gebhart/patrepeval huggingface dataset:
Analysis of the Dynamics of Magnetic Core–Shell Nanoparticles and Self-Assembly of Crystalline Superstructures in Gradient Fields (2015)

A method is presented for controlling the field-directed self-assembly of colloidal magnetic core–shell nanoparticles into three-dimensional (3D) crystalline superstructures with nanoscale feature resolution. This level of resolution is obtained using submicron soft-magnetic template elements to guide the assembly in the presence of a uniform bias field. The use of a bias field combined with template-induced gradient fields is a critical feature of this process as it provides highly localized regions of attractive and repulsive magnetic force that enable nanoscale control of particle placement during assembly. We demonstrate proof-of-concept using a computational model that predicts the dynamics of individual particles during assembly as well as the final assembled structure. Our predictions are consistent with reported experimental observations and demonstrate for the first time that 3D crystalline superstructures can be assembled within milliseconds. Uniform hexagonal close packed (hcp), face centered cubic (fcc), and mixed phase hcp-fcc structures can be obtained depending on the template geometry. We further show that the structure and resolution of the assembled particles as well as the rate of assembly can be controlled via careful selection of key parameters including the template geometry, particle constituents, core–shell dimensions, and the particle volume fraction. The proposed assembly method is very versatile as it broadly applies to arbitrary template geometries and multilayered core–shell particles that have at least one magnetic component. The magnetic component enables control to drive self-assembly, while the nonmagnetic components can provide desired functionality, e.g., photonic, electronic, biological, etc. Moreover, the process is reversible in that the particles can be repeatedly assembled and redisperesed by applying and removing the bias field, thereby enabling the reversible creation of functional media on demand. Alternatively, assembled structures can be transferred intact to a substrate to form thin films. As such, the method opens up opportunities for the scalable bottom-up fabrication of nanostructured materials with unprecedented functionality for a broad range of applications. The computational model is very general and can be applied to many forms of self-assembly to provide a fundamental understanding of underlying mechanisms and enable the rational design of novel media.
Verification of Finger Motion Discrimination using k-NN method for Myoelectric Hands (2019)

In society more and more delicate work is required, to make an artificial hand more convenient, it must support more works. To accomplish this, increase in the number of motion that the users can control is necessary. By using current motion discrimination method, the users can’t manipulate the fingers freely because the method can’t discriminate finger motions. Therefore, this study is set to development of a motion discrimination method that supports wrist-motion, finger-motion and hand-motion. The method is verified with cross validation in those nine and eleven motions.
1P1-T08 Control of Robot Arm by Considering Biological Limb Tip Compliance Characteristic (2015)

Organism use monoarticular muscles and biarticular muscles when driving the joints. Compliance with monoarticular muscles and biarticular muscles are doing the control of limb tip compliance of the biological. Previous studies have confirmed this characteristic by adding a mechanism corresponding to biarticular muscles to the robot arm. Generally, the direction of the trajectory match against any direction of the external force of the arm tip at the compliance characteristics of the arm circularity. In this paper, 2-link arm which has two motors showed approach to meet this characteristic. Also, we control the size of the tip compliance that varies with position. As a result, we have confirmed by simulation to satisfy this characteristic when tip displacement amount is small.
Growth-Inhibitory Antibodies Are Not Necessary for Protective Immunity to Malaria Infection (2009)

The absence of a validated surrogate marker for the immune state has complicated the design of a subunit vaccine against asexual stages of Plasmodium falciparum. In particular, it is not known whether the capacity to induce antibodies that inhibit parasite growth in vitro is an important criterion for selection of P. falciparum proteins to be assessed in human vaccine trials. We examined this issue in the Plasmodium yoelii rodent malaria model using the 19-kDa C-terminal fragment of merozoite surface protein 1 (MSP1(19)). To examine the relationship between inhibitory antibodies in immunized mice and the immune state, as indicated by resistance to a blood-stage challenge, we used an allelic replacement strategy to generate a transgenic P. falciparum line that expresses MSP1(19) from P. yoelii. We show that MSP1(19) is functionally conserved across these two divergent Plasmodium species, and replacing PfMSP1(19) with PyMSP1(19) has no detectable effect on parasite growth in vitro. By comparing growth rates of this transgenic line with a matched transgenic line that expresses the endogenous PfMSP1(19), we developed an assay to measure the specific growth-inhibitory activity directed exclusively to the PyMSP1(19) protein in the sera from vaccinated animals. To validate this assay, sera from rabbits immunized with recombinant PyMSP1(19) were tested and showed specific inhibitory activity in a concentration-dependent manner. In mice that were immunized with recombinant PyMSP1(19), the levels of PyMSP1(19)-specific inhibitory activity did not correlate with the total antibody levels measured by enzyme-linked immunosorbent assay. Furthermore, they did not correlate with resistance to subsequent blood-stage infection, and some mice with complete protection showed no detectable inhibitory activity in their prechallenge sera. These data indicated that growth-inhibitory activity measured in vitro was not a reliable predictor of immune status in vivo, and the reliance on this criterion to select vaccine candidates for human clinical trials may be misplaced. The transgenic lines further offer useful tools for comparing the efficacy of MSP1(19)-based vaccines that utilize different immunization regimens and antigen formulations.
Computer extracted features of tumor-infiltrating lymphocytes (TILs) architecture are prognostic of progression-free survival in stage III colon cancer (2022)

Stage III Colorectal cancer (CRC) is treated with surgery followed by chemotherapy. Yet &gt;20% of clinically low-risk patients develop recurrence. It is critical to identify high-risk stage III patients who can benefit from closer monitoring and escalation of therapy. Previous studies showed promising results in predicting risk from H&E slides in CRC using deep learning based algorithms. One biomarker which was heavily studied and showed good results in predicting risk is Tumor Infiltrating Lymphocytes (TILs). In CRC, TIL density has been shown to be significantly and independently associated with overall patient survival<sup>1</sup>. Furthermore, additional studies have demonstrated that analyzing spatial organization of TILs could be more informative than density alone<sup>2</sup>. Hence, our study aimed to stratify stage III CRC patients into distinct risk groups based on features derived from TILs and to determine if this classification could have independent prognostic significance. The training set (D<sub>1</sub>) included 50 patients and validation set (D<sub>2</sub>) consisted of 70 patients from an independent site. A survival model was trained to predict the risk of recurrence in stage III CRC patients. First, a deep learning (DL) model was used to segment TILs on WSIs. Next, 1036 features related to spatial architecture (SpaTIL) and density of TILs (DenTIL) were extracted. A Cox proportional hazards regression model in conjunction with the least absolute shrinkage and selection operator (Lasso) was used to find top 5 features and the feature coefficients associated with progression free survival (PFS) and provide risk scores to each patient. The risk scores for the training dataset were computed using the selected features with their respective coefficients. A cut-off value was determined according to these risk scores, above which patients were labelled high-risk and below was low risk. In the validation set, the median PFS for the high-risk group was 15.1mos and in the low-risk group was 27mos. The model was able to accurately predict higher incidence of progression in patients in the high-risk group (HR = 3.76, 95% CI 1.3-10.9, p-value=0.0053, c-index=0.687) in the validation set. Future work will entail additional multi-site, multi-institutional validation of our biomarker to further understand its strengths and applications.
Reduced-complexity RLS estimation for shallow-water channels (2002)

An adjustable complexity, recursive least squares (RLS) estimation algorithm is presented, which is suitable for adaptive equalization and source localization in shallow-water acoustic channels. The algorithm adjusts its computational complexity, measured in FLOPS per update, in a decreasing fashion with the relative signal strength, by ignoring "insignificant" dimensions of the channel. The algorithm reverts to the well-known fast RLS algorithms when the signal quality is weak, and may be combined with reduced period updating techniques. Examples illustrate computational savings in excess of one order of magnitude, permitting a tripling of the maximum data rate through these complexity-limited communication channels.
DFM rules! (2005)

For sub-100nm processes, predictions are putting initial process yields in the single digits. At the same time, at 130nm, we saw that two chips designed with the same methodology and same design rules could deliver completely different manufacturing yields.This panel will discuss the reasons for these phenomena and talk about future trends in DFM that will need to be addressed for success below 100nm.
Angiotensin II type 1 receptors and the intestinal microvascular dysfunction induced by ischemia and reperfusion (2006)

The acute phase of intestinal ischemia-reperfusion (I/R) injury is mediated by leukocytes and is characterized by oxidative stress and blood cell recruitment. Upregulation of angiotensin II type 1 receptors (AT1-R) has been implicated in the pathogenesis of conditions associated with oxidative stress. The AT1-R-antagonist Losartan (Los) attenuates leukocyte recruitment following I/R. However, the role of AT1-R in intestinal I/R injury and the associated platelet-leukocyte interactions remains unclear. The objective of this study was to define the contribution of AT1-R to I/R-induced blood cell recruitment in intestinal venules. Leukocyte and platelet adhesion were quantified by intravital microscopy in the small bowel of C57Bl/6 [wild-type (WT)] mice exposed to sham operation or 45 min of ischemia and 4 h of reperfusion. A separate WT group received Los for 7 days before gut I/R (WT-I/R + Los). AT1-R bone marrow chimeras that express AT1-R on the vessel wall but not blood cells also underwent I/R. Platelet and leukocyte adhesion as well as AT1-R expression in the gut microvasculature were significantly elevated after I/R. All of these responses were attenuated in the WT-I/R + Los group, compared with untreated I/R mice. A comparable abrogation of I/R-induced blood cell adhesion was noted in AT1-R bone marrow chimeras. I/R-induced platelet adhesion was unaltered in mice overexpressing Cu,Zn-SOD or mice deficient in NAD(P)H oxidase. These data suggest that although gut I/R upregulates endothelial expression of AT1-R, engagement of these angiotensin II receptors on blood cells is more important in eliciting the prothrombogenic and proinflammatory state observed in postischemic gut venules, through a superoxide-independent pathway.
Thermal diffusivity imaging with the thermal lens microscope (2011)

A coaxial thermal lens microscope was used to generate images based on both the absorbance and thermal diffusivity of histological samples. A pump beam was modulated at frequencies ranging from 50 kHz to 5 MHz using an acousto-optic modulator. The pump and a CW probe beam were combined with a dichroic mirror, directed into an inverted microscope, and focused onto the specimen. The change in the transmitted probe beam's center intensity was detected with a photodiode. The photodiode's signal and a reference signal from the modulator were sent to a high-speed lock-in amplifier. The in-phase and quadrature signals were recorded as a sample was translated through the focused beams and used to generate images based on the amplitude and phase of the lock-in amplifier's signal. The amplitude is related to the absorbance and the phase is related to the thermal diffusivity of the sample. Thin sections of stained liver and bone tissues were imaged; the contrast and signal-to-noise ratio of the phase image was highest at frequencies from 0.1-1 MHz and dropped at higher frequencies. The spatial resolution was 2.5 μm for both amplitude and phase images, limited by the pump beam spot size.
Subtyping Botulinum Neurotoxins by Sequential Multiple Endoproteases In-Gel Digestion Coupled with Mass Spectrometry (2012)

Botulinum neurotoxin (BoNT) is one of the most toxic substances known. BoNT is classified into seven distinct serotypes labeled A-G. Among individual serotypes, researchers have identified subtypes based on amino acid variability within a serotype and toxin variants with minor amino acid sequence differences within a subtype. BoNT subtype identification is valuable for tracing and tracking bacterial pathogens. A proteomics approach is useful for BoNT subtyping since botulism is caused by botulinum neurotoxin and does not require the presence of the bacteria or its DNA. Enzymatic digestion and peptide identification using tandem mass spectrometry determines toxin protein sequences. However, with the conventional one-step digestion method, producing sufficient numbers of detectable peptides to cover the entire protein sequence is difficult, and incomplete sequence coverage results in uncertainty in distinguishing BoNT subtypes and toxin variants because of high sequence similarity. We report here a method of multiple enzymes and sequential in-gel digestion (MESID) to characterize the BoNT protein sequence. Complementary peptide detection from toxin digestions has yielded near-complete sequence coverage for all seven BoNT serotypes. Application of the method to a BoNT-contaminated carrot juice sample resulted in the identification of 98.4% protein sequence which led to a confident determination of the toxin subtype.
Inhibition of Ebola Virus Entry by a C-peptide Targeted to Endosomes (2011)

Ebola virus (EboV) and Marburg virus (MarV) (filoviruses) are the causative agents of severe hemorrhagic fever. Infection begins with uptake of particles into cellular endosomes, where the viral envelope glycoprotein (GP) catalyzes fusion between the viral and host cell membranes. This fusion event is thought to involve conformational rearrangements of the transmembrane subunit (GP2) of the envelope spike that ultimately result in formation of a six-helix bundle by the N- and C-terminal heptad repeat (NHR and CHR, respectively) regions of GP2. Infection by other viruses employing similar viral entry mechanisms (such as HIV-1 and severe acute respiratory syndrome coronavirus) can be inhibited with synthetic peptides corresponding to the native CHR sequence ("C-peptides"). However, previously reported EboV C-peptides have shown weak or insignificant antiviral activity. To determine whether the activity of a C-peptide could be improved by increasing its intracellular concentration, we prepared an EboV C-peptide conjugated to the arginine-rich sequence from HIV-1 Tat, which is known to accumulate in endosomes. We found that this peptide specifically inhibited viral entry mediated by filovirus GP proteins and infection by authentic filoviruses. We determined that antiviral activity was dependent on both the Tat sequence and the native EboV CHR sequence. Mechanistic studies suggested that the peptide acts by blocking a membrane fusion intermediate.
Validation and test–retest repeatability performance of parametric methods for [11C]UCB-J PET (2022)

[<sup>11</sup>C]UCB-J is a PET radioligand that binds to the presynaptic vesicle glycoprotein 2A. Therefore, [<sup>11</sup>C]UCB-J PET may serve as an in vivo marker of synaptic integrity. The main objective of this study was to evaluate the quantitative accuracy and the 28-day test-retest repeatability (TRT) of various parametric quantitative methods for dynamic [<sup>11</sup>C]UCB-J studies in Alzheimer's disease (AD) patients and healthy controls (HC). Eight HCs and seven AD patients underwent two 60-min dynamic [<sup>11</sup>C]UCB-J PET scans with arterial sampling over a 28-day interval. Several plasma-input based and reference-region based parametric methods were used to generate parametric images using metabolite corrected plasma activity as input function or white matter semi-ovale as reference region. Different parametric outcomes were compared regionally with corresponding non-linear regression (NLR) estimates. Furthermore, the 28-day TRT was assessed for all parametric methods. Spectral analysis (SA) and Logan graphical analysis showed high correlations with NLR estimates. Receptor parametric mapping (RPM) and simplified reference tissue model 2 (SRTM2) BP<sub>ND</sub>, and reference Logan (RLogan) distribution volume ratio (DVR) regional estimates correlated well with plasma-input derived DVR and SRTM BP<sub>ND</sub>. Among the multilinear reference tissue model (MRTM) methods, MRTM1 had the best correspondence with DVR and SRTM BP<sub>ND</sub>. Among the parametric methods evaluated, spectral analysis (SA) and SRTM2 were the best plasma-input and reference tissue methods, respectively, to obtain quantitatively accurate and repeatable parametric images for dynamic [<sup>11</sup>C]UCB-J PET.
Induction of Broad CD4+and CD8+T-Cell Responses and Cross- Neutralizing Antibodies against Hepatitis C Virus by Vaccination with Th1-Adjuvanted Polypeptides Followed by Defective Alphaviral Particles Expressing Envelope Glycoproteins gpE1 and gpE2 and Nonstructural Proteins 3, 4, and 5 (2008)

Broad, multispecific CD4(+) and CD8(+) T-cell responses to the hepatitis C virus (HCV), as well as virus-cross-neutralizing antibodies, are associated with recovery from acute infection and may also be associated in chronic HCV patients with a favorable response to antiviral treatment. In order to recapitulate all of these responses in an ideal vaccine regimen, we have explored the use of recombinant HCV polypeptides combined with various Th1-type adjuvants and replication-defective alphaviral particles encoding HCV proteins in various prime/boost modalities in BALB/c mice. Defective chimeric alphaviral particles derived from the Sindbis and Venezuelan equine encephalitis viruses encoding either the HCV envelope glycoprotein gpE1/gpE2 heterodimer (E1E2) or nonstructural proteins 3, 4, and 5 (NS345) elicited strong CD8(+) T-cell responses but low CD4(+) T helper responses to these HCV gene products. In contrast, recombinant E1E2 glycoproteins adjuvanted with MF59 containing a CpG oligonucleotide elicited strong CD4(+) T helper responses but no CD8(+) T-cell responses. A recombinant NS345 polyprotein also stimulated strong CD4(+) T helper responses but no CD8(+) T-cell responses when adjuvanted with Iscomatrix containing CpG. Optimal elicitation of broad CD4(+) and CD8(+) T-cell responses to E1E2 and NS345 was obtained by first priming with Th1-adjuvanted proteins and then boosting with chimeric, defective alphaviruses expressing these HCV genes. In addition, this prime/boost regimen resulted in the induction of anti-E1E2 antibodies capable of cross-neutralizing heterologous HCV isolates in vitro. This vaccine formulation and regimen may therefore be optimal in humans for protection against this highly heterogeneous global pathogen.
Energy Outage-Aware Power Distribution Scheme for Off-Grid Base Station Operation (2017)

This letter describes a theoretical framework for power distribution to minimize an energy outage (EO) of off-grid base stations (BSs) powered by renewable energy sources and battery storage without direct support of an electrical grid. Here, EOs may occur when off-grid BSs cannot meet the power demand. Thus, considering the transmission power of the BS according to the traffic load and battery capacity, we represent an EO probability model. Using this model, we propose an energy outage-aware power distribution scheme (EO-PDS) for off-grid BSs. The convex optimization problem for minimizing the EO in off-grid BSs is formulated and solved. Numerical results reveal that the proposed scheme significantly reduces the EO probability compared with other existing schemes and has an acceptable convergence time.
Myocardial Engineering in Vivo : Formation and Characterization of Contractile, Vascularized Three-Dimensional Cardiac Tissue (2005)

Engineering cardiac tissue in three dimensions is limited by the ability to supply nourishment to the cells in the center of the construct. This limits the radius of an in vitro engineered cardiac construct to approximately 40 microm. This study describes a method of engineering contractile three-dimensional cardiac tissue with the incorporation of an intrinsic vascular supply. Neonatal cardiac myocytes were cultured in vivo in silicone chambers, in close proximity to an intact vascular pedicle. Silicone tubes were filled with a suspension of cardiac myocytes in fibrin gel and surgically placed around the femoral artery and vein of adult rats. At 3 weeks, the tissues in the chambers were harvested for in vitro contractility evaluation and processed for histologic analysis. By 3 weeks, the chambers had become filled with living tissue. Hematoxylin and eosin staining showed large amounts of muscle tissue situated around the femoral vessels. Electron micrographs revealed well-organized intracellular contractile machinery and a high degree of intercellular connectivity. Immunostaining for von Willebrand factor demonstrated neovascularization throughout the constructs. With electrical stimulation, the constructs were able to generate an average active force of 263 microN with a maximum of 843 microN. Electrical pacing was successful at frequencies of 1 to 20 Hz. In addition, the constructs exhibited positive inotropy in response to ionic calcium and positive chronotropy in response to epinephrine. As engineering of cardiac replacement tissue proceeds, vascularization is an increasingly important component in the development of three-dimensional structures. This study demonstrates the in vivo survival, vascularization, organization, and functionality of transplanted myocardial cells.
Evaluation of new base‐labile2‐(4‐nitrophenylsulfonyl)ethoxycarbonyl (Nsc)‐amino acids for solid‐phase peptide synthesis (2000)

The 2-(4-nitrophenylsulfonyl)ethoxycarbonyl (Nsc) group is a new base-labile protecting group for solid-phase peptide synthesis, completely interchangeable with the fluorenylmethoxycarbonyl (Fmoc) protecting group, but with certain advantages. In this paper, we report a methodology with Nalpha-Nsc-protected amino acids for the synthesis of some melanotropins important to our research, namely, gamma-melanocyte-stimulating hormone (gamma-MSH), its [Nle3]-analogue, and a cyclic alpha-MSH/beta-MSH hybrid. We developed an efficient protocol for the synthesis of the cyclic MSH analogue that yielded this peptide in >98% purity. The gamma-MSH synthesis, which gave problems with both the Boc and Fmoc strategies, yielded the desired peptide by Nsc-chemistry but was accompanied by side products. Finally, the Nle3-gamma-MSH analogue was synthesized more efficiently using the Fmoc strategy, suggesting that Nsc-chemistry might not be the best methodology for certain sequences.