder architecture with three novel components: (i) 3D depthwise separable convolutions to improve the network efficiency by factorising each regular 3D convolution into two simpler operations; (ii) dilated residual dense blocks to efficiently expand the receptive field of the network and aggregate multi-scale contextual information for segmentation; and (iii) input reinforcement at each downsampled resolution to compensate for the loss of spatial information due to convolutional and downsampling operations. We evaluated the proposed PLS-Net on a multi-institutional dataset that consists of 210 CT images acquired from patients with a wide range of lung abnormalities. Experimental results show that our PLS-Net achieves state-of-the-art performance with better computational efficiency. Further experiments confirm the effectiveness of each novel component of the PLS-Net.
Exploiting Social Media to enhance Clinical Decision Support (2019)

Social media are increasingly used to collect data and report on the personal health status, on health issues, symptoms and experiences with treatments. The health data that is, thus, becoming available represents a valuable source for continuous health monitoring and prevention, and clinical decision making.
Ferrier Carbocyclization Reaction (2015)

The Ferrier carbocyclization reaction is an important carbohydrate-based transformation in organic synthesis. The reaction is highly effective for the conversion of readily available aldohexoses into enantiomerically pure cyclohexanones. This chapter focuses on the Ferrier carbocyclization reaction and its applications to natural product synthesis. Chiral cyclohexanones obtained by the Ferrier carbocyclization reaction are useful precursors for the synthesis of cyclitols and aminocyclitols, some of which are found in clinically important aminoglycoside antibiotics. The substrates for the Ferrier carbocyclization reaction are 6-deoxy-hex-5-enopyrano side derivatives. The chapter provides an overview of some representative syntheses of 5-enopyranosides. The applications of Ferrier carbocyclization reaction include the syntheses of hygromycin A, lycoricidine, (-)- and (+)-actinoboline, galanthamine, rapamycin, and morphine.
Forward Time Domain Ground Penetrating Radar Modeling of Scattering from Anomalies in the Presence of Steel Reinforcements (2009)

Ground penetrating radar (GPR) for nondestructive testing is applied to civil infrastructure such as bridges and roadways. Conventional methods of processing and analyzing GPR data for civil infrastructure are often qualitative, using relative reflection amplitude from subsurface boundaries or reinforcing steel (rebars) as an indicator of health. A Finite Difference Time Domain (FDTD) simulation of GPR is used to generate a bridge deck response of a heterogeneous model of a healthy bridge deck. The result is a healthy deck background that can be removed from measured data to bring anomalies to attention. For the purpose of this article, the measured data is also simulated. In lieu of modeling the identified rebars as perfect electrical conductors (PECs), they are modeled as hard point source excitations to allow for examination of the effect that the scattered waves from the rebar can have on an anomaly. This is an important consideration for application of many inversion methods.
TEXTAL TM : Artificial Intelligence Techniques for Automated Protein Structure Determination. (2003)

X-ray crystallography is the most widely used method for determining the three-dimensional structures of proteins and other macromolecules. One of the most difficult steps in crystallography is interpreting the 3D image of the electron density cloud surrounding the protein. This is often done manually by crystallographers and is very time-consuming and error-prone. The difficulties stem from the fact that the domain knowledge required for interpreting electron density data is uncertain. Thus crystallographers often have to resort to intuitions and heuristics for decision-making. The problem is compounded by the fact that in most cases, data available is noisy and blurred. TEXTAL ™ is a system designed to automate this challenging process of inferring the atomic structure of proteins from electron density data. It uses a variety of AI and pattern recognition techniques to try to capture and mimic the intuitive decision-making processes of experts in solving protein structures. The system has been quite successful in determining various protein structures, even with average quality data. The initial structure built by TEXTAL ™ can be used for subsequent manual refinement by a crystallographer, and combined with post-processing routines to generate a more complete model.
Low Threshold Current and High Relaxation Oscillation Frequency of Short-Cavity Integrable InP/InGaAsP BRS Laser (1990)

We describe the fabrication and modulation characteristics of short cavity InP/InGaAsP buried ridge stripe (BRS) lasers with ion beam etched facets. A CW threshold current as low as 9 mA is achieved for 50 µm-long cavity laser. A relaxation oscillation frequency in excess of 17 GHz is observed in such laser for an output optical power of only 9 mW/facet. The small signal -3 dB modulation frequency of such device is 11.5 GHz and is limited by the parasitic impedances of the BRS structure.
An Improved Device for X-Ray Diffraction Studies at Low Temperatures (1951)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Benjamin Post, Robert S. Schwartz, I. Fankuchen; An Improved Device for X‐Ray Diffraction Studies at Low Temperatures. Rev. Sci. Instrum. 1 March 1951; 22 (3): 218–219. https://doi.org/10.1063/1.1745893 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioReview of Scientific Instruments Search Advanced Search |Citation Search
Innentitelbild: Molecularly Imprinted Nanogels Acquire Stealth In Situ by Cloaking Themselves with Native Dysopsonic Proteins (Angew. Chem. 25/2017) (2017)

Durch Albumin getarnte Nanogele als unsichtbare Nanotransporter: In der Zuschrift auf S. 7194 beschreiben T. Takeuchi et al. die regulierte Bildung einer Proteinhülle durch molekulares Prägen polymerer Nanogele. Die Nanogele tarnen sich nach intravenöser Injektion in situ durch Anlagerung einer Albumin-reichen Hülle. Da sie passiv in Tumorgewebe akkumulieren, könnte diese Strategie zur Entwicklung von Wirkstofftransportsystemen für die Krebstherapie beitragen.
Granuloma Formation, a Rare Complication after PDO Threads Lifting, and Adjuvant Treatment Using Dual-Frequency Ultrasound (LDM®-MED) (2019)

Thread-lifting is a minimally invasive procedure that shows good results and fewer complications as compared with those results and complications of standard surgery. Many procedures and techniques have been developed to create a younger appearance of facial/neck skin for aging people, and the demand for an improved aesthetic appearance is increasing. Since the incidence of side effects is much less than that of non-absorbable threads, which can lead to complications such as foreign body reactions, polydioxanone (PDO) threads are predominantly used for face lift procedures. A 66-year-old woman presented to our clinic with inflamed palpable masses. She had undergone a face lift with absorbable threads in our clinic 5 months previously. Excisional biopsy was performed with the patient under local anesthesia. During the operation, any threads were not detected and there was both fibrotic scar tissue and granulomatous tissue. For effectively promoting healing and managing the scars, treatment with LDM®-MED was performed on the day after surgery. The treatment was performed according to the author’s protocol. Although foreign body granuloma as a complication after using non-absorbable thread types have been previously reported, it is relatively rare to find this type of complication after using absorbable thread. In this report, we present a case in which a 66-year-old female with foreign body granuloma after undergoing a face lift using absorbable threads was treated with the application of dual-frequency ultrasound, which promoted wound healing.
Assessing ranking and effectiveness of evolutionary algorithm hyperparameters using global sensitivity analysis methodologies (2022)

We present a comprehensive global sensitivity analysis of two single-objective and two multi-objective state-of-the-art global optimization evolutionary algorithms as an algorithm configuration problem. That is, we investigate the quality of influence hyperparameters have on the performance of algorithms in terms of their direct effect and interaction effect with other hyperparameters. Using three sensitivity analysis methods, Morris LHS, Morris, and Sobol, to systematically analyze tunable hyperparameters of covariance matrix adaptation evolutionary strategy, differential evolution, non-dominated sorting genetic algorithm III, and multi-objective evolutionary algorithm based on decomposition, the framework reveals the behaviors of hyperparameters to sampling methods and performance metrics. That is, it answers questions like what are hyperparameters influence patterns, how they interact, how much they interact, and how much their direct influence is. Consequently, the ranking of hyperparameters suggests their order of tuning, and the pattern of influence reveals the stability of the algorithms.
Shape shifting pain: chronification of back pain shifts brain representation from nociceptive to emotional circuits (2013)

Chronic pain conditions are associated with abnormalities in brain structure and function. Moreover, some studies indicate that brain activity related to the subjective perception of chronic pain may be distinct from activity for acute pain. However, the latter are based on observations from cross-sectional studies. How brain activity reorganizes with transition from acute to chronic pain has remained unexplored. Here we study this transition by examining brain activity for rating fluctuations of back pain magnitude. First we compared back pain-related brain activity between subjects who have had the condition for ∼2 months with no prior history of back pain for 1 year (early, acute/subacute back pain group, n = 94), to subjects who have lived with back pain for >10 years (chronic back pain group, n = 59). In a subset of subacute back pain patients, we followed brain activity for back pain longitudinally over a 1-year period, and compared brain activity between those who recover (recovered acute/sub-acute back pain group, n = 19) and those in which the back pain persists (persistent acute/sub-acute back pain group, n = 20; based on a 20% decrease in intensity of back pain in 1 year). We report results in relation to meta-analytic probabilistic maps related to the terms pain, emotion, and reward (each map is based on >200 brain imaging studies, derived from neurosynth.org). We observed that brain activity for back pain in the early, acute/subacute back pain group is limited to regions involved in acute pain, whereas in the chronic back pain group, activity is confined to emotion-related circuitry. Reward circuitry was equally represented in both groups. In the recovered acute/subacute back pain group, brain activity diminished in time, whereas in the persistent acute/subacute back pain group, activity diminished in acute pain regions, increased in emotion-related circuitry, and remained unchanged in reward circuitry. The results demonstrate that brain representation for a constant percept, back pain, can undergo large-scale shifts in brain activity with the transition to chronic pain. These observations challenge long-standing theoretical concepts regarding brain and mind relationships, as well as provide important novel insights regarding definitions and mechanisms of chronic pain.
Getting Started (2014)

I spend a great deal of time working with Oracle technology. Often I’m called in to assist with diagnosing and resolving performance issues. Many of the applications I’ve worked with have experienced problems in part due to the developers (and to some degree database administrators) treating the database as if it was a black box. In other words, the team hadn’t spent any time becoming familiar with the database technology that was at the core of their application. In this regard, a fundamental piece of advice I have is do not treat the database as a nebulous piece of software to which you simply feed queries and receive results. The database is the most critical piece of most applications. Trying to ignore its internal workings and database vendor–specific features results architectural decisions from which high performance cannot be achieved.
N-version programming: a unified modeling approach (2002)

This paper presents an unified approach aimed at modeling the joint behavior of the N version system and its operational environment. Our objective is to develop reliability model that considers both functional and performance requirements which is particularly important for real-time applications. The model is constructed in two steps. First, the Markov model of N version failure and execution behavior is developed. Next, we develop the user-oriented model of the operational environment. In accounting for dependence we use the idea that the influence of the operational environment on versions failures and execution times induces correlation. The model addresses a number of basic issues and yet yields closed-form solutions that provide considerable insight into how reliability is affected by both versions characteristics and the operational environment.
A comparison between pure active pharmaceutical ingredients and therapeutic deep eutectic solvents: Solubility and permeability studies (2017)

THEDES, so called therapeutic deep eutectic solvents are here defined as a mixture of two components, which at a particular molar composition become liquid at room temperature and in which one of them is an active pharmaceutical ingredient (API). In this work, THEDES based on menthol complexed with three different APIs, ibuprofen (ibu), BA (BA) and phenylacetic acid (PA), were prepared. The interactions between the components that constitute the THEDES were studied by NMR, confirming that the eutectic system is formed by H-bonds between menthol and the API. The mobility of the THEDES components was studied by PFGSE NMR spectroscopy. It was determined that the self-diffusion of the species followed the same behavior as observed previously for ionic liquids, in which the components migrate via jumping between voids in the suprastructure created by punctual thermal fluctuations. The solubility and permeability of the systems in an isotonic solution was evaluated and a comparison with the pure APIs was established through diffusion and permeability studies carried out in a Franz cell. The solubility of the APIs when in the THEDES system can be improved up to 12 fold, namely for the system containing ibu. Furthermore, for this system the permeability was calculated to be 14×10<sup>-5</sup>cm/s representing a 3 fold increase in comparison with the pure API. With the exception of the systems containing PA an increase in the solubility, coupled with an increase in permeability was observed. In this work, we hence demonstrate the efficiency of THEDES as a new formulation for the enhancement of the bioavailability of APIs by changing the physical state of the molecules from a solid dosage to a liquid system.
Fast Video Search Algorithm for Large Video Database Using Adjacent Pixel Intensity Difference Quantization Histogram Feature (2009)

†† Summary In this paper, we present a fast and robust video search algorithm for large video database using the histogram feature which is essentially different from conventional ones. This algorithm is based on the adjacent pixel intensity difference quantization (APIDQ) algorithm, which had been reliably applied to human face recognition previously. An APIDQ histogram is utilized as the feature vector of a frame image. Combined with active search [4], a temporal pruning algorithm, fast and robust video search can be achieved. The proposed search algorithm has been evaluated by 6 hours of video to search for given 200 video clips which having a each length of 15 seconds. Experimental results show the proposed algorithm can detect the similar video clip in merely 80ms, and is more accurate and robust against Gaussian noise than conventional fast video search algorithm.