gebhart/patrepeval huggingface dataset:
Total Lymphocyte and Natural Killer (NK) Cell Count Day 30 Post-Transplant Strongly Predict Transplant Outcome after T Cell Depleted Allogeneic Stem Cell Transplantation. (2006)

Abstract One hundred and fifty-seven patients with leukemia (80 CML, 48 AML/MDS, 29 ALL) received a T cell depleted myeloablative allogeneic stem cell transplantation (SCT) from an HLA-matched sibling between 09/1993–09/2005. Conditioning consisted of TBI (12–13.6 Gy) + cyclophosphamide (96) or cyclophosphamide and fludarabine (61). The stem cell source was G-CSF mobilized peripheral blood stem cell (PBSC) in 129 and bone marrow in 28 patients. T cell dose with graft ranged from 0.2 – 2 × 105/kg CD3+ cells. GVHD prophylaxis was with low dose cyclosporine (level 100–200 ng/ml) in 103 and standard dose in 54. Patients without ≥ grade II acute GVHD received 1–2 donor lymphocyte infusion of 107 CD3+ cells/kg between days 45 and 100. Absolute lymphocytes on day 30 (LC30) was available in 154 patients (3 patients died before day 30) and 54 day +30 post-transplant samples were available for lymphocyte subset analysis. Median lymphocyte count on day +30 (LC30) was 400/μl, (range 10–3295) and 150/μl, (range 6–1005) for CD56+, CD16+ CD3− NK cells (NK30). Statistical analysis was performed on SPSS14 software. Median age of the group was 34 years (range 10–56). 78 patients had standard risk (SR) disease in first remission or first chronic phase of CML. The remaining 79 had high risk (HR) disease. At the time of analysis 85 patients are (51.5±4%) are alive with median follow-up of surviving patients 1392 days (range 147–4208). Only 9 patients (3 above median LC30) developed aGVHD before day+30. Patients with ≥ median LC30 had significantly better transplant outcome: survival 71±5 vs. 36 ±5.5%, p&lt;0.0001; DFS 71±5 vs. 31±5 %, p&lt;0.0001; NRM 10±3.5 vs. 38 ±6%, p&lt;0.0001; relapse 22±5 vs. 51±7.5%, p=0.004; ≥ II aGVHD 34 ±5 vs. 51±6%, p=0.05. In multivariate analysis only disease risk and LC30 emerged as independent prognostic factors: LC30 above 400/μl was associated with improved survival (RR 4.3), DFS (RR 4.5), less relapse (RR 10.3), NRM (RR 3.3) and aGVHD (RR 2.3). LC30 impacted on outcome of both HR and SR disease groups (Figure). LC30 and NK30 were highly correlated (r2– 0.45, p&lt;0.0001) and NK30 above 150/μl was also associated with improved transplant outcome: In multivariate analysis of this subset of 54 patients, SR disease and NK30 emerged as the only independent factors with better outcome for NK30 &gt;150/μl: higher survival (RR 3), and DFS (RR 3), less relapse (RR 4.8), less NRM (RR 3) and less aGVHD (RR 5.3). This study does not define whether LC30 is a surrogate for NK cell count or whether both are a surrogate for some other undetected prognostic factor. However the inverse relationship between NK count and aGVHD suggests an NK-mediated effect through elimination of host antigen presenting cells as has been described in mismatched SCT but also in HLA identical SCT by Cook et al (Blood2004, 103, 1521) Prospective studies to correlate transplant outcome with NK cell recovery and function after HLA identical SCT are indicated. Figure Figure
Analysis of aflatoxins in foods retailed in Saudi Arabia using immunoaffinity column cleanup and high-performance liquid chromatography-fluorescence detection (2019)

A liquid–liquid extraction based high performance liquid chromatography-fluorescence method has been proposed for the quantitation of naturally producing aflatoxins in nuts and nut based products. Aflatoxins extraction from nuts and nut products was involved methanol – water extraction, immunoaffinity column cleanup followed by post column derivatization technique. The gel contents of monoclonal antibody of the column are very specific to the toxins of interest, which makes the extraction experiment rapid, simple, highly specific and sensitive. Additionally, the improve concentration of toxins from complex nuts and nut product matrices helps to reduced chromatography interference and lower limit of detection. The proposed method was authenticated to evaluate the performance in terms of linearity of the calibration, limit of detection, recovery, run-to-run (repeatability) and day-to-day precision (reproducibility). Good quality parameters with LOD between 0.003 and 0.007 ppb, recovery from 89 to 98%, linearity in the range of 0.02 to 100 ppb (r2 > 0.989) and precisions with RSDs were achieved below 4.5% at concentration level of 1.0 and 30.0 ppb. The developed method was effectively used to the analysis of aflatoxins (AFB1, AFB2, AFG1, and AFG2) in twenty nuts and nut products and were found up to 120.1 ng/mL AFB1 and 11.2 ppb AFB2 in few of the samples.
Radical Polymerization of Vinyl Acetate with Bis(tetramethylheptadionato)cobalt(II): Coexistence of Three Different Mechanisms (2009)

The complex [Co(II)(tmhd)(2)] (4; tmhd = 2,2,6,6-tetramethylhepta-3,5-dionato) has been investigated as a mediator for controlled radical polymerization of vinyl acetate (VAc) and compared with the analogue [Co(II)(acac)(2)] (1; acac = acetylacetonato). A relatively well controlled process occurs, after an induction time, with 2,2'-azobis(4-methoxyl-2,4-dimethylvaleronitrile) (V-70) as radical initiator at 30 degrees C. However, whereas the polymerization essentially stops after about six initiator half-lives in the presence of 1, it continues with a first-order rate law in the presence of 4. The successful simulation of the kinetic data shows that 4 operates simultaneously by associative (degenerative transfer, DT) and dissociative (organometallic radical polymerization, OMRP) mechanisms. The occurrence of OMRP was confirmed by an independent polymerization experiment starting from an isolated and purified [Co(tmhd)(2)](PVAc) macroinitiator. The polymer molecular weight evolves linearly with conversion in accordance with the expected values for one chain per Co atom when DT is the predominant mechanism and also during the pure OMRP process; however, observation of stagnating molecular weights at long reaction times with concomitant breakdown of the first-order rate law for monomer consumption indicates a competitive chain-transfer process catalyzed by an increasing amount of Co(II). In the presence of external donors L (water, pyridine, triethylamine) the DT pathway is blocked and the OMRP pathway is accelerated, and polymerization with complex 4 is then about five times slower than with complex 1. The reversal of relative effective OMRP rate constants k(eff) (4>1 in the absence of external donors, 4<1 in their presence) is rationalized through competitive steric effects on Co(III)-C and Co(II)-L bond strengths. These propositions are supported by (1)H NMR studies and by DFT calculations.
Most microbe-specific naïve CD4 + T cells produce memory cells during infection (2016)

Infection elicits CD4(+) memory T lymphocytes that participate in protective immunity. Although memory cells are the progeny of naïve T cells, it is unclear that all naïve cells from a polyclonal repertoire have memory cell potential. Using a single-cell adoptive transfer and spleen biopsy method, we found that in mice, essentially all microbe-specific naïve cells produced memory cells during infection. Different clonal memory cell populations had different B cell or macrophage helper compositions that matched effector cell populations generated much earlier in the response. Thus, each microbe-specific naïve CD4(+) T cell produces a distinctive ratio of effector cell types early in the immune response that is maintained as some cells in the clonal population become memory cells.
Dilated Cardiomyopathy: Phosphorus 31 MR Spectroscopy at 7 T (2016)

Purpose To test whether the increased signal-to-noise ratio of phosphorus 31 (<sup>31</sup>P) magnetic resonance (MR) spectroscopy at 7 T improves precision in cardiac metabolite quantification in patients with dilated cardiomyopathy (DCM) compared with that at 3 T. Materials and Methods Ethical approval was obtained, and participants provided written informe consent. In a prospective study, <sup>31</sup>P MR spectroscopy was performed at 3 T and 7 T in 25 patients with DCM. Ten healthy matched control subjects underwent <sup>31</sup>P MR spectroscopy at 7 T. Paired Student t tests were performed to compare results between the 3-T and 7-T studies. Results The phosphocreatine (PCr) signal-to-noise ratio increased 2.5 times at 7 T compared with that at 3 T. The PCr to adenosine triphosphate (ATP) concentration ratio (PCr/ATP) was similar at both field strengths (mean ± standard deviation, 1.48 ± 0.44 at 3 T vs 1.54 ± 0.39 at 7 T, P = .49), as expected. The Cramér-Rao lower bounds in PCr concentration (a measure of uncertainty in the measured ratio) were 45% lower at 7 T than at 3 T, reflecting the higher quality of 7-T <sup>31</sup>P spectra. Patients with dilated cardioyopathy had a significantly lower PCr/ATP than did healthy control subjects at 7 T (1.54 ± 0.39 vs 1.95 ± 0.25, P = .005), which is consistent with previous findings. Conclusion 7-T cardiac <sup>31</sup>P MR spectroscopy is feasible in patients with DCM and gives higher signal-to-noise ratios and more precise quantification of the PCr/ATP than that at 3 T. PCr/ATP was significantly lower in patients with DCM than in control subjects at 7 T, which is consistent with previous findings at lower field strengths.
Understanding and mitigating refresh overheads in high-density DDR4 DRAM systems (2013)

Recent DRAM specifications exhibit increasing refresh latencies. A refresh command blocks a full rank, decreasing available parallelism in the memory subsystem significantly, thus decreasing performance. Fine Granularity Refresh (FGR) is a feature recently announced as part of JEDEC's DDR4 DRAM specification that attempts to tackle this problem by creating a range of refresh options that provide a trade-off between refresh latency and frequency.
Leveraging Process-Mining Techniques (2012)

Semi-structured processes are data-driven, human-centric, flexible processes whose execution between instances can vary dramatically. Due to their unpredictability and data-driven nature, it's becoming increasingly important to mine traces of events collected from these processes. This enables the extraction of mined process models that could help users handle new process instances. Process-mining techniques can help facilitate this goal, but it can be daunting for users new to process-aware analytics to sift through the literature and available software to determine which process-mining algorithm to use. The authors compare five process-mining algorithms and present a decision tree to help readers determine which mining algorithm to use for a specific problem. Semi-structured processes, however, present challenges that these mining techniques don't address. So, the authors also identify three key characteristics of semi-structured processes and the mining challenges they present, highlighting a selection of emerging mining approaches that can address these challenges.
Geometric Tools for Perspective Taking for Human-Robot Interaction (2008)

Psychological studies on human interactions made surface the notion Perspective Taking. This notion, referring to reason on other persons' points of view, eases the communication between interacting individuals. For a robot interacting with people, we believe that Perspective Taking can play an important role that will allow the robot to understand , reason and act according to human's point of view thus allowing an efficient communication and cooperation. In this paper, we propose a group of algorithms to evaluate and generate robot configurations that are not only collision free but also obeying HRI constraints by reasoning explicitly on human's perspective.
Lipid Droplet-Binding Protein TIP47 Regulates Hepatitis C Virus RNA Replication through Interaction with the Viral NS5A Protein (2013)

The nonstructural protein NS5A has emerged as a new drug target in antiviral therapies for Hepatitis C Virus (HCV) infection. NS5A is critically involved in viral RNA replication that takes place at newly formed membranes within the endoplasmic reticulum (membranous web) and assists viral assembly in the close vicinity of lipid droplets (LDs). To identify host proteins that interact with NS5A, we performed a yeast two-hybrid screen with the N-terminus of NS5A (amino acids 1-31), a well-studied α-helical domain important for the membrane tethering of NS5A. Our studies identified the LD-associated host protein, Tail-Interacting Protein 47 (TIP47) as a novel NS5A interaction partner. Coimmunoprecipitation experiments in Huh7 hepatoma cells confirmed the interaction of TIP47 with full-length NS5A. shRNA-mediated knockdown of TIP47 caused a more than 10-fold decrease in the propagation of full-length infectious HCV in Huh7.5 hepatoma cells. A similar reduction was observed when TIP47 was knocked down in cells harboring an autonomously replicating HCV RNA (subgenomic replicon), indicating that TIP47 is required for efficient HCV RNA replication. A single point mutation (W9A) in NS5A that disrupts the interaction with TIP47 but preserves proper subcellular localization severely decreased HCV RNA replication. In biochemical membrane flotation assays, TIP47 cofractionated with HCV NS3, NS5A, NS5B proteins, and viral RNA, and together with nonstructural viral proteins was uniquely distributed to lower-density LD-rich membrane fractions in cells actively replicating HCV RNA. Collectively, our data support a model where TIP47--via its interaction with NS5A--serves as a novel cofactor for HCV infection possibly by integrating LD membranes into the membranous web.
A Quantitative Comparison of Epistemic Uncertainty Maps Applied to Multi-Class Segmentation (2021)

Uncertainty assessment has gained rapid interest in medical image analysis. A popular technique to compute epistemic uncertainty is the Monte-Carlo (MC) dropout technique. From a network with MC dropout and a single input, multiple outputs can be sampled. Various methods can be used to obtain epistemic uncertainty maps from those multiple outputs. In the case of multi-class segmentation, the number of methods is even larger as epistemic uncertainty can be computed voxelwise per class or voxelwise per image. This paper highlights a systematic approach to define and quantitatively compare those methods in two different contexts: class-specific epistemic uncertainty maps (one value per image, voxel and class) and combined epistemic uncertainty maps (one value per image and voxel). We applied this quantitative analysis to a multi-class segmentation of the carotid artery lumen and vessel wall, on a multi-center, multi-scanner, multi-sequence dataset of (MR) images. We validated our analysis over 144 sets of hyperparameters of a model. Our main analysis considers the relationship between the order of the voxels sorted according to their epistemic uncertainty values and the misclassification of the prediction. Under this consideration, the comparison of combined uncertainty maps reveals that the multi-class entropy and the multi-class mutual information statistically out-perform the other combined uncertainty maps under study. In a class-specific scenario, the one-versus-all entropy statistically out-performs the class-wise entropy, the class-wise variance and the one versus all mutual information. The class-wise entropy statistically out-performs the other class-specific uncertainty maps in terms of calibration. We made a python package available to reproduce our analysis on different data and tasks.
Neural Network–Based Clustering (2008)

This chapter contains sections titled: Introduction Hard Competitive Learning Clustering Soft Competitive Learning Clustering Applications Summary
Synthesis of a new nanocrystalline titanium aluminum fluoride phase by reaction of Ti2AlC with hydrofluoric acid (2011)

A new nanocrystalline phase of titanium aluminum fluoride, with a stoichiometry of Ti2AlF9—exact stoichiometry measured herein is Ti2.1Al0.9F9,—was synthesized by the fluorination of Ti2AlC in anhydrous hydrofluoric acid at 55 °C for 2 h. The results from X-ray diffraction, scanning and high-resolution transmission electron microscopy and selected area diffraction, together with crystal structure solution via simulated annealing, confirmed the formation of a nanocrystalline material with a trigonal structure belonging to the R3 space group. The structure can also be viewed as being comprised of corner-sharing octahedra that are arranged in a distorted simple cubic arrangement. Thermogravimetric analysis, in argon, indicates that this phase is stable up to ≈ 850 °C. Density functional theory calculations estimate the band gap to be ≈ 5 eV and the bulk modulus to be ≈ 109 GPa.
Tandem solar cell cost relations (2016)

Tandem solar cells overcome conversion efficiency limitations of conventional single-junction solar cells by using multiple absorber materials with different band gap energies. The absorber materials are stacked in sequence with decreasing band gap energy, thus reducing thermalization losses in the conversion process. The improved conversion efficiency of a tandem solar cell comes at increased fabrication complexity and, hence, production cost. More fabrication steps and more materials are needed to produce a tandem solar cell than to produce a single-junction solar cell. Economically, a tandem solar cell is of interest if it generates electricity at a lower cost than either of its comprising single-junction counter parts. In this paper we present cost relations that link the costs and efficiencies of two single junction solar cells to those of a dual-junction tandem solar cell made from the combination of the two cells. In doing so, we establish criteria under which tandem solar cells are economically viable.
Lack of Visual Field Improvement After Initiation of Intraocular Pressure Reducing Treatment in the Early Manifest Glaucoma Trial (2016)

Observed visual field changes among glaucoma patients receiving initial IOP-reducing therapy were not significantly different to changes seen in patients who received no treatment. Thus, our results did not support the idea that visual field status improves after initiation of IOP- reducing therapy in glaucoma individuals, at least not in individuals with initially normal to moderately elevated IOPs.
Optical Implementation of the stream cipher based on one dimensional Cellular Automata (1997)

Rapid expansion of computer networks in all aspects of today’s society brings undeniable benefits but also serious security problems. Cryptography is one of the tools which ensures security, integrity and authentication of electronic data. Ever increasing standards for data security urge introducing new, complicated algorithms, or increasing of the key length, which require more computing power and time. Together with the increasing amount of data to be protected this may turn into system bottleneck. To avoid this, new algorithms and architectures are being extensively researched. Optical computing systems may offer valuable alternative with the inherent parallelism and high interconnectivity, allowing encryption of large block of data in parallel using very long key. In this way variety of biometrical data such as fingerprint, retinal or facial images can be used as a key, instead of a short password. This will lead to increase of the security not compromising the speed at the same time. One of the most promising optical architecture is the cellular. A number of optical cellular architectures have been proposed mainly for image processing [3-10]. A promising new application field can be cryptography and random pattern generation. As first attempt in this direction we propose optical implementation of CA rule a i ' = a i −1 X O R ( a i O R a i +1 ) based Stream Cipher, suggested by S. Wolfram [1].
Figure S4 from PET Reporter Gene Imaging and Ganciclovir-Mediated Ablation of Chimeric Antigen Receptor T Cells in Solid Tumors (2023)

&lt;p&gt;Figure S4 shows long-term monitoring of mice following GCV treatment, confirming persistent T-cell ablation&lt;/p&gt;
SoCurity: A Design Approach for Enhancing SoC Security (2023)

We propose SoCurity, the first NoC counter-based hardware monitoring approach for enhancing heterogeneous SoC security. With SoCurity, we develop a fast, lightweight anomalous activity detection system leveraging semi-supervised machine learning models that require no prior attack knowledge for detecting anomalies. We demonstrate our techniques with a case study on a real SoC for a connected autonomous vehicle system and find up to 96% detection accuracy.
Combining Speech, Gaze, and Micro-gestures for the Multimodal Control of In-Car Functions (2016)

Modern cars are already incredibly smart environments today due to the sheer number of sensors and processors packed into a small space. Likewise, new technologies in human-computer interaction increasingly find their way inside, e.g. eye tracking, speech interaction and gesture recognition. The support of new modalities is promising a reduction of driver distraction and a better handling of an increasing number of functions offered by in-vehicle systems. With multiple modalities to choose from, which can be combined arbitrarily via multimodal fusion, drivers can make a free choice depending on the demands of the situation and their preferences. Our paper presents a prototype in-car system that allows car features (like turning lights and windows) to be controlled by combinations of speech, gaze, and micro-gestures. We propose an interaction concept, sketch our architecture based on a domain-independent multimodal dialogue platform, and draw some first conclusions on the outcome.
Operative versus Conservative Treatment of Back Pain in Adults with Scoliosis (2008)

INTRODUCTION: Back pain is the most common complaint among adult patients with scoliosis and undoubtedly influences the decision to pursue operative management. Previous studies suggest that overall pain and function are improved by surgery. The purpose of this study was to assess the degree to which back pain is improved with surgery and whether this improvement is durable. METHODS: This study is a retrospective review of a prospective multicenter database of adults with spinal deformity. At the time of enrollment and follow-up, patients completed standardized questionnaires, including Oswestry Disability Index (ODI) and specific assessment of back pain using the visual analog score (VAS). Initial plan for surgical or conservative treatment was made at the time of enrollment. Statistical comparisons of ODI and VAS for back pain at baseline and 2 years were assessed both within and between patients treated surgically and those treated conservatively. RESULTS: Of 344 patients, 320 (93%) had back pain (VAS > 0) at presentation (mean VAS, 5.5). Of these 320 patients, 149 (47%) were managed surgically. Compared with patents managed conservatively, operative patients had greater baseline mean VAS for back pain (6.3 versus 4.8, P < 0.001) and greater mean ODI (35 versus 27, P < 0.001). At the 2-year follow-up, conservatively managed patients did not have significant change in ODI (P = 0.8) or VAS for back pain (P = 0.9). In contrast, at the 2-year follow-up, surgically treated patients had significant improvement in mean VAS for back pain (2.6 versus 6.3, P < 0.001) and ODI (20 versus 35, P < 0.001). Compared with conservatively treated patients, at the 2-year follow-up, operative patients had lower VAS for back pain (P < 0.001) and ODI (P = 0.001). CONCLUSION: Despite having started with significantly greater back pain and disability, surgically treated patients at the 2-year follow-up had significantly less back pain and disability than conservatively-treated patients. Compared with conservative treatment, surgery offers significant improvement of back pain for adults with scoliosis.