gebhart/patrepeval huggingface dataset:
Extended Successive Convex Approximation for Phase Retrieval with Dictionary Learning (2021)

Phase retrieval aims at reconstructing unknown signals from magnitude measurements of linear mixtures. In this paper, we consider the phase retrieval with dictionary learning problem, which includes an additional prior information that the measured signal admits a sparse representation over an unknown dictionary. The task is to jointly estimate the dictionary and the sparse representation from magnitude-only measurements. To this end, we study two complementary formulations and develop efficient parallel algorithms by extending the successive convex approximation framework using a smooth majorization. The first algorithm is termed compact-SCAphase and is preferable in the case of less diverse mixture models. It employs a compact formulation that avoids the use of auxiliary variables. The proposed algorithm is highly scalable and has reduced parameter tuning cost. The second algorithm, referred to as SCAphase, uses auxiliary variables and is favorable in the case of highly diverse mixture models. It also renders simple incorporation of additional side constraints. The performance of both methods is evaluated when applied to blind sparse channel estimation from subband magnitude measurements in a multi-antenna random access network. Simulation results demonstrate the efficiency of the proposed techniques compared to state-of-the-art methods.
Hydrogen Absorption in Wet NH4HS Environment (2000)

Abstract This paper addresses hydrogen absorption of carbon steels caused by wet ammonium bi-sulfide (NH4HS) corrosion that occurs in effluent condensers of hydroprocessing units in refineries. Although it had been considered that hydrogen absorption of steels in wet H2S solution would be negligible in non-acidic conditions except for those containing cyanide (CN-), our previous study confirmed that hydrogen absorption of steels was accelerated even in CN- free non-acidic wet H2S environment at elevated temperature1). In this study, hydrogen absorption of steels in a wet NH4HS environment was investigated. Hydrogen absorption in low and high NH4HS solutions at elevated temperatures was observed which appeared to be associated with flow velocity and solution temperature.
Hardware experiments of humanoid robot safe fall using Aldebaran NAO (2012)

Although the fall of a humanoid robot is rare in controlled environments, it cannot be avoided in the real world where the robot may physically interact with the environment. Our earlier work [1], [2] introduced the strategy of direction-changing fall, in which the robot attempts to reduce the chance of human injury by changing its default fall direction in real-time and falling in a safer direction. The current paper reports further theoretical developments culminating in a successful hardware implementation of this fall strategy conducted on the Aldebaran NAO robot[3]. This includes new algorithms for humanoid kinematics and Jacobians involving coupled joints and a complete estimation of the body frame attitude using an additional inertial measurement unit. Simulations and experiments are smoothly handled by our platform independent humanoid control software package called Locomote. We report experiment scenarios where we demonstrate the effectiveness of the proposed strategies in changing humanoid fall direction.
A unified view of diffusion maps and signal processing on graphs (2017)

In this paper we explore the connection between diffusion maps and signal processing on graphs. We aim to create a common terminology for both approaches and formulate the diffusion map interpretation of operations developed for signal processing. In particular we show the advantages of using the transition matrix of a Markov chain defined on the graph as the graph shift operator in the signal processing on graphs framework.
Gene therapy and neural grafting: Keeping the message switched on (1995)

Abstract A major problem in developing an effective gene therapy for the nervous system lies in understanding the principles that maintain or turn off the expression of genes following their transfer into the CNS.
Toward a Quantitative Colorimeter for Point-of-Care Nitrite Detection (2022)

This paper reports on a low-cost, quantitative, point-of-care solution for the early detection of nitrite, a common biomarker for urinary tract infections (UTIs). In a healthy individual, nitrite is not found in the urine. However, a subject with a suspected UTI will produce nitrite in their urine since the bacteria present will convert nitrate into nitrite. Traditionally, nitrite is monitored by urinary dipsticks that are either read by eye or using a reflectance spectrophotometer. Both methods provide a semiquantitative positive or negative result at best. In this paper, we described a novel, affordable, portable transmission-based colorimeter for the quantitative measurement of nitrite. A unique permutation of the Griess reaction was optimized for the clinical detection of nitrite in urine and is reported. By using nitrite spiked in a salt buffer, artificial, and human urine samples, the performance of the colorimeter was evaluated against dipsticks read using two commercial dipstick analyzers, Urisys 1100 (Roche Diagnostics) and Clinitek Status+ (Siemens Medical Solutions). The colorimeter was able to detect the clinically relevant range of nitrite from 0.78 to 200 μM in a salt buffer. The detection limit in artificial urine was determined as 1.6 μM, which is ∼16× more sensitive than commercial dipstick reflectance analyzers, enabling the possibility for earlier detection of urinary infections. The colorimeter is assembled using off-the-shelf components (<$80) and controlled by a smartphone application <i>via</i> low-energy bluetooth. It has a built-in color correction algorithm and is designed to enable for a turbidity correction in samples containing bacteria or other cellular debris as well. The mobile application can display the nitrite concentration for a single sample or display the results over a period of time. Tracking urinalysis results longitudinally can help identify trends such as increases in nitrite concentrations over an individual's baseline and identify possible infections earlier. While the detection of nitrite was showcased here, this portable analyzer can be expanded to other colorimetric-based chemistries to detect a panel of biomarkers, which can improve the overall sensitivity and specificity of the desired assay.
Method for minimizing lens breathing with one moving group (2022)

Lens breathing in movie cameras is the change in the overall content of a scene while bringing subjects located at different depths into focus. This paper presents a method for minimizing lens breathing or changing angular field-of-view while maintaining perspective by moving only one lens group. To maintain perspective, the stop is placed in a fixed position where no elements between the scene and the stop can move, thus fixing the entrance pupil in one location relative to the object fields. The result is perspective invariance while refocusing the lens. Using paraxial optics, we solve for the moving group's position to focus on every object position and eliminate breathing between the minimum and maximum object distances. We investigate the solution space for optical systems with two positive groups or a positive and a negative group (i.e., retrofocus and telephoto systems). We explain how to apply this paraxial solution to existing systems to minimize breathing. The results for two systems altered using this method are presented. Breathing improved by two orders of magnitude in both cases, and performance specifications were still met when compared to the initial systems.
Discovery, optimization, and cellular activities of 2-(aroylamino)cinnamamide derivatives against colon cancer cells (2019)

ABSTRACT Curcumin and trans- cinnamaldehyde are acrolein-based Michael acceptor compounds that are commonly found in domestic condiments, and known to cause cancer cell death via redox mechanisms. Based on the structural features of these compounds we designed and synthesized several 2-cinnamamido-N-substituted-cinnamamide (bis-cinnamamide) compounds. One of the derivatives, ( Z )-2-[( E )-cinnamamido]-3-phenyl-N-propylacrylamide ( 1512) showed a moderate antiproliferative potency (HT116 cell line inhibition of 32.0 µM ± 2.6) with proven cellular activities leading to apoptosis. Importantly, 1512 exhibited good selectivity toxicity on cancer cells over noncancerous cells (IC 50 of C-166 cell lines &gt;100 µM), and low cancer cell resistance at 100 µM dose (growth rate 10.1±1.1%). We subsequently carried out structure activity relationship studies with 1512 . Derivatives with electron rich moiety at the aryl ring of the 2-aminocinnamaide moiety exhibited strong antiproliferative action while electron withdrawing groups caused loss of activity. Our most promising compound, 4112 [( Z )-3-(1 H -indol-3-yl)- N -propyl-2-[( E )-3-(thien-2-yl)propenamido)propenamide] killed cancer cells at IC 50 = 0.89 ± 0.04 µM (Caco-2), 2.85 ± 1.5 (HCT-116) and 1.65 ± 0.07 (HT-29), while exhibiting much weaker potency on C-166 and BHK normal cell lines (IC 50 = 71 ± 5.12 and 77.6 ± 6.2 µM, respectively). Cellular studies towards identifying the compounds mechanism of cytotoxic activities revealed that apoptotic induction occurs in part due to oxidative stress. Importantly, the compounds showed inhibition of cancer stem cells that are critical for maintaining the potential for self-renewal and stemness. The results presented here show discovery of Michael addition compounds that potently kill cancer cells by a defined mechanism, with minimal effect on normal noncancerous cell.
Near‐Field Energy Transfer into Silicon Inversely Proportional to Distance Using Quasi‐2D Colloidal Quantum Well Donors (2021)

Abstract Silicon is the most prevalent material system for light‐harvesting applications; however, its inherent indirect bandgap and consequent weak absorption limits its potential in optoelectronics. This paper proposes to address this limitation by combining the sensitization of silicon with extraordinarily large absorption cross sections of quasi‐2D colloidal quantum well nanoplatelets (NPLs) and to demonstrate excitation transfer from these NPLs to bulk silicon. Here, the distance dependency, d , of the resulting Förster resonant energy transfer from the NPL monolayer into a silicon substrate is systematically studied by tuning the thickness of a spacer layer (of Al 2 O 3 ) in between them (varied from 1 to 50 nm in thickness). A slowly varying distance dependence of d −1 with 25% efficiency at a donor–acceptor distance of 20 nm is observed. These results are corroborated with full electromagnetic solutions, which show that the inverse distance relationship emanates from the delocalized electric field intensity across both the NPL layer and the silicon because of the excitation of strong in‐plane dipoles in the NPL monolayer. These findings pave the way for using colloidal NPLs as strong light‐harvesting donors in combination with crystalline silicon as an acceptor medium for application in photovoltaic devices and other optoelectronic platforms.
Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2 (2021)

COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.
Dynamic task scheduling using online optimization (2000)

Algorithms for scheduling independent tasks on to the processors of a multiprocessor system must trade-off processor load balance, memory locality, and scheduling overhead. Most existing algorithms, however, do not adequately balance these conflicting factors. This paper introduces the self-adjusting dynamic scheduling (SADS) class of algorithms that use a unified cost model to explicitly account for these factors at runtime. A dedicated processor performs scheduling in phases by maintaining a tree of partial schedules and incrementally assigning tasks to the least-cost schedule. A scheduling phase terminates whenever any processor becomes idle, at which time partial schedules are distributed to the processors. An extension of the basic SADS algorithm, called DBSADS, controls the scheduling overhead by giving higher priority to partial schedules with more task-to-processor assignments. These algorithms are compared to two distributed scheduling algorithms within a database application on an Intel Paragon distributed memory multiprocessor system.
Relaxation inS=1/2 quantum spin chains: The role of second neighbor interactions (1996)

Most of the existing dynamical studies in one dimension on magnetic insulators have considered the simplest spin models with nearest-neighbor interactions. In real systems, however, it is possible that longer range interactions are not entirely negligible. It is expected that the inclusion of next-nearest-neighbor interactions between spins in one-dimensional spin models will introduce a multitude of new frequencies in addition to the ones already present in the dynamics that arises due to nearest-neighbor interactions. We first present an exact solution for the dynamical xx-spin-pair correlations in an Ising chain with both nearest- and next-nearest-neighbor interactions to confirm our expectation. We next show, via an approximate analytical calculation, that the dynamical zz-spin-pair correlations in the next-nearest-neighbor transverse Ising chain when plotted as a function of time is noticeably different with respect to the exactly solvable nearest-neighbor transverse Ising chain at T\ensuremath{\rightarrow}\ensuremath{\infty} when the next-nearest-neighbor interaction is \ensuremath{\gtrsim}1/2 of the magnitude of the nearest-neighbor interaction. The effects could be fairly subtle in the time domain representation and in the spectral function when these additional interactions are weak (i.e., 1/2 of the nearest-neighbor interaction magnitude). The general conclusions reached in this work are expected to be valid for other simple quantum spin models such as the XY and XXZ models in one dimension. \textcopyright{} 1996 The American Physical Society.
Expression of simple epithelial cytokeratins in bovine pulmonary microvascular endothelial cells (1990)

Polypeptides of bovine aortic, pulmonary artery, and pulmonary microvascular endothelial cells, as well as vascular smooth muscle cells and retinal pericytes were evaluated by two-dimensional gel electrophoresis. The principal cytoskeletal proteins in all of these cell types were actin, vimentin, tropomyosin, and tubulin. Cultured pulmonary microvascular endothelial cells also expressed 12 unique polypeptides including a 41 kd acidic type I and two isoforms of a 52 kd basic type II simple epithelial cytokeratin microvascular endothelial cell expression of the simple epithelial cytokeratins was maintained in cultured in the presence or absence of retinal-derived growth factor, and regardless of whether cells were cultured on gelatin, fibronectin, collagen I, collagen IV, laminin, basement membrane proteins, or plastic. Cytokeratin expression was maintained through at least 50 population doublings in culture. The expression of cytokeratins was found to be regulated by cell density. Pulmonary microvascular endothelial cells seeded at 2.5 X 10(5) cell/cm2 (confluent seeding) expressed 3.5 times more cytokeratins than cells seeded at 1.25 X 10(4) cells/cm2 (sparse seeding). Vimentin expression was not altered by cell density. By indirect immunofluorescence microscopy it was determined that the cytokeratins were distributed cytoplasmically at subconfluent cell densities but that cytokeratin 19 sometimes localized at regions of cell-cell contact after cells reached confluence. Vimentin had a cytoplasmic distribution regardless of cell density. These results suggest that pulmonary microvascular endothelial cell have a distinctive cytoskeleton that may provide them with functionally unique properties when compared with endothelial cells derived from the macrovasculature. In conjunction with conventional endothelial cell markers, the presence of simple epithelial cytokeratins may be an important biochemical criterion for identifying pulmonary microvascular endothelial cells.
12/15-lipoxygenase–mediated enzymatic lipid oxidation regulates DC maturation and function (2015)

DCs are able to undergo rapid maturation, which subsequently allows them to initiate and orchestrate T cell-driven immune responses. DC maturation must be tightly controlled in order to avoid random T cell activation and development of autoimmunity. Here, we determined that 12/15-lipoxygenase-meditated (12/15-LO-mediated) enzymatic lipid oxidation regulates DC activation and fine-tunes consecutive T cell responses. Specifically, 12/15-LO activity determined the DC activation threshold via generation of phospholipid oxidation products that induced an antioxidative response dependent on the transcription factor NRF2. Deletion of the 12/15-LO-encoding gene or pharmacologic inhibition of 12/15-LO in murine or human DCs accelerated maturation and shifted the cytokine profile, thereby favoring the differentiation of Th17 cells. Exposure of 12/15-LO-deficient DCs to 12/15-LO-derived oxidized phospholipids attenuated both DC activation and the development of Th17 cells. Analysis of lymphatic tissues from 12/15-LO-deficient mice confirmed enhanced maturation of DCs as well as an increased differentiation of Th17 cells. Moreover, experimental autoimmune encephalomyelitis in mice lacking 12/15-LO resulted in an exacerbated Th17-driven autoimmune disease. Together, our data reveal that 12/15-LO controls maturation of DCs and implicate enzymatic lipid oxidation in shaping the adaptive immune response.
Goals in Nutrition Science 2015–2020 (2015)

With the definition of goals in Nutrition Science, we are taking a brave step and a leap of faith with regard to predicting the scope and direction of nutrition science over the next five years. The content of this editorial has been discussed, refined and evaluated with great care by the Frontiers in Nutrition editorial board. We feel the topics described represent the key opportunities, but also the biggest challenges in our field. We took a clean-slate, bottom-up approach to identify and address these topics and present them in eight categories. For each category the authors listed take responsibility, and deliberately therefore this document is a collection of thoughts from active minds, rather than a complete integration or consensus.At Frontiers in Nutrition, we are excited to develop and share a platform for this discussion. Healthy Nutrition for all – an ambition too important to be handled by detached interest groups and behind closed doors.
Approximate Absolute Rate Constants for 5-Exo and 6-Exo Cyclizations of 1°-Radicals to Acyl(triphenyl)germanes (1992)

Rate measurements indicate that acyl(triphenyl)-germanes are excellent acceptors in both 5-exo and 6-exo radical cyclizations.
Supplementary Figures 1 - 5 from Exploratory Clinical Trial of (4<i>S</i>)-4-(3-[<sup>18</sup>F]fluoropropyl)-l-glutamate for Imaging x<sub>C</sub><sup>−</sup> Transporter Using Positron Emission Tomography in Patients with Non–Small Cell Lung or Breast Cancer (2023)

&lt;p&gt;PDF file, 358K, S1: System xC� and CD44 in glutathione biosynthesis and the cysteine-cystine redox cycle; S2: 18FFSPG distribution in normal organs and cancer; S3: Correlation between 18FFDG and 18FFSPG; S4: 18FFDG and 18FFSPG PET in a breast cancer patient; S5: Correlation analysis between the staining intensity of xC� transporter and CD44 expression.&lt;/p&gt;
Troubleshooting When Using γ-Valerolactone (GVL) in Green Solid-Phase Peptide Synthesis (2019)

The synthesis of peptides for both research and API production is conveniently carried out using the solid-phase strategy. However, the main drawback of this approach is the large amounts of hazardous solvents required. In this regard, several pharmaceutical industries participating in the ACS Green Chemistry Institute Pharmaceutical Roundtable have shown interest in identifying green solvents for solid-phase peptide synthesis. In a previous study, our group proposed γ-valerolactone (GVL) as a replacement for the hazardous DMF. However, during Fmoc removal of the less hindered Gly residue, acylation with GVL can take place. Here we demonstrate that this side reaction can be circumvented by the incorporation of the corresponding dipeptides that carry Gly as the C-terminal. These dipeptides were conveniently prepared using CTC resin, which can be reused after activation. Using this strategy, GVL proved to be slightly superior to DMF for the synthesis of the demanding ABRF 1992 peptide, which contains five Gly residues.
Supplementary Figure 3 from Molecular Photoacoustic Imaging of Follicular Thyroid Carcinoma (2023)

&lt;p&gt;PDF file - 159K, Cleavage specificity&lt;/p&gt;
Antenna optimization for vehicular environments (2011)

This paper presents a multi-antenna optimization for communication in a Rockwell T-39 Sabreliner, a mid-size aircraft with a metallic body. The aircraft channel at 2.45 GHz is modeled using site specific 3D ray-tracing software. Added effects from system details including the antenna radiation patterns, mutual coupling, etc. are incorporated into a network theory based detailed signal model. The paper considers traditional antennas including dipoles, square patches, PIFAs, and polarization agile patches along with some more complex shaped patches and PIFAs. A random search algorithm was used to optimize capacity for arrays with widely divergent element count, element type, matching, directivity, polarization alignment, efficiency, spatial correlation and coupling. The polarization agile patch provides the best capacity for locations near the aircraft ceiling while the PIFAs with more variety in shape (spiral shapes) provide the best capacity for locations near the floor. This is because the signals reaching the roof and sides contain more polarization diversity than those in the center of the body where the nonconductive floor is located.