gebhart/patrepeval huggingface dataset:
Abstract 5361: Deep learning models capture high dimensional features for cell morphology analysis (2023)

Abstract Many methods for imaging and sorting tumor cells require biomarker labels that perturb cells and may create a selection bias. The Deepcell platform can characterize and sort cells using only brightfield images of unlabeled single cells, thereby enabling more comprehensive and unbiased assessment of tumor cell morphology and heterogeneity. Cells are imaged with a high-speed camera during microfluidic flow and brightfield images are analyzed in real-time by deep learning models to generate quantitative embeddings, which are reproducible and multi-dimensional descriptions of cell morphology. One of the key technical challenges in building this platform was the development of an AI model to extract features from cell images from diverse human cells without prior knowledge of specific cell types, cell preparation, or other application-specific knowledge for an exploratory approach. Deepcell’s ‘Human Foundation Model’ (HFM) is a feature encoder that transforms cell images into 128 dimensional embedding vectors. The model backbone, responsible for extracting image features, is based on the ResNet18 convolutional deep neural network architecture. Training utilizes a multi-task semi-supervised training framework that combines the VicReg self-supervised learning model, which learns images features without labels, along with supervised auxiliary models using labeled data. These sub-models enable the backbone model to recognize specific cell attributes such as granulation, pigmentation, characteristics of malignancy, attributes related to cellular states like apoptosis and necrosis. We augment the deep learning embeddings with computer vision derived cellular features, such as area, perimeter, intensity, and texture features to improve model interpretability and accuracy. Here, we describe how the HFM self-supervised backbone model was trained, the discriminatory power added by the supervised tasks, and validation of the reproducibility and generalization capabilities of the resulting model. We also demonstrate how the resulting embeddings can be visualized using the Deepcell Cloud software and how clusters of cells in our embedding space can be related to cell images, interpretable morphological features, and actionable biological characteristics. Potential applications of the Deepcell platform are diverse and promising, such as label-free enrichment of malignant cells and discovery of morphologically distinct subpopulations of heterogeneous cancer cell samples. Citation Format: Kevin B. Jacobs, Kiran Saini, Nianzhen Li, Senzeyu Zhang, Ryan Carelli, Amy Wong-Thai, Stephane C. Boutet, Anastasia Mavropoulos, Andreja Jovic, Jeanette Mei, Mahyar Salek, Maddison Masaeli. Deep learning models capture high dimensional features for cell morphology analysis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5361.
JustRunIt: experiment-based management of virtualized data centers (2009)

Managing data centers is a challenging endeavor. State-of-the-art management systems often rely on analytical modeling to assess the performance, availability, and/or energy implications of potential management decisions or system configurations. In this paper, we argue that actual experiments are cheaper, simpler, and more accurate than models for many management tasks. To support this claim, we built an infrastructure for experimentbased management of virtualized data centers, called JustRunIt. The infrastructure creates a sandboxed environment in which experiments can be run--on a very small number of machines--using real workloads and real system state, but without affecting the on-line system. Automated management systems or the system administrator herself can leverage our infrastructure to perform management tasks on the on-line system. To evaluate the infrastructure, we apply it to two common tasks: server consolidation/expansion and evaluating hardware upgrades. Our evaluation demonstrates that JustRunIt can produce results realistically and transparently, and be nicely combined with automated management systems.
Scale-Driven Iterative Optimization for Brain Extraction and Registration (2006)

We present a novel framework to automatically separate brain region from other non-brain regions in head images. The idea of the proposed method is to estimate larger scale patterns in an image and then correct the boundaries iteratively. The scale estimation is based on the recently proposed total variation (TV) regularized L^1 functional. An iterative optimization method is used to refine non-convex and acute angle boundaries. The final algorithm is able to extract large scale patterns with arbitrary shapes, which is particularly suitable for brain extraction. In order to reduce the computation overhead in 3D data, a multi-level technique is proposed to exponentially improve the speed of the brain extraction process. Based on accurate results of brain extraction, a non-rigid brain registration algorithm is proposed to improve accuracy and consistency of existing registration methods. Experimental results on real 3D brain MR images demonstrate that the proposed methods outperform existing solutions. In addition, results are provided to show that the proposed algorithm can also be used to segment large scale patterns in general images.
Use of Inhaled Anticholinergic Agents in Obstructive Airway Disease (2007)

In the last 2 decades, anticholinergic agents have been generally regarded as the first-choice bronchodilator therapy in the routine management of stable chronic obstructive pulmonary disease (COPD) and, to a lesser extent, asthma. Anticholinergics are particularly important bronchodilators in COPD, because the vagal tone appears to be the only reversible component of airflow limitation in COPD. The inhaled anticholinergics approved for clinical use are synthetic quaternary ammonium congeners of atropine, and include ipratropium bromide, oxitropium bromide, and tiotropium bromide. This article reviews the most current evidence for inhaled anticholinergics in obstructive airway disease and summarizes outcomes reported in randomized controlled trials.
Screening of tau protein kinase inhibitors in a tauopathy-relevant cell-based model of tau hyperphosphorylation and oligomerization (2020)

Tauopathies are a class of neurodegenerative disorders characterized by abnormal deposition of post-translationally modified tau protein in the human brain. Tauopathies are associated with Alzheimer's disease (AD), chronic traumatic encephalopathy (CTE), and other diseases. Hyperphosphorylation increases tau tendency to aggregate and form neurofibrillary tangles (NFT), a pathological hallmark of AD. In this study, okadaic acid (OA, 100 nM), a protein phosphatase 1/2A inhibitor, was treated for 24h in mouse neuroblastoma (N2a) and differentiated rat primary neuronal cortical cell cultures (CTX) to induce tau-hyperphosphorylation and oligomerization as a cell-based tauopathy model. Following the treatments, the effectiveness of different kinase inhibitors was assessed using the tauopathy-relevant tau antibodies through tau-immunoblotting, including the sites: pSer202/pThr205 (AT8), pThr181 (AT270), pSer202 (CP13), pSer396/pSer404 (PHF-1), and pThr231 (RZ3). OA-treated samples induced tau phosphorylation and oligomerization at all tested epitopes, forming a monomeric band (46-67 kDa) and oligomeric bands (170 kDa and 240 kDa). We found that TBB (a casein kinase II inhibitor), AR and LiCl (GSK-3 inhibitors), cyclosporin A (calcineurin inhibitor), and Saracatinib (Fyn kinase inhibitor) caused robust inhibition of OA-induced monomeric and oligomeric p-tau in both N2a and CTX culture. Additionally, a cyclin-dependent kinase 5 inhibitor (Roscovitine) and a calcium chelator (EGTA) showed contrasting results between the two neuronal cultures. This study provides a comprehensive view of potential drug candidates (TBB, CsA, AR, and Saracatinib), and their efficacy against tau hyperphosphorylation and oligomerization processes. These findings warrant further experimentation, possibly including animal models of tauopathies, which may provide a putative Neurotherapy for AD, CTE, and other forms of tauopathy-induced neurodegenerative diseases.
Carbon Nanotube Synthesis Using Mesoporous Silica Templates (2002)

Well-aligned carbon nanotubes (CNTs) were grown on mesoporous silica films by chemical vapor deposition (CVD). Ethylene was used as the carbon source and CVD was performed at 1023 K and atmospheric pressure. The films were doped with Fe during sol−gel synthesis, and three different structure directing agents were used for mesoporous silica preparation: polyoxyethylene (10) cetyl ether (C16EO10), Pluronic tri-block copolymer (P123), and cetyltriethylammonium chloride (CTAC). A high degree of CNT alignment on C16EO10 mesoporous silica films was produced at Fe:Si molar ratio of 1.80. Similar alignment of CNTs was achieved in the other preparations, but on CTAC-derived films CNTs only grew parallel to the substrate surface because the in-plane arrangement of the pore structure limited CNT growth to crack domains. We also show that the diameter of the CNTs can be controlled by changing the Fe concentration in the mesoporous silica substrate.
Realistic hair simulation (2008)

The last five years have seen a profusion of innovative solutions to one of the most challenging tasks in character synthesis: hair simulation. This class covers both recent and novel research ideas in hair animation and rendering, and presents time tested industrial practices that resulted in spectacular imagery.
Encapsulated Cells Expressing a Chemotherapeutic Activating Enzyme Allow the Targeting of Subtoxic Chemotherapy and Are Safe and Efficacious: Data from Two Clinical Trials in Pancreatic Cancer (2014)

Despite progress in the treatment of pancreatic cancer, there is still a need for improved therapies. In this manuscript, we report clinical experience with a new therapy for the treatment of pancreatic cancer involving the implantation of encapsulated cells over-expressing a cytochrome P450 enzyme followed by subsequent low-dose ifosfamide administrations as a means to target activated ifosfamide to the tumor. The safety and efficacy of the angiographic instillation of encapsulated allogeneic cells overexpressing cytochrome P450 in combination with low-dose systemic ifosfamide administration has now been evaluated in 27 patients in total. These patients were successfully treated in four centers by three different interventional radiologists, arguing strongly that the treatment can be successfully used in different centers. The safety of the intra-arterial delivery of the capsules and the lack of evidence that the patients developed an inflammatory or immune response to the encapsulated cells or encapsulation material was shown in all 27 patients. The ifosfamide dose of 1 g/m2/day used in the first trial was well tolerated by all patients. In contrast, the ifosfamide dose of 2 g/m2/day used in the second trial was poorly tolerated in most patients. Since the median survival in the first trial was 40 weeks and only 33 weeks in the second trial, this strongly suggests that there is no survival benefit to increasing the dose of ifosfamide, and indeed, a lower dose is beneficial for quality of life and the lack of side effects. This is supported by the one-year survival rate in the first trial being 38%, whilst that in the second trial was only 23%. However, taking the data from both trials together, a total of nine of the 27 patients were alive after one year, and two of these nine patients were alive for two years or more.
Resistance of macrophages to the suppressive effect of interleukin-10 following thermal injury (2001)

The activation of a macrophage (Mphi)-dependent proinflammatory cascade following thermal injury plays an important role in the development of immunosuppression and increased susceptibility to subsequent sepsis in burn patients. In contrast, although interleukin (IL)-10, an anti-inflammatory cytokine that can downregulate M phi activity, has also been implicated in postburn immune dysfunction, its role in the regulation of M phi function postburn remains unclear. To study this, C57BL/6 female mice were subjected to a 25% total body surface area third-degree scald burn, and splenic Mphis were isolated 7 days later. Lipopolysaccharide (LPS)-stimulated IL-10, IL-6, tumor necrosis factor (TNF)-alpha, and nitric oxide (NO) production were significantly increased in the burn group compared with shams. Blockade of endogenous IL-10 activity enhanced IL-6 and TNF-alpha release, but not NO release, in both groups. The addition of exogenous IL-10 to the M phi cultures dose dependently suppressed production of these inflammatory mediators in both groups. The timing of IL-10 addition to the cultures in relation to LPS stimulation, however, was critical. The suppressive effect of exogenous IL-10 was attenuated in both groups when the cells were exposed to IL-10 at 4-6 h after LPS stimulation; however, Mphis from injured mice were significantly better able to maintain inflammatory mediator-productive capacity. The resistance of Mphis from injured mice to IL-10-mediated suppression correlated with decreased IL-10 receptor (IL-10R) expression and increased CD11b expression. These findings suggest that Mphis, following thermal injury, display resistance to suppression by IL-10 due in part to downregulation of IL-10R expression.
Early results of high‐flex total knee arthroplasty: comparison study at 1 year after surgery (2006)

We compared clinical [including maximal flexion and range of motion (ROM)] and radiographical outcomes of high-flex versus conventional implants for total knee arthroplasty (TKA) after 1 year. We also analyzed the factors affecting postoperative ROM in high-flex implants. The high-flex group (n=90) had an average maximal flexion of 129.8 degrees (standard deviation (SD), 5.2 degrees ) significantly higher than the 124.3 degrees (SD, 9.2 degrees ) of the conventional group (n=90), especially for patients with less than 90 degrees of knee flexion (P<0.05). There was no significant difference in hospital for special surgery (HSS) score between the two groups. No knee developed osteolysis, aseptic loosening, or other complications. We found that, for high-flex implants, preoperative ROM had a significant effect on postoperative ROM.
Flow Field Analysis and Defrosting Cycle Optimization in a Large-scale Industrial Cold- storage Facility (2014)

We report a joint theoretical and experiment analysis of an industrial cold-storage unit for a large-scale poultry processing enterprise in the Central Plains Economic Zone of China. The flow field inside the unit was analyzed using computational fluid dynamics, which identified an optimum forced air supply of 2.05 m s<SUP>-1</SUP>. The defrosting cycle was then optimized experimentally, resulting in an improved defrosting method and a monthly saving of 5,530 RMB in electricity costs. Furthermore, we achieved a reduction in the temperature variation of 1.82% and in the coefficient of performance variation of 1.89%. The refrigerating capacity and electricity costs per unit of production were decreased by 8.30% and 10.20%, respectively.
A Diabetes Dashboard and Physician Efficiency and Accuracy in Accessing Data Needed for High-Quality Diabetes Care (2011)

Using a patient-specific diabetes dashboard improves both the efficiency and accuracy of acquiring data needed for high-quality diabetes care. Usability analysis tools can provide important insights into the value of optimizing physician use of health information technologies.
A Variational Approach to Video Registration with Subspace Constraints (2013)

This paper addresses the problem of non-rigid video registration, or the computation of optical flow from a reference frame to each of the subsequent images in a sequence, when the camera views deformable objects. We exploit the high correlation between 2D trajectories of different points on the same non-rigid surface by assuming that the displacement of any point throughout the sequence can be expressed in a compact way as a linear combination of a low-rank motion basis. This subspace constraint effectively acts as a trajectory regularization term leading to temporally consistent optical flow. We formulate it as a robust soft constraint within a variational framework by penalizing flow fields that lie outside the low-rank manifold. The resulting energy functional can be decoupled into the optimization of the brightness constancy and spatial regularization terms, leading to an efficient optimization scheme. Additionally, we propose a novel optimization scheme for the case of vector valued images, based on the dualization of the data term. This allows us to extend our approach to deal with colour images which results in significant improvements on the registration results. Finally, we provide a new benchmark dataset, based on motion capture data of a flag waving in the wind, with dense ground truth optical flow for evaluation of multi-frame optical flow algorithms for non-rigid surfaces. Our experiments show that our proposed approach outperforms state of the art optical flow and dense non-rigid registration algorithms.
Quality-of-service oriented medium access control for wireless ATM networks (1997)

The medium access control (MAC) protocol and the underlying traffic scheduling algorithm developed within project Magic WAND (Wireless ATM Network Demonstrator) are presented. Magic WAND is investigating wireless ATM technology for customer premises networks in the framework of the Advanced Communications Technologies and Services (ACTS) program funded by the European Union. The MAC protocol, known as MASCARA, is a hub-based, adaptive TDMA scheme which combines reservation- and contention-based access methods to provide multiple access efficiency and quality-of-service guarantees to wireless ATM terminal connections sharing a common radio channel. The traffic scheduling algorithm is delay-oriented to meet the requirements of the various traffic classes defined by the ATM architecture. The results of the simulation of a number of scenarios are presented to assess the performance of the proposed algorithm.
The relationship between brain activity and accuracy of replicating actions in the process of embodied knowledge acquisition (2016)

In this paper, we analyze the relationship between brain activity and accuracy of replicating actions in the process of embodied knowledge acquisition. Subjects learned a series of actions as fundamental embodied knowledge as a experiment. Remembering and executing the actions, oxy hemoglobin increase in dorsolateral prefrontal area and decrease in frontal pole. Subjects watched a video crip of a working procedure, and executed the same series of actions as another experiment.. We conducted this experiment twice. After the first experiment, we set up three practice terms. In the observation task, oxy hemoglobin stabilize at a low level in dorsolateral prefrontal area and frontal pole with elevation of accuracy of replicating actions. In the execution task, oxy hemoglobin increase in dorsolateral prefrontal area and decrease in frontal pole with elevation of accuracy of replicating actions. These results suggest frontal pole relate self body imaging and dorsolateral prefrontal area relate working memory, and activity in these areas changes during the process of embodied knowledge acquisition.
High transmission float glass for solar applications (2000)

Antireflective quarter-wave single layers with an improved abrasion resistance were prepared from sols by dip coating of float glasses, which can be used for covering solar cells and collectors. The coating sols are based on tetraalkoxysilane hydrolyzed in the presence of different organic additives, eg. polymers. This kind of sols lead to a stable pore structure in the pre-annealed film, which allows to treat it even at temperatures neccessary for glass strengthening. A heat treatment above 600 °C improved the abrasion resistance, but was not accompained by a reduction of the pore volume as would commonly be expected. The resulting porous film therefore showed the required effective refractive index of &lt; 1.3, and increased the transmission of such coated low-iron glass up to 99.6 % in the visible spectral range and 97.0 % in the solar spectral range.
Market Impact of Domestic Offset Programs (2010)

Three recent reports have estimated the market impacts of domestic offset programs, including afforestation, contained in the American Clean Energy and Security Act (ACES). The magnitude of these estimated impacts motivates this study. We show that with carbon prices as low as $30 per metric ton, a significant number of U.S. crop acres would be used to grow trees and this would cause price increases for some U.S. commodities. Although we present only one carbon price scenario, the modeling approach that we use suggests that the acreage and price impacts we describe here would increase at higher carbon prices.
Modification of paclitaxel metabolism in a cancer patient by induction of cytochrome P450 3A4. (1998)

Biliary, plasma, and urinary disposition of paclitaxel and paclitaxel metabolites were determined simultaneously in a patient with percutaneous biliary drain. The complete chemical structures of the major metabolites were established by mass spectrometry and NMR spectroscopy. A nonlinear elimination model was indicated by the fact that the rate of biliary excretion of paclitaxel rose as plasma concentrations fell. Dihydroxypaclitaxel was the predominant biliary metabolite, in contrast to the barely detectable levels in two previous patients. This derivative results from hydroxylation at the C6 position of the taxane ring and at the phenyl C3'-position on the C13 side chain mediated by cytochrome P450 2C8 and 3A4, respectively. In line with this mechanism, the two other main metabolites corresponded to 6alpha-hydroxypaclitaxel and to the paclitaxel derivative hydroxylated in the para-position on the phenyl ring at the C3'-position of the C13. A high CYP3A4 activity in the patient is consistent with the repeated administration of methylprednisolone for 14 days before paclitaxel treatment, a compound known to induce the CYP3A isoform, and with the increased ratio of 6beta-hydroxycortisol/cortisol in urine, an index of CYP3A activity. These findings emphasize the influence of pretreatment with corticoids on the disposition of paclitaxel.