gebhart/patrepeval huggingface dataset:
Reconstruction from free‐breathing cardiac MRI data using reproducing kernel Hilbert spaces (2009)

This paper describes a rigorous framework for reconstructing MR images of the heart, acquired continuously over the cardiac and respiratory cycle. The framework generalizes existing techniques, commonly referred to as retrospective gating, and is based on the properties of reproducing kernel Hilbert spaces. The reconstruction problem is formulated as a moment problem in a multidimensional reproducing kernel Hilbert spaces (a two-dimensional space for cardiac and respiratory resolved imaging). Several reproducing kernel Hilbert spaces were tested and compared, including those corresponding to commonly used interpolation techniques (sinc-based and splines kernels) and a more specific kernel allowed by the framework (based on a first-order Sobolev RKHS). The Sobolev reproducing kernel Hilbert spaces was shown to allow improved reconstructions in both simulated and real data from healthy volunteers, acquired in free breathing.
Abstract W MP90: Suppression of Endothelial Cell Alpha5Beta1 Integrin Prevents Ischemic Stroke Injury in Mice (2015)

Although breakdown of the blood-brain barrier (BBB) leads to significant injury after ischemic stroke, therapies that target this breakdown have been unsuccessful in improving patient outcomes. We hypothesize that the α5β1 integrin, a receptor that is conditionally upregulated in brain endothelial cells following ischemic stroke, could play a critical role in worsening ischemic injury and functional outcome by contributing to BBB breakdown. To investigate this hypothesis, we performed transient CCA/MCA occlusion in endothelial cell specific α5 integrin knockout (α5 KO) mice and wild-type (WT) mice treated with a α5β1 small peptide inhibitor ATN-161. Following experimental stroke, while WT control mice showed significant TTC-visualized infarcts by post-stroke day (PSD) 3, α5 KO mice and WT mice treated with ATN-161 had minimal to no discernible infarcts. Cresyl violet neuronal stain further demonstrated little to no tissue disruption and neuronal injury on PSD 1-3 in the α5 KO stroked brains. Furthermore, the BBB remained intact in the stroked α5 KO mice as evidenced by absent IgG staining in the brain parenchyma which was otherwise abundant in stroked WTs. Likewise, several markers of BBB stability such as the tight junction proteins Claudin-5 and ZO-1 were found to be upregulated in the α5 KO mice after stroke. Importantly, α5 KO mice did not have any difference in cerebrovascular anatomy or collateral brain blood flow that could otherwise account for these results. Finally, in vitro assays of brain endothelial cells exposed to oxygen-glucose deprivation (OGD) demonstrated that ATN-161 could prevent OGD-mediated increased endothelial cell permeability as measured by TEER and FITC-dextran, and enhanced beneficial Claudin-5 rearrangement at the cell surface. Taken together, these results suggest that suppression of α5 integrin in brain endothelial cells conveys significant resistance to experimental ischemic stroke injury due, at least in part, to enhanced BBB stability, and suggest that α5β1 integrin represents a novel and very promising therapeutic target for stroke.
Biointegrated flexible inorganic light emitting diodes (2012)

Abstract: The use of light-emitting diodes (LEDs) as therapeutic tools has been actively studied over the past few decades due to their advantages of high safety, low cost, excellent portability, and wide bandwidth. In addition, their application in biomedical fields has been expanded to such areas as nerve stimulation, photodynamic therapy, and LED-based biosensors, and LED lights are thus receiving attention as alternatives to conventional biomedical light sources such as lasers. Recently, several developments in the area of flexible inorganic LEDs along with advanced nanoelectronic technologies have pointed toward the possibility of new innovative biomethodologies in the near future. In this paper, we review the salient features of high-performance biointegrated LED applications, together with future challenges for the realization of implantable, flexible biointegrated electronic devices. Keywords: flexible, inorganic, biointegrated, light-emitting diodes, nerve stimulation, photodynamic therapy, biosensor
Obtaining and determination of the concentration in the culture fluid of phaecin – peptide bacteriocin Enterococcus faecium (2020)

Phaecin, a peptide bacteriocin with a molecular mass of ~5 kDa, was obtained and purified to an electrophoretically pure state with a yield of ~70% of the total activity in the culture fluid. The method of time-of-flight mass spectrometry (MALDI) showed that bacteriocin consists of two components A and B with similar molecular mass. In previously published works, the yield of purified bacteriocins, usually did not exceed 4–5% of the total activity in the culture fluid. The authors believe that the increase in yield is due to the fact that not only the similarity of bacteriocins with high molecular mass proteins was taken into account, but also differences associated with low molecular mass, the ability to hydrophobic interaction at slightly alkaline pH values and resistance to denaturation. Using the Scopes method, it was possible to determine the concentration of phaecin in the final stage of purification and in the culture fluid in absolute units (mg/l). The methods of the purification with high yield described in this work are probably applicable to other bacteriocins due to the proximity of their physicochemical properties. Key words: Enterococcus faecium, Listeria monocytogenes, bacteriocin, phaecin, culture liquid, adsorption chromatography, Scopes equation
Covalent 2D Patterning, Local Electronic Structure and Polarization Switching of Graphene at the Nanometer Level (2021)

A very facile and efficient protocol for the covalent patterning and properties tuning of graphene is reported. Highly reactive fluorine radicals were added to confined regions of graphene directed by laser writing on graphene coated with 1-fluoro-3,3-dimethylbenziodoxole. This process allows for the realization of exquisite patterns on graphene with resolutions down to 200 nm. The degree of functionalization, ranging from the unfunctionalized graphene to extremely high functionalized graphene, can be precisely tuned by controlling the laser irradiation time. Subsequent substitution of the initially patterned fluorine atoms afforded an unprecedented graphene nanostructure bearing thiophene groups. This substitution led to a complete switch of both the electronic structure and the polarization within the patterned graphene regions. This approach paves the way towards the precise modulation of the structure and properties of nanostructured graphene.
High Numerical Aperture Real and Fourier Space Investigation of Planar Photonic Devices Operating below the Light Cone (2007)

We will demonstrate that Fourier space imaging technique of the light diffracted from a photonic crystal (PhC) device allows the direct measurement of important physical properties of the PhC such as dispersion curves, equi-frequency surfaces, group indices and the characterization of the device performances in a complex environment. Advance techniques based on size effect super-resolution or coupling to an evanescent probe grating allow the extension of the measurement of such quantities even to propagating states lying below the light cone. We will illustrate such technique with three examples: 1) a PhC tile exhibiting self-collimated light propagation; 2) a polarization splitter device and 3) a modified Wl waveguide exhibiting slow light propagation.
Potential microRNA-related Targets for Therapeutic Intervention with Ovarian Cancer Metastasis (2018)

Treatment of disseminated epithelial ovarian cancer (EOC) is an unmet medical need. Therefore, the identification along with preclinical and clinical validation of new targets is an issue of high importance. In this review we focus on microRNAs that mediate metastasis of EOC. We summarize up-regulated metastasis-promoting and down-regulated metastasis-suppressing microRNAs. We focus on preclinical in vitro and in vivo functions as well as their metastasis-related clinical correlations. Finally, we outline modalities for therapeutic intervention and critical issues of microRNA-based therapeutics in the context of metastatic EOC.
Ultrafast Metal Electrodeposition Revealed by In Situ Optical Imaging and Theoretical Modeling towards Fast‐Charging Zn Battery Chemistry (2022)

Metallic Zn is a preferred anode material for rechargeable aqueous batteries towards a smart grid and renewable energy storage. Understanding how the metal nucleates and grows at the aqueous Zn anode is a critical and challenging step to achieve full reversibility of Zn battery chemistry, especially under fast-charging conditions. Here, by combining in situ optical imaging and theoretical modeling, we uncover the critical parameters governing the electrodeposition stability of the metallic Zn electrode, that is, the competition among crystallographic thermodynamics, kinetics, and Zn<sup>2+</sup> -ion diffusion. Moreover, steady-state Zn metal plating/stripping with Coulombic efficiency above 99 % is achieved at 10-100 mA cm<sup>-2</sup> in a reasonably high concentration (3 M) ZnSO<sub>4</sub> electrolyte. Significantly, a long-term cycling-stable Zn metal electrode is realized with a depth of discharge of 66.7 % under 50 mA cm<sup>-2</sup> in both Zn||Zn symmetrical cells and MnO<sub>2</sub> ||Zn full cells.
Figure S1-S8 from TIGIT and PD-1 Mark Intratumoral T Cells with Reduced Effector Function in B-cell Non-Hodgkin Lymphoma (2023)

&lt;p&gt;Supplementary figures S1-S8.&lt;/p&gt;
2011 Workshop on Visual Analytics in Healthcare (2012)

This paper presents a review and summary of the 2011 Workshop on Visual Analytics in Healthcare (VAHC 2011). This was the second annual VAHC workshop and it was held in late October in conjunction with the IEEE VisWeek Conference. The primary goal of the VAHC workshop is to bring together researchers and clinicians to discuss the areas in healthcare that can benefit the most from advances in visualization and analytic systems. This review summarizes the event and provides information on how to access the electronic proceedings. In addition, we seek volunteers who are interested in helping to organize future VAHC workshops.
Poly-ligand profiling (PLP) to differentiate pancreatic cancer patients who benefit from gemcitabine+evofosfamide versus gemcitabine+placebo treatment. (2018)

12067 Background: The MAESTRO trial randomized 693 locally advanced or metastatic pancreatic cancer patients to gemcitabine (G) + placebo vs G + evofosfamide (GE). OS hazard ratio (HR) was 0.84; p = 0.059. We developed a PLP assay that identifies patients most likely to benefit from GE vs G alone. By capitalizing on ssDNA aptamer binding properties, PLP measures network changes in tumors, including those that predict drug response. Methods: FFPE tissues of pancreatic cancer patients from the MAESTRO trial with good (OS > 13 mos) or poor (OS < 7 mos) outcome from GE were used for PLP assay development. Assay cut-points were determined using a training set (n = 12) and performance metrics were then determined using an independent blinded test set (n = 172). The study population enrolled in MAESTRO was divided into four cohorts based on treatment and benefit (cut-point = 240 days). The assay performance from the blinded test set was used to generate 1000 different possible patient subsets. Each simulation represents one possible trial outcome if the PLP assay had been used to enroll patients. We used the average value of the simulated median increase in OS from the 1000 random selections to estimate the impact the PLP assay would have had on MAESTRO. Results: 97% of the simulations yielded log-rank p < 0.05. Compared to MAESTRO, the average median OS increase for GE improved by 116±38% (simulation s.d.) with an average HR of 0.72±0.04. Moreover, the sample size in the simulations was 49% smaller compared to the original study, reflecting the percentage of test positive patients in the blinded test set. When only data from primary tumors were used, 100% of the permutations yielded log-rank p < 0.05 with an average median OS increase of 216±36% compared to MAESTRO and an average HR of 0.63±0.03. Conclusions: This retrospective study demonstrates that PLP, if prospectively applied, likely would have resulted in a successful study comparing GE to G pancreatic cancer patients. PLP is a powerful, flexible and facile platform warrants further study of additional therapies and in prospective trials.
Helping patients travel by air. (1991)

Although safe and rapid, air travel may present problems for people with certain medical conditions. Most medical emergencies that occur during a flight are preventable by judicious screening and preparation. We provide guidelines for physicians who are consulted about the wisdom of undertaking a journey by air. Potential stresses before, during and after the flight are outlined, including decreased atmospheric pressure, low humidity, turbulence, inactivity and time changes. We recommend precautionary measures for passengers with certain medical conditions, such as recent myocardial infarction, pulmonary disorders, pneumothorax, cerebrovascular accidents and diabetes and for those who have recently had surgery. The policy regarding air travel for pregnant women varies with each airline, but for certain conditions associated with pregnancy supplemental oxygen should be ordered before the trip. The special equipment and care that most airlines offer to ill or disabled people are described.
Exploring novel strategies for AIDS protozoal pathogens: α-helix mimetics targeting a key allosteric protein–protein interaction in C. hominis thymidylate synthase-dihydrofolate reductase (TS-DHFR) (2013)

The bifunctional enzyme thymidylate synthase-dihydrofolate reductase (TS-DHFR) from the protozoal parasite <i>Cryptosporidium hominis</i> is a potential molecular target for the design of antiparasitic therapies for AIDS-related opportunistic infections. The enzyme exists as a homodimer with each monomer containing a unique swap domain known as a "crossover helix" that binds in a cleft on the adjacent DHFR active site. This crossover helix is absent in species containing monofunctional forms of DHFR such as human. An in-depth understanding of protein-protein interactions between the crossover helix and adjacent DHFR active site that might modulate enzyme integrity or function would allow for insights into rational design of species-specific allosteric inhibitors. Mutational analysis coupled with structural studies and biophysical and kinetic characterization of crossover helix mutants identifies this domain as essential for full enzyme stability and catalytic activity, and pinpoints these effects to distinct faces of the crossover helix important in protein-protein interactions. Moreover, targeting this helical protein interaction with α-helix mimetics of the crossover helix leads to selective inhibition and destabilization of the <i>C. hominis</i> TS-DHFR enzyme, thus validating this region as a new avenue to explore for species-specific inhibitor design.
Preclinical Safety Evaluation of Ophthalmic Viscosurgical Devices in Rabbits and a Novel Mini-Pig Model (2019)

Johnson & Johnson Surgical Vision, Inc.
10-GHz High-Repetition Optical Short Pulse Generation from Wavelength-Tunable Quantum Dot Optical Frequency Comb Laser (2013)

The quantum dot optical frequency comb laser (QD-CML) is an attractive photonic device for generating a stable emission of fine multiple-wavelength peaks. In the present paper, 1.0-GHz and ∼10-ps-order short optical pulsation is successfully demonstrated from a hybrid mode-locked QD-CML with an ultrabroadband wavelength tuning range in the T+O band. In addition, 10-GHz high-repetition intensity-stable short optical pulse generation with a high S/N ratio is successfully demonstrated using an external-cavity QD-CML with a 10th-harmonic mode-locking technique.
Atypical opioid receptors: unconventional biology and therapeutic opportunities (2021)

Endogenous opioid peptides and prescription opioid drugs modulate pain, anxiety and stress by activating four opioid receptors, namely μ (mu, MOP), δ (delta, DOP), κ (kappa, KOP) and the nociceptin/orphanin FQ receptor (NOP). Interestingly, several other receptors are also activated by endogenous opioid peptides and influence opioid-driven signaling and biology. However, they do not meet the criteria to be recognized as classical opioid receptors, as they are phylogenetically distant from them and are insensitive to classical non-selective opioid receptor antagonists (e.g. naloxone). Nevertheless, accumulating reports suggest that these receptors may be interesting alternative targets, especially for the development of safer analgesics. Five of these opioid peptide-binding receptors belong to the family of G protein-coupled receptors (GPCRs)-two are members of the Mas-related G protein-coupled receptor X family (MrgX1, MrgX2), two of the bradykinin receptor family (B<sub>1,</sub> B<sub>2</sub>), and one is an atypical chemokine receptor (ACKR3). Additionally, the ion channel N-methyl-d-aspartate receptors (NMDARs) are also activated by opioid peptides. In this review, we recapitulate the implication of these alternative receptors in opioid-related disorders and discuss their unconventional biology, with members displaying signaling to scavenging properties. We provide an overview of their established and emerging roles and pharmacology in the context of pain management, as well as their clinical relevance as alternative targets to overcome the hurdles of chronic opioid use. Given the involvement of these receptors in a wide variety of functions, including inflammation, chemotaxis, anaphylaxis or synaptic transmission and plasticity, we also discuss the challenges associated with the modulation of both their canonical and opioid-driven signaling.
Impact of Plastic Blends on the Gaseous Product Composition from the Co-Pyrolysis Process (2023)

The co-pyrolysis of various biomasses mixed with two types of plastic waste was investigated in this study. Mixture M1 consisted of 30% m/m styrene–butadiene rubber (SBR), 40% m/m polyethylene terephthalate (PET), and 30% m/m polypropylene (PP). M2 consisted of 40% m/m PET, 30% m/m PP, and 30% m/m acrylonitrile–butadiene–styrene copolymer (ABS). The SBR, ABS, and PP used in this study were from the automotive industry, while the PET originated from scrap bottles. Co-pyrolysis was performed using wood biomass, agricultural biomass, and furniture trash. Thermal treatment was performed on samples from room temperature to 400 or 600 °C at a heating rate of 10 °C/min under N2 at a flow rate of 3 dm3/min. Based on the findings of the experiments, an acceptable temperature was found for the fixed-bed pyrolysis of biomass–plastic mixtures with varying ratios, and the raw materials were pyrolyzed under the same conditions. The composition of the derived gaseous fraction was investigated. The co-pyrolysis studies and variance analysis revealed that combining biomass with plastic materials had a good influence on the gaseous fraction, particularly in the presence of 6.6–7.5% v/v hydrogen and a lower heating value of 15.11 MJ/m3. This type of gaseous product has great potential for use as a replacement for coke oven gas in metallurgy and other applications.
The Convenient Synthesis of Hydrogen‐Bonded Ureidopyrimidinones (2004)

Abstract Blocked isocytosine isocyanates are conveniently obtained by the reaction of 1,1′‐carbonyldiimidazole (CDI) with isocytosines. The resulting precursors for quadruple hydrogen‐bonded structures can be isolated and stored for further use. Reaction with either aliphatic or aromatic amines gives the corresponding mono‐, bi‐, or trifunctional ureidopyrimidinone derivatives in good to excellent isolated yields. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
The Influenza Virus Protein PB1-F2 Inhibits the Induction of Type I Interferon at the Level of the MAVS Adaptor Protein (2011)

PB1-F2 is a 90 amino acid protein that is expressed from the +1 open reading frame in the PB1 gene of some influenza A viruses and has been shown to contribute to viral pathogenicity. Notably, a serine at position 66 (66S) in PB1-F2 is known to increase virulence compared to an isogenic virus with an asparagine (66N) at this position. Recently, we found that an influenza virus expressing PB1-F2 N66S suppresses interferon (IFN)-stimulated genes in mice. To characterize this phenomenon, we employed several in vitro assays. Overexpression of the A/Puerto Rico/8/1934 (PR8) PB1-F2 protein in 293T cells decreased RIG-I mediated activation of an IFN-β reporter and secretion of IFN as determined by bioassay. Of note, the PB1-F2 N66S protein showed enhanced IFN antagonism activity compared to PB1-F2 wildtype. Similar observations were found in the context of viral infection with a PR8 PB1-F2 N66S virus. To understand the relationship between NS1, a previously described influenza virus protein involved in suppression of IFN synthesis, and PB1-F2, we investigated the induction of IFN when NS1 and PB1-F2 were co-expressed in an in vitro transfection system. In this assay we found that PB1-F2 N66S further reduced IFN induction in the presence of NS1. By inducing the IFN-β reporter at different levels in the signaling cascade, we found that PB1-F2 inhibited IFN production at the level of the mitochondrial antiviral signaling protein (MAVS). Furthermore, immunofluorescence studies revealed that PB1-F2 co-localizes with MAVS. In summary, we have characterized the anti-interferon function of PB1-F2 and we suggest that this activity contributes to the enhanced pathogenicity seen with PB1-F2 N66S- expressing influenza viruses.
Second Cancers Among 104760 Survivors of Cervical Cancer: Evaluation of Long-Term Risk (2007)

Cervical cancer patients treated with radiotherapy are at increased risk of second cancers at sites in close proximity to the cervix beyond 40 years of follow-up.
Delivery of viral-vectored vaccines by B cells represents a novel strategy to accelerate CD8+ T-cell recall responses (2013)

Rapid boosting of memory CD8(+) T cells (TM) is essential in cancer immunotherapy and the control of certain infectious diseases. However, effector T cells (TE) are a barrier to booster vaccination because they can rapidly kill antigen-bearing antigen-presenting cells (APCs) before TM are engaged. We demonstrate that viral-vectored vaccines delivered by B cells elicit robust TM expansion in the presence of TE, enabling booster immunizations to bypass TE-mediated negative feedback regulation. Our data indicate that viral vector-loaded B cells home to the follicular regions in secondary lymphoid organs, which are anatomically separated from TE and in close proximity to TM. The B cells, however, do not serve as APCs in this area. Rather, classic CD11c(+) dendritic cells serve to stimulate the secondary CD8(+) T-cell response. Our data reveal that B cells represent a novel and readily accessible delivery system that can effectively engage secondary CD8(+) T-cell activation for prime-boost strategies.