gebhart/patrepeval huggingface dataset:
An illustrated comparison of processing methods for phase MRI and QSM: removal of background field contributions from sources outside the region of interest (2016)

The elimination of so-called background fields is an essential step in phase MRI and quantitative susceptibility mapping (QSM). Background fields, which are caused by sources outside the region of interest (ROI), are often one to two orders of magnitude stronger than tissue-related field variations from within the ROI, hampering quantitative interpretation of field maps. This paper reviews the current literature on background elimination algorithms for QSM and provides insights into similarities and differences between the many algorithms proposed. We discuss the basic theoretical foundations and derive fundamental limitations of background field elimination. Copyright © 2016 John Wiley & Sons, Ltd.
Effect of Viscoelasticity of PVA Brush on Friction during Post-CMP Cleaning: A Guideline for Nodule Configuration (2014)

The application of new materials and three-dimensional structures are being used to achieve next-generation semiconductor devices. Hence, the role of the chemical-mechanical planarization (CMP) process has gained importance. Polyvinyl acetal (PVA) brushes are widely used as scrubbers during post-CMP cleaning. However, the mechanisms of brush scrubber cleaning are still a matter of debate because direct observation is difficult. Many researchers have proposed the removal mechanisms that operate during brush cleaning based on investigations of the forces acting on particles, friction, and the lubrication characteristics. Hydrodynamic drag forces and direct contact between the brush and the particles have been proposed as cleaning mechanisms [1–5]. Philipossian et al. [6] and Sun et al. [7] focused on the brush design and suggested that the existence of nodules or eccentricity of the roller brush had a significant effect on the friction. The friction system between the roller brush and the surface is complex because of the collision of nodules with the surface. Hence, the shapes of the nodules have been designed through trial and error. In this study, we focus on the friction of a single nodule to investigate the role of nodules in roller brush cleaning. The normal and friction forces are measured during brush sliding. In particular, we focus on the viscoelastic properties of a PVA brush and discuss its effects on friction.
Treatment of hypertension in patients with comorbiditiesResults from the study of hypertensive prescribing practices (SHyPP) (1999)

Approximately 50 million people have hypertension. Many agents with differing efficacy, side effects, dosing schedules, and costs are available to treat hypertension. Joint National Committee (JNC) guidelines attempt to simplify this decision by recommending specific agents based on special considerations such as comorbidities. The objective of this study was to survey primary care physicians' antihypertensive prescribing practices and their treatment recommendations for patients with comorbidities. A direct mail survey was sent to a national random sample of 500 office-based primary care internists, family practitioners, and general practitioners. There were no significant differences between initial treatment recommendations at the time of the survey and those recommended before the survey. However, there were several therapeutic classes whose reported utilization for specific comorbidities significantly changed over 18 months. Angiotensin converting enzyme (ACE) inhibitors reportedly increased in patients with congestive heart failure and diabetes. In addition, the reported use of selective β-blockers increased for patients with a history of myocardial infarction. Physicians did not follow JNC recommendations when initiating treatment in black patients, older patients, or those with mild renal failure. Younger physicians were more likely than older physicians to select agents consistent with guideline recommendations. Physicians did not adhere to JNC guidelines when initiating treatment in patients with comorbidities; however, more physicians are prescribing recommended agents today as compared to 18 months ago. Younger physicians were more likely to prescribe agents consistent with the guidelines. More direct efforts are needed to ensure awareness and compliance with these guidelines. Am J Hypertens 1999;12:333–340 © 1999 American Journal of Hypertension, Ltd.
Methods for Low Bitrate Coding Enhancement Part I: Spectral Restoration (2017)

Perceptual audio coders are widely used when storage space or streaming bandwidth for audio content is limited. If the used bitrate is low, various coding artifacts can be introduced that degrade the perceived audio quality. A suite of algorithms has been developed to conceal these coding artifacts and to improve the perceived sound quality in automotive environments. This paper is a continuation of a previous paper and introduces two post-processing algorithms for restoring the spatial signal quality of decoded compressed audio signals. Both algorithms work single-ended, i.e. without access to the bitrate or other side information. The merit of the algorithms is demonstrated by listening tests. A second part of the paper describes algorithms that enhance the spatial image.
Preliminary results on the instrumental polarization of NIKA2-Pol at the IRAM 30m telescope (2020)

Clarifying the role of magnetic fields in the star formation process is crucial. Observations have already shown that magnetic fields play an important role in the early stages of star formation. The high spatial resolution (∼0.01 to 0.05 pc) provided by NIKA2-Pol 1.2 mm imaging polarimetry of nearby clouds will help us clarify the geometry of the B-field within dense cores and molecular filaments as part of the IRAM 30m large program B-FUN. There are numerous challenging issues in the validation of NIKA2-Pol such as the calibration of instrumental polarization. The commissioning phase of NIKA2-Pol is underway and is helping us characterize the intensity-to-polarization “leakage” pattern of the instrument. We present a preliminary analysis of the leakage pattern and its dependence with elevation. We also present the current leakage correction made possible by the NIKA2 pipeline in polarization mode based on the NIKA2-Pol commissioning data taken in December 2018. Based on reduced Stokes I, Q, U data we find that the leakage pattern of NIKA2-Pol depends on elevation and is sensitive to the focus of the telescope.
Nanoscopic Polymer Film (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
NFX1 Interacts with mSin3A/Histone Deacetylase To Repress hTERT Transcription in Keratinocytes (2008)

Transcription of the catalytic subunit of telomerase (hTERT) in keratinocytes can be induced by human papillomavirus type 16 (HPV16) E6/E6AP ubiquitin ligase through degradation of the repressor, NFX1-91. Here, we demonstrate that NFX1-91 interacts with the corepressor complex mSin3A/histone deacetylase (HDAC) at the hTERT promoter. By degrading NFX1-91, E6/E6AP changes the chromatin structure at the hTERT promoter as indicated by enhanced acetylation of histones H3 and H4 as well as dimethylation of H3K4. Knockdown of NFX1-91 by short hairpin RNA (shRNA) mimics the effect of E6 and leads to acetylation of histones H3 and H4. Conversely, knockdown of E6AP by shRNA suppresses histone acetylation at the hTERT promoter. These data demonstrate that targeted degradation of NFX1-91 by E6/E6AP dissociates the mSin3A/HDAC complex from the hTERT promoter and induces hTERT transcription.
Parallel computation of GA search for the artery shape determinants with CFD (2010)

We studied which factors play important role to determine the shape of arteries at the carotid artery bifurcation by performing multi-objective optimization with computation fluid dynamics (CFD) and the genetic algorithm (GA). To perform it, the most difficult problem is how to reduce turn-around time of the GA optimization with 3D unsteady computation of blood flow. We devised two levels of parallel computation method with the following features: level 1: parallel CFD computation with appropriate number of cores; level 2: parallel jobs generated by "master", which finds quickly available job cue and dispatches jobs, to reduce turn-around time. As a result, the turn-around time of one GA trial, which would have taken 462 days with one core, was reduced to less than two days on RIKEN supercomputer system, RICC, with 8192 cores. We performed a multi-objective optimization to minimize the maximum mean WSS and to minimize the sum of circumference for four different shapes and obtained a set of trade-off solutions for each shape. In addition, we found that the carotid bulb has the feature of the minimum local mean WSS and minimum local radius. We confirmed that our method is effective for examining determinants of artery shapes.
UAV Command and Control, Navigation and Surveillance: A Review of Potential 5G and Satellite Systems (2019)

Drones, unmanned aerial vehicles (UAVs), or unmanned aerial systems (UAS)are expected to be an important component of 5G/beyond 5G (B5G) communications. This includes their use within cellular architectures (5G UAVs), in which they can facilitate both wireless broadcast and point-to-point transmissions, usually using small UAS (sUAS). Allowing UAS to operate within airspace along with commercial, cargo, and other piloted aircraft will likely require dedicated and protected aviation spectrum-at least in the near term, while regulatory authorities adapt to their use. The command and control (C2), or control and non-payload communications (CNPC)link provides safety critical information for the control of the UAV both in terrestrial-based line of sight (LOS)conditions and in satellite communication links for so-called beyond LOS (BLOS)conditions. In this paper, we provide an overview of these CNPC links as they may be used in 5G and satellite systems by describing basic concepts and challenges. We review new entrant technologies that might be used for UAV C2 as well as for payload communication, such as millimeter wave (mmWave)systems, and also review navigation and surveillance challenges. A brief discussion of UAV-to-UAV communication and hardware issues are also provided.
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline (2023)

Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between <sup>15</sup>N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform.
Metabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months (2020)

Sparse data exist regarding the normal range of composition of maternal milk beyond the first postnatal weeks. This single timepoint, observational study in collaboration with the 'Parenting Science Gang' citizen science group evaluated the metabolite and bacterial composition of human milk from 62 participants (infants aged 3-48 months), nearly 3 years longer than previous studies. We utilised rapid evaporative ionisation mass spectrometry (REIMS) for metabolic fingerprinting and 16S rRNA gene metataxonomics for microbiome composition analysis. Milk expression volumes were significantly lower beyond 24 months of lactation, but there were no corresponding changes in bacterial load, composition, or whole-scale metabolomic fingerprint. Some individual metabolite features (~14%) showed altered abundances in nursling age groups above 24 months. Neither milk expression method nor nursling sex affected metabolite and metataxonomic fingerprints. Self-reported lifestyle factors, including diet and physical traits, had minimal impact on metabolite and metataxonomic fingerprints. Our findings suggest remarkable consistency in human milk composition over natural-term lactation. The results add to previous studies suggesting that milk donation can continue up to 24 months postnatally. Future longitudinal studies will confirm the inter-individual and temporal nature of compositional variations and the use of donor milk as a personalised therapeutic.
Quantification of the Deformation of the Human Iliac Arteries With Hip and Knee Flexion: Implications for Stent-Graft Design (2008)

Abdominal aortic aneurysm stent grafts have been reported to fracture at a rate as high as 8% [1]. Iliac artery deformation induced by cardiac pulsation or musculoskeletal motions has been hypothesized to cause these fractures, but little in vivo data has been available heretofore to test this hypothesis. We have utilized magnetic resonance angiography and image-processing methods to quantify in vivo deformation of the human iliac arteries due to maximal hip flexion.
CCDC 989051: Experimental Crystal Structure Determination (2015)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Preventing antiblastic drug-related cardiomyopathy (2016)

Because of the recent advances in chemotherapeutic protocols, cancer survival has improved significantly, although cardiovascular disease has become a major cause of morbidity and mortality among cancer survivors: in addition to the well-known cardiotoxicity (CTX) from anthracyclines, biologic drugs that target molecules that are active in cancer biology also interfere with cardiovascular homeostasis.Pharmacological and non-pharmacological strategies to protect the cardiovascular structure and function are the best approaches to reducing the prevalence of cardiomyopathy linked to anticancer drugs. Extensive efforts have been devoted to identifying and testing strategies to achieve this end, but little consensus has been reached on a common and shared operability.Timing, dose and mode of chemotherapy administration play a crucial role in the development of acute or late myocardial dysfunction. Primary prevention initiatives cover a wide area that ranges from conventional heart failure drugs, such as β-blockers and renin-angiotensin-aldosterone system antagonists to nutritional supplementation and physical training. Additional studies on the pathophysiology and cellular mechanisms of anticancer-drug-related CTX will enable the introduction of novel therapies.We present various typologies of prevention strategies, describing the approaches that have already been used and those that could be effective on the basis of a better understanding of pharmacokinetic and pharmacodynamic CTX mechanisms.
AIMMX (2020)

Despite all of the power that machine learning and artificial intelligence (AI) models bring to applications, much of AI development is currently a fairly ad hoc process. Software engineering and AI development share many of the same languages and tools, but AI development as an engineering practice is still in early stages. Mining software repositories of AI models enables insight into the current state of AI development. However, much of the relevant metadata around models are not easily extractable directly from repositories and require deduction or domain knowledge. This paper presents a library called AIMMX that enables simplified AI Model Metadata eXtraction from software repositories. The extractors have five modules for extracting AI model-specific metadata: model name, associated datasets, references, AI frameworks used, and model domain. We evaluated AIMMX against 7,998 open-source models from three sources: model zoos, arXiv AI papers, and state-of-the-art AI papers. Our platform extracted metadata with 87% precision and 83% recall. As preliminary examples of how AI model metadata extraction enables studies and tools to advance engineering support for AI development, this paper presents an exploratory analysis for data and method reproducibility over the models in the evaluation dataset and a catalog tool for discovering and managing models. Our analysis suggests that while data reproducibility may be relatively poor with 42% of models in our sample citing their datasets, method reproducibility is more common at 72% of models in our sample, particularly state-of-the-art models. Our collected models are searchable in a catalog that uses existing metadata to enable advanced discovery features for efficiently finding models.
Defining Nonadherence and Nonpersistence to Anti–Vascular Endothelial Growth Factor Therapies in Neovascular Age-Related Macular Degeneration (2021)

This classification system provides a framework for assessing treatment nonadherence and nonpersistence over time and across different health settings in the treatment of nAMD with current intravitreal anti-vascular endothelial growth factor treatments. This may have additional importance, given the potential association of the coronavirus pandemic on adherence to treatment in patients with nAMD.
Improvements in Alzheimer' Disease Diagnosis using Principal Component Analysis (PCA) in Combination with Raman Spectroscopy (2007)

The significant achievements of medical science over the last century are evident in the increasing age of the global population, however this now brings new problems, the most prominent being the growth in the number of people suffering from dementia. Over half the people with dementia in the UK are sufferers of Alzheimer’s disease1, a condition in which intraneuronal neurofibrillary tangles and extraneuronal senile tangles take over neurons prompting their death. A definitive diagnosis is still only currently available post-mortem, whilst current symptom based processes of elimination are far from perfect, especially when the only treatments available are symptom inhibiting drugs. Principal component analysis (PCA) of the Raman spectra taken from brain tissue has proved to be a potential tool in the diagnosis. However, this work now has to be refined in order to progress to tissue less associated with the symptoms of Alzheimer’s disease. The first step of this has already been taken in progressing from frontal tissue to occipital tissue point spectra taken at random positions from bulk tissue. Now we present initial work into acquiring Raman spectral maps from across a tissue area, in pursuit of identifying unique plaque and tangle spectra. These spectra are presented alongside synthetic β-Amyloid spectra, in a study of the role that the peptide plays in the biomarker spectra, and how this information can aid the PCA of bulk tissue, and point towards a Raman spectroscopic test on less sensitive tissue, such as blood.
1.3 µm InAs/GaAs multilayer quantum-dot laser with extremely low room-temperature threshold current density (2004)

A high growth temperature step used for the GaAs spacer layer is shown to significantly improve the performance of 1.3 µm multilayer InAs/GaAs quantum-dot lasers. Extremely low room-temperature continuous-wave threshold current densities of 32.5 and 17 A/cm2 are achieved for a three-layer device with as-cleaved facets and high-reflectivity coated facets, respectively.
The Membrane Glycoprotein IIb/IIIa Complex Mediates Deposition of Thrombin-stimulated Blood Platelets on Polystyrene Plastic Under Static Conditions (1994)

A major challenge in the use of artificial materials for implant devices, artificial organs, and extra-corporeal circulation systems, is the adhesion of platelets and the subsequent formation of platelet aggregates on the non-biological surface. The mechanism of platelet attachment to artificial surfaces is not completely understood. Using an enzyme immunoassay, we examined platelet deposition to the polystyrene plastic of microtiter plate wells under static conditions. Following thrombin stimulation, platelets adhered to the wells. This adhesion process was suppressible by the use of different substances known to interfere with the function of the platelet surface glycoprotein IIb/IIIa complex (GPIIb/IIIa). The substances we used were ethylenediaminetetraacetic acid (EDTA), tetrapeptide RGDS (Arg-Gly-Asp-Ser), and a monoclonal antibody directed against the IIIa moiety of the GPIIb/IIIa complex. Our results indicate that the GPIIb/IIIa complex is the platelet receptor which mediates platelet adhesion to polystyrene plastic under such static conditions. The GPIIb/IIIa complex should consequently be regarded as a multifunctional platelet regulator which, depending on the circumstances, may support platelet adhesion as well as platelet aggregation. By contrast, a monoclonal antibody directed against the platelet surface glycoprotein complex Ib/IX (GPIb/IX) did not under the same static conditions inhibit platelet deposition to the polystyrene plastic. In the microtiter wells, platelet alpha-granular proteins were detected either on the surface of adherent platelets or, when platelet deposition was inhibited by EDTA directly on the polystyrene plastic. In the latter case, fibrinogen and thrombospondin were definitely the dominating proteins. The presence of platelet-derived proteins in the microtiter wells significantly enhanced the adhesion of thrombin-stimulated platelets but not of non-stimulated platelets.