gebhart/patrepeval huggingface dataset:
Patient-specific deep deformation models (PsDDM) to register planning and interventional ultrasound volumes in image fusion-guided interventions (2020)

Image fusion-guided interventions often require planning MR/CT and interventional U/S images to be registered in realtime. Organ motion, patient breathing and inconsistent ultrasound probe positioning during intervention, all contribute to the challenges of real-time 3D deformable registration, where alignment accuracy and computation time are often mutual trade-offs. In this work, we propose a novel framework to align planning and interventional 3D U/S by training patientspecific deep-deformation models (PsDDM) at the planning stage. During intervention, planning 3D U/S volumes are efficiently warped onto the interventional 3D U/S volumes using the trained deep-deformation model, thus enabling the transfer of other modality (planning MR/CT) information in real-time on interventional images. The alignment of planning MR/CT to planning U/S is not time-critical as these can be aligned before the intervention with desired accuracy using any known multimodal deformable registration method. The feasibility of training PsDDM is shown on liver U/S data acquired with a custom-built MR-compatible, hands-free 3D ultrasound probe that allows simultaneous acquisition of planning MR and U/S. Liver U/S volumes exhibit large motion in time due to respiration and therefore serve as a good anatomy to quantify the accuracy of the PsDDM. For quantitative evaluation of the PsDDM, a large vessel bifurcation was manually annotated on 9 U/S volumes that were not used for training the PsDDM but from the same subject. Mean target registration error (TRE) between the centroids was 0.84mm &plusmn; 0.39mm, mean Hausdorff distance (HD) was 1.80mm &plusmn; 0.29mm and mean surface distance (MSD) was 0.44mm &plusmn; 0.06mm for all volumes. In another experiment, the PsDDM was trained using liver volumes from one scanning session, while the model was tested on data from a separate scanning session of the same patient, for which qualitative alignment results were presented.
Emotional ratings and skin conductance response to visual, auditory and haptic stimuli (2018)

The human emotional reactions to stimuli delivered by different sensory modalities is a topic of interest for many disciplines, from Human-Computer-Interaction to cognitive sciences. Different databases of stimuli eliciting emotional reaction are available, tested on a high number of participants. Interestingly, stimuli within one database are always of the same type. In other words, to date, no data was obtained and compared from distinct types of emotion-eliciting stimuli from the same participant. This makes it difficult to use different databases within the same experiment, limiting the complexity of experiments investigating emotional reactions. Moreover, whereas the stimuli and the participants' rating to the stimuli are available, physiological reactions of participants to the emotional stimuli are often recorded but not shared. Here, we test stimuli delivered either through a visual, auditory, or haptic modality in a within participant experimental design. We provide the results of our study in the form of a MATLAB structure including basic demographics on the participants, the participant's self-assessment of his/her emotional state, and his/her physiological reactions (i.e., skin conductance).
1-Tbyte/s 1-Gbit DRAM Architecture Using 3-D Interconnect for High-Throughput Computing (2011)

Aiming to resolve memory bottlenecks in multi-core system, novel 1-Tbyte/s 1-Gbit DRAM architecture based on a multi-core configuration and 3-D interconnects was developed. The DRAM stacked on a multi-core CPU has 512-bit I/Os with through-silicon-via (TSV) distributed in 16 memory cores. Five-stage pipelined architecture in the compact DRAM core was developed to reduce the operation cycle of the data-bus to 2 ns. A low-noise early-bar-write scheme for an 8-ns cycle array operation and 16-Gbit/s I/O circuits on TSV were also developed. The proposed DRAM architecture greatly improves power efficiency. TSV scheme reduces the parasitic capacitance of the interconnects between the DRAM and CPU, and multi-core architecture reduces the length of the data bus on the DRAM. A 1-Gbit DRAM was designed based on the 45-nm stand-alone DRAM process. Chip size is 51.6 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> assuming 4F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> memory cells, and the density is about 5 times higher than that of embedded DRAM. Circuit simulations confirmed the 2-ns operation of the data bus, 8-ns operation of the memory array, and 16-Gbit/s operation of I/O circuits. Power consumption is 19.5 W, providing power efficiency of 51.3 Gbyte/s/W, which is an order of magnitude higher than that of conventional DRAMs.
Metabolism of human articular chondrocytes cultured in alginate beads. Longterm effects of interleukin 1beta and nonsteroidal antiinflammatory drugs. (2002)

The mechanism of action of NSAID seems to be multifactorial and not limited to the inhibition of cyclooxygenases. Further, in our culture conditions, at the Cmax and by comparison with other NSAID, ACECLO and INDO show an advantageous activity profile. They fully blocked PGE2 production, inhibited IL-6 synthesis, and increased aggrecan synthesis. These effects appear advantageous for the longterm treatment of chronic joint diseases such as osteoarthritis.
Hybrid Adipogenic Implants from Adipose Stem Cells for Soft Tissue Reconstruction In Vivo (2010)

A critical barrier in tissue regeneration is scale-up. Bioengineered adipose tissue implants have been limited to ∼10 mm in diameter. Here, we devised a 40-mm hybrid implant with a cellular layer encapsulating an acellular core. Human adipose-derived stem cells (ASCs) were seeded in alginate. Poly(ethylene)glycol-diacrylate (PEGDA) was photopolymerized into 40-mm-diameter dome-shaped gel. Alginate-ASC suspension was painted onto PEGDA surface. Cultivation of hybrid constructs ex vivo in adipogenic medium for 28 days showed no delamination. Upon 4-week in vivo implantation in athymic rats, hybrid implants well integrated with host subcutaneous tissue and could only be surgically separated. Vascularized adipose tissue regenerated in the thin, painted alginate layer only if ASC-derived adipogenic cells were delivered. Contrastingly, abundant fibrous tissue filled ASC-free alginate layer encapsulating the acellular PEGDA core in control implants. Human-specific peroxisome proliferator-activated receptor-γ (PPAR-γ) was detected in human ASC-seeded implants. Interestingly, rat-specific PPAR-γ was absent in either human ASC-seeded or ASC-free implants. Glycerol content in ASC-delivered implants was significantly greater than that in ASC-free implants. Remarkably, rat-specific platelet/endothelial cell adhesion molecule (PECAM) was detected in both ASC-seeded and ASC-free implants, suggesting anastomosis of vasculature in bioengineered tissue with host blood vessels. Human nuclear staining revealed that a substantial number of adipocytes were of human origin, whereas endothelial cells of vascular wall were of chemaric human and nonhuman (rat host) origins. Together, hybrid implant appears to be a viable scale-up approach with volumetric retention attributable primarily to the acellular biomaterial core, and yet has a biologically viable cellular interface with the host. The present 40-mm soft tissue implant may serve as a biomaterial tissue expander for reconstruction of lumpectomy defects.
Quantization of Distributed Data for Learning (2021)

We consider machine learning applications that train a model by leveraging data distributed over a trusted network, where communication constraints can create a performance bottleneck. A number of recent approaches propose to overcome this bottleneck through compression of gradient updates. However, as models become larger, so does the size of the gradient updates. In this paper, we propose an alternate approach to learn from distributed data that quantizes data instead of gradients, and can support learning over applications where the size of gradient updates is prohibitive. Our approach leverages the dependency of the computed gradient on data samples, which lie in a much smaller space in order to perform the quantization in the smaller dimension data space. At the cost of an extra gradient computation, the gradient estimate can be refined by conveying the difference between the gradient at the quantized data point and the original gradient using a small number of bits. Lastly, in order to save communication, our approach adds a layer that decides whether to transmit a quantized data sample or not based on its importance for learning. We analyze the convergence of the proposed approach for smooth convex and non-convex objective functions and show that we can achieve order optimal convergence rates with communication that mostly depends on the data rather than the model (gradient) dimension. We use our proposed algorithm to train ResNet models on the CIFAR-10 and ImageNet datasets, and show that we can achieve an order of magnitude savings over gradient compression methods. These communication savings come at the cost of increasing computation at the learning agent, and thus our approach is beneficial in scenarios where communication load is the main problem.
Long-Term Outcome of Patients with Acromegaly and Congestive Heart Failure (2004)

Cardiovascular complications are a major cause of morbidity and mortality in patients with acromegaly. Normalization of GH secretion is associated with an improvement in structural and functional cardiac abnormalities. However, the long-term cardiac effects of treatment for acromegaly have not been studied in patients who have already developed chronic congestive heart failure (CHF). We reviewed the charts of 330 consecutive patients with acromegaly treated in two French and Belgian centers since 1985. Ten patients with both acromegaly and CHF (eight men, two women, mean age 49.7 yr) were studied retrospectively. One of them was excluded because CHF was due to severe aortic stenosis.CHF (New York Heart Association stages III-IV and echocardiography showing dilated hypokinetic cardiomyopathy with left ventricular systolic dysfunction and a left ventricular ejection fraction less than 45%) was diagnosed before, concomitantly, or after acromegaly in, respectively, two, five, and two patients. Three patients were referred with terminal heart failure requiring transplantation.One patient had transient CHF associated with a hypertensive crisis. The other eight patients had symptomatic chronic CHF. Control of GH hypersecretion failed, totally or partially, in three patients: one had a long-term survival, and the two others died at 1 and 5 yr. Good GH control was achieved in five patients: four of these are still alive 2-16 yr after diagnosis of CHF, their clinical status is stable or improved, and their quality of life is good. Overall, the 1- and 5-yr mortality (or transplantation) rates for patients with chronic symptomatic CHF were 25% (2 of 8 patients) and 37.5% (3 of 8 patients), respectively. In conclusion, less than 3% of acromegalic patients developed CHF in this study. Although effective treatment of acromegaly improved short-term cardiovascular status, its impact on long-term survival is questionable.
Membrane curvature regulates the spatial distribution of bulky glycoproteins (2022)

The glycocalyx is a shell of heavily glycosylated proteins and lipids distributed on the cell surface of nearly all cell types. Recently, it has been found that bulky transmembrane glycoproteins such as MUC1 can modulate membrane shape by inducing membrane protrusions. In this work, we examine the reciprocal relationship of how membrane shape affects MUC1's spatial distribution on the cell membrane and its biological significance. By employing nanopatterned surfaces and membrane-sculpting proteins to manipulate membrane curvature, we show that MUC1 avoids positively-curved membranes (membrane invaginations) and accumulates on negatively-curved membranes (membrane protrusions). MUC1's curvature sensitivity is dependent on the length and the extent of glycosylation of its ectodomain, with large and highly glycosylated forms preferentially staying out of positive curvature. Interestingly, MUC1's avoidance of positive membrane curvature enables it to escape from endocytosis and being removed from the cell membrane. These findings also suggest that the truncation of MUC1's ectodomain, often observed in breast and ovarian cancers, may enhance its endocytosis and potentiate its intracellular accumulation and signaling.
Effects of acute and repeated administration of the selective M 4 PAM VU0152099 on cocaine versus food choice in male rats (2022)

Ligands that stimulate muscarinic acetylcholine receptors 1 and 4 (M<sub>1</sub> , M<sub>4</sub> ) have shown promising effects as putative pharmacotherapy for cocaine use disorder in rodent assays. We have previously shown reductions in cocaine effects with acute M<sub>4</sub> stimulation, as well as long-lasting, delayed reductions in cocaine taking and cocaine seeking with combined M<sub>1</sub> /M<sub>4</sub> receptor stimulation or with M<sub>1</sub> stimulation alone. M<sub>4</sub> stimulation opposes dopaminergic signalling acutely, but direct dopamine receptor antagonists have proved unhelpful in managing cocaine use disorder because they lose efficacy with long-term administration. It is therefore critical to determine whether M<sub>4</sub> approaches themselves can remain effective with repeated or chronic dosing. We assessed the effects of repeated administration of the M<sub>4</sub> positive allosteric modulator (PAM) VU0152099 in rats trained to choose between intravenous cocaine and a liquid food reinforcer to obtain quantitative measurement of whether M<sub>4</sub> stimulation could produce delayed and lasting reduction in cocaine taking. VU0152099 produced progressively augmenting suppression of cocaine choice and cocaine intake, but produced neither rebound nor lasting effects after treatment ended. To compare and contrast effects of M<sub>1</sub> versus M<sub>4</sub> stimulation, we tested whether the M<sub>4</sub> PAM VU0152100 suppressed cocaine self-administration in mice lacking CalDAG-GEFI signalling factor, required for M<sub>1</sub> -mediated suppression of cocaine self-administration. CalDAG-GEFI ablation had no effect on M<sub>4</sub> -mediated suppression of cocaine self-administration. These findings support the potential usefulness of M<sub>4</sub> PAMs as pharmacotherapy to manage cocaine use disorder, alone or in combination with M<sub>1</sub> -selective ligands, and show that M<sub>1</sub> and M<sub>4</sub> stimulation modulate cocaine-taking behaviour by distinct mechanisms.
Spin wave instability by spin-polarized current injection (2005)

Magnetic domain wall motion by spin polarized current injection has been studied. The critical current for instability of uniform magnetization is investigated by micromagnetic computer simulation.
Simulation of Lithium-Ion Battery Performance in Hybrid Electric Vehicles (2002)

&lt;div class="htmlview paragraph"&gt;In this study, three batteries were designed and these designs were evaluated in a hybrid vehicle simulation program. The battery designs were based on laboratory tests of 18650 cells for which a Lumped Parameter Battery Model was employed to correlate the cell impedance data. The three battery designs were each tested on three driving cycles, the Federal Urban Driving Schedule, the Highway Fuel Economy Test, and a special cycle developed to test the full power of the vehicle. The results of these simulation tests showed that the battery impedances were low for much of the time because the discharging and charging currents are not maintained at high levels for long periods of time on these cycles. For these conditions, the rates of heat generation in the batteries that were calculated by the simulation programs were low and may not be a serious problem.&lt;/div&gt;
Symmetric Designs (1983)

Symmetric designs are an important class of combinatorial structures which arose first in the statistics and are now especially important in the study of finite geometries. This book presents some of the algebraic techniques that have been brought to bear on the question of existence, construction and symmetry of symmetric designs – including methods inspired by the algebraic theory of coding and by the representation theory of finite groups – and includes many results. Rich in examples and containing over 100 problems, the text also provides an introduction to many of the modern algebraic approaches used, through six lengthy appendices and supplementary problems. The book will be of interest to both combinatorialists and algebraists, and could be used as a course text for a graduate course.
WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans (2022)

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.
Abstract 685: Wnt5a/JNK Signaling Mediates Endothelial Insulin Resistance in Human Diabetes (2015)

Diabetes mellitus (DM) is associated with endothelial dysfunction that contributes to the development of atherosclerosis and promotes cardiovascular disease. Recent work has identified the secreted Wnt5a as a pro-inflammatory mediator of metabolic dysfunction in obesity acting through a non-canonical signaling pathway involving JNK activation. In animal models, JNK activity has been widely described to be involved in systemic insulin resistance. However, the relevance of Wnt5a/JNK axis in the vasculature is unknown. Our study aimed to evaluate the involvement of Wnt5a/JNK in endothelial dysfunction, studying its potential role in altered eNOS activation and insulin signaling in patients with DM. We measured protein expression, and insulin response in freshly isolated endothelial cells (ECs) from patients with DM (n=26) and non-diabetic controls (n=32). ECs from patients with DM displayed impaired insulin-mediated eNOS activation and reduced NO release in conjunction with higher expression of Wnt5a (P=0.01). This effect was accompanied with an enhanced activation of JNK (P&lt;0.01). In endothelial cells from non-diabetic subjects, Wnt5a treatment increased JNK activation and reduced insulin-mediated activation of eNOS (P&lt;0.001). In ECs from patients with DM, treatment with a JNK chemical inhibitor (SP600125) restored eNOS activation and insulin response (P&lt;0.001). In summary, our data provide evidence for the presence of altered endothelial Wnt5a and JNK activity in human diabetes, suggesting that Wnt5a/JNK signaling pathway contributes to endothelial insulin resistance in DM and support further studies of Wnt5a inhibitors to restore endothelial function.
Electrochemotherapy as a treatment for melanoma and other cutaneous malignancies (1997)

Heller, R; Jaroszeski, M; DeConti, R; Reintgen, D; Gilbert, R; Glass, F Author Information
Supplementary table 2 from <i>WRN</i> Promoter CpG Island Hypermethylation Does Not Predict More Favorable Outcomes for Patients with Metastatic Colorectal Cancer Treated with Irinotecan-Based Therapy (2023)

&lt;p&gt;Clinical characteristics of patients included in the present study and of all patients that participated the original CAIRO study&lt;/p&gt;
Potassium and Magnesium Changes Associated with Programmed Electrical Stimulation (1989)

Serum potassium and magnesium concentrations decrease secondary to an increase in catecholamine concentrations. We hypothesized that during programmed electrical stimulation (PES), where stress of the procedure may elevate catecholamine levels, potassium and magnesium concentrations would decrease. To test this hypothesis, potassium and magnesium concentrations were measured at baseline, during, and after PES in 16 patients. Potassium concentrations (mean ± standard deviation) decreased from 4.5 ± 0.3 (mEq/L) at baseline to 3.9 ± 0.2 during PES (P &lt; 0.05). At 2 hours post‐PES, serum potassium concentrations returned to baseline values (mean 4.2 ± 0.5 mEq/L, P &gt; 0.05 compared to baseline). Mean magnesium concentrations (mmol/L) decreased from 0.84 ± 0.07 at baseline to 0.81 ± 0.07 at the end of PES (P &lt; 0.05) but did not decrease significantly during PES. In conclusion, potassium concentrations decreased significantly during PES, whereas magnesium concentrations decreased slightly but significantly at the end of PES. These changes in electrolyte concentrations may be due to catecholamine influence secondary to the PES procedure. In light of these observations, serum concentrations of potassium and magnesium should be normalized prior to PES procedure in order to prevent hypokalemia and hypomagnesemia.
Fluidic Topology Optimization with an Anisotropic Mixture Model (2022)

Fluidic devices are crucial components in many industrial applications involving fluid mechanics. Computational design of a high-performance fluidic system faces multifaceted challenges regarding its geometric representation and physical accuracy. We present a novel topology optimization method to design fluidic devices in a Stokes flow context. Our approach is featured by its capability in accommodating a broad spectrum of boundary conditions at the solid-fluid interface. Our key contribution is an anisotropic and differentiable constitutive model that unifies the representation of different phases and boundary conditions in a Stokes model, enabling a topology optimization method that can synthesize novel structures with accurate boundary conditions from a background grid discretization. We demonstrate the efficacy of our approach by conducting several fluidic system design tasks with over four million design parameters.