gebhart/patrepeval huggingface dataset:
Understanding Optomagnetic Interactions in Fe Nanowire–Au Nanoring Hybrid Structures Synthesized through Coaxial Lithography (2020)

Ferromagnetic Fe nanowires surrounded by two plasmonic Au nanorings (FeAuNRsNWs) were synthesized by coaxial lithography (COAL). They were characterized under irradiation (three different wavelengths) and an external magnetic field applied either parallel or perpendicular to the long axes of the wires using magnetic force microscopy (MFM) and Kelvin probe force microscopy (KPFM). The field directs the magnetic spin alignment of the nanowires. Through these studies, two important properties of FeAuNRsNWs, which derive from plasmon–spin interactions, have been discovered. First, with both parallel and perpendicular spin alignments (relative to the wire axis), hot-electron-enhanced magnetization is observed, as evidenced by plasmon-induced changes in both the surface potential and MFM phase values. Second, the observed enhancement when the spin alignment is perpendicular to the wire axis is smaller than that observed for parallel alignment. Both of these observations are a consequence of hot electron transfer from the Au nanorings to the Fe nanowire and the interaction between the plasmon-induced internal magnetic field and the external magnetic field in the FeAuNRsNW. This conclusion is further supported by finite-difference time domain (FDTD) and finite element method (FEM) simulations. In addition to being an excellent testbed for examining plasmon–spin interactions as a way to control magnetic spins with light, these FeAuNRsNWs, and their ring structure-dependent properties point toward a pathway for tailoring plasmon–spin interactions.
Surprisingly High Conductivity and Efficient Exciton Blocking in Fullerene/Wide-Energy-Gap Small Molecule Mixtures (2015)

We find that mixtures of C60 with the wide energy gap, small molecular weight semiconductor bathophenanthroline (BPhen) exhibit a combination of surprisingly high electron conductivity and efficient exciton blocking when employed as buffer layers in organic photovoltaic cells. Photoluminescence quenching measurements show that a 1:1 BPhen/C60 mixed layer has an exciton blocking efficiency of 84 ± 5% compared to that of 100% for a neat BPhen layer. This high blocking efficiency is accompanied by a 100-fold increase in electron conductivity compared with neat BPhen. Transient photocurrent measurements show that charge transport through a neat BPhen buffer is dispersive, in contrast to nondispersive transport in the compound buffer. Interestingly, although the conductivity is high, there is no clearly defined insulating-to-conducting phase transition with increased insulating BPhen fraction. Thus, we infer that C60 undergoes nanoscale (<10 nm domain size) phase segregation even at very high (>80%) BPhen fractions.
Origami-like folded mems for realization of TIMU: fabrication technology and initial demonstration (2015)

This paper reports a prototype of miniature, <50 mm3, Timing and Inertial Measurement Unit (TIMU), implemented utilizing a Folded MEMS concept. The approach is based on a wafer-level fabrication of high aspect ratio single-axis sensors, interconnected by flexible polyimide hinges, and then folded into a 3-D configuration, typically in a shape of cube or prism. Co-fabricated thru-wafer interconnects enable interfacing sensors on the device side of the TIMU with signal conditioning electronics potentially integrated inside a folded 3-D structure. We report a TIMU prototype with all 7 sensors operational, thus demonstrating a feasibility of the proposed fabrication approach. In this paper, we emphasize the characterization of the low-noise accelerometers, implemented on the TIMU sidewalls, demonstrating VRW of 0.057 m=s2= p h and bias instability of <0.2 mg.
Imaging in alpha-1 antitrypsin deficiency: a window into the disease (2021)

Imaging modalities such as plain chest radiograph and computed tomography (CT) are important tools in the assessment of patients with chronic obstructive pulmonary disease (COPD) of any etiology. These methods facilitate differential diagnoses and the assessment of individual lung pathologies, such as the presence of emphysema, bullae, or fibrosis. However, as emphysema is the core pathological consequence in the lungs of patients with alpha-1 antitrypsin deficiency (AATD), and because AATD is associated with the development of other lung pathologies such as bronchiectasis, there is a greater need for patients with AATD than those with non-AATD-related COPD to undergo more detailed assessment using CT. In the field of AATD, CT provides essential information regarding the presence, distribution, and morphology of emphysema. In addition, it offers the option to quantify the extent of emphysema. These data have implications for treatment decisions such as initiation of alpha-1 antitrypsin (AAT) therapy, or suitability for surgical or endoscopic interventions for reducing lung volume. Furthermore, CT has provided vital insight regarding the natural history of emphysema progression in AATD, and CT densitometry has underpinned research into the efficacy of AAT therapy. Moving forward, hyperpolarized xenon gas (<sup>129</sup>Xe) lung magnetic resonance imaging (MRI) is emerging as a promising complement to CT by adding comprehensive measures of regional lung function. It also avoids the main disadvantage of CT: the associated radiation. This chapter provides an overview of technological aspects of imaging in AATD, as well as its role in the management of patients and clinical research. In addition, perspectives on the future potential role of lung MRI in AATD are outlined.
In vitro Prevention of Vaccinia and Herpesvirus Infection Spread in Explanted Human Corneas by N-Chlorotaurine (2009)

Smallpox has been known as a major cause of blindness in historical outbreaks. NCT could therefore provide an additional supportive means for treating orthopoxvirus-associated keratitis. Additionally, biocompatible local antiseptics like NCT could also serve as an experimental treatment in other keratitis of suspected viral origin.
Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires (2018)

Summary Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.
In Situ Detection of Regulatory T Cells in Human Genital Herpes Simplex Virus Type 2 (HSV-2) Reactivation and Their Influence on Spontaneous HSV-2 Reactivation (2016)

The association of a high Treg to Tconv ratio with high viral shedding suggests that the balance between regulatory and effector T cells influences human HSV-2 disease.
Refinement of MIMO limited-feedback using second best codeword (2009)

This paper presents a new low complexity method of providing improved channel state information at the transmitter within closed-loop MIMO systems. We propose to feedback the second best codeword in addition to the best codeword. At the transmitter, these two precoding codewords are interpolated using geodesic. The optimal interpolation parameter is derived in closed-form for single-stream transmission. The performance of the proposed method with b-bit codewords is shown to be close to a codebook with 2b-bit codewords, while our method has significantly lower computational complexity.
S-Figure-1 from Gemcitabine and Chk1 Inhibitor AZD7762 Synergistically Suppress the Growth of Lkb1-Deficient Lung Adenocarcinoma (2023)

&lt;p&gt;Lkb1-null and shRNA library synthetic lethal genetic screen identified Chek1 as a putative candidate&lt;/p&gt;
New Chiral Ether Derivatives of 2-Arylidene-p-Menthane-3-Ones as Components of Induced Ferroelectric Systems (2001)

Abstract New 2-arylidene-p-menthane-3-ones containing the ether bridging group in the arylidene fragment have been synthesized and studied as chiral dopants in ferroelectric liquid crystal mixtures. The ferroelectric properties of these compositions were compared with those for compositions including chiral dopants that do not contain any bridging group. The influence of bridging group and terminal alkyl substituent length in the dopant molecule on the ferroelectric parameters of systems studied is discussed.
Visual field progression in glaucoma (1998)

Editor,—We read with interest the article by Viswanathan et al .1 

We were surprised by the authors’ progression criteria for theprogressor method; their criteria are extremely sensitive and very non-specific: only one point needs to show significantly negative slope when tested on the 5% level, together with an observed slope of <−1 dB/year and <−2 dB/year for inner and outer points, respectively. With 74 test points, it goes without saying that one here faces a problem with mass significance testing, which explains the very low specificity. It is obvious that almost any stable glaucoma patient would be detected as progressing with the reported method.

To illustrate the effect, we studied 10 patients with manifest glaucoma which, after at least 5 year follow up studies and at least eight visual fields, did not show visual field progression on the same clinical grounds as those used by Viswanathan et al . We had used same type of visual field test as the authors—that is, Humphrey 30-2 full threshold. In order to eliminate the possibility of any significant subclinical progression, the order of field tests were randomised before tests were analysed by the progressormethod. This randomisation secures that all significant progression would be the results of pure chance. Using the progression criteria of Viswanathan et al , stated above, five visual fields showed progression at the fourth visit, and already at the sixth visit eight eyes (80%) had shown false progression at one or more visits.

Further, we performed a Monte Carlo simulation study with the same criteria: 10 000 fields were simulated and tested 10 times and the regression slope was tested at each point starting at the third test occasion. The field was divided into two regions with 50 inner points and …
Direction Finding in Partly Calibrated Arrays Exploiting the Whole Array Aperture (2022)

We consider the problem of direction finding using partly calibrated arrays, a distributed subarray with position errors between subarrays. The key challenge is to enhance angular resolution in the presence of position errors. To achieve this goal, existing algorithms, such as subspace separation and sparse recovery, have to rely on multiple snapshots, which increases the burden of data transmission and the processing delay. Therefore, we aim to enhance angular resolution using only a single snapshot. To this end, we exploit the orthogonality of the signals of partly calibrated arrays. Particularly, we transform the signal model into a special multiple-measurement model, show that there is approximate orthogonality between the source signals in this model, and then use blind source separation to exploit the orthogonality. Simulation and experiment results both verify that our proposed algorithm achieves high angular resolution as distributed arrays without position errors, inversely proportional to the whole array aperture.
Dendritic Cells Engineered to Express Defined Allo‐HLA Peptide Complexes Induce Antigen‐specific Cytotoxic T Cells Efficiently Killing Tumour Cells (2008)

Most tumour-associated antigens (TAA) are non-mutated self-antigens. The peripheral T cell repertoire is devoid of high-avidity TAA-specific cytotoxic T lymphocytes (CTL) due to self-tolerance. As tolerance is major histocompatibility complex-restricted, T cells may be immunized against TAA presented by a non-self human leucocyte antigen (HLA) molecule and transferred to cancer patients expressing that HLA molecule. Obtaining allo-restricted CTL of high-avidity and low cross-reactivity has, however, proven difficult. Here, we show that dendritic cells transfected with mRNA encoding HLA-A*0201, efficiently present externally loaded peptides from the antigen, Melan-A/MART-1 to T cells from HLA-A*0201-negative donors. CD8(+) T cells binding HLA-A*0201/MART-1 pentamers were detected already after 12 days of co-culture in 11/11 donors. The majority of cells from pentamer(+) cell lines were CTL and efficiently killed HLA-A*0201(+) melanoma cells, whilst sparing HLA-A*0201(+) B-cells. Allo-restricted CTL specific for peptides from the leukaemia-associated antigens CD33 and CD19 were obtained with comparable efficiency. Collectively, the results show that dendritic cells engineered to express defined allo-HLA peptide complexes are highly efficient in generating CTL specifically reacting with tumour-associated antigens.
Effects of lonising radiation on deoxyribonucleic acid. Part 2. The influence of nitroimidazole drugs on the course of radiation damage to aqueous deoxyribonucleic acid (1985)

Exposure of frozen aqueous solutions of calf-thymus DNA to 60Co γ-irradiation at 77 K gave electron-gain centres localised on thymine (T–) and electron-loss centres localised on guanine (G+), in approximately equal yields as judged from their e.s.r. spectra. The presence of metronidazole or misonidazole resulted in a marked reduction in the yield of T–, the drug anions being detected in their place. The yield of G+ was not enhanced, in contrast to the results of others. Similar treatment of frozen aqueous solutions of plasmid DNA (pBR 322) was shown by gel electrophoresis to result in extensive single- and double-strand breaks in the absence of drug. Inclusion of metronidazole significantly reduced the number of strand breaks, double-strand breaks being reduced by a proportionately greater amount. An explanation is offered for this. At the molecular level these drugs clearly protect DNA from radiation damage (at least in terms of radical yield and strand breaks), despite the fact that they are known to be efficient radiosensitisers at the cellular level. These observations are discussed with regard to the various proposals for the mechanism of action of these drugs.
Loquat Leaf Extract Inhibits Oxidative Stress-Induced DNA Damage and Apoptosis via AMPK and Nrf2/HO-1 Signaling Pathways in C2C12 Cells (2022)

Loquat (Eriobotrya japonica) leaf extract exhibits bioactive properties against a variety of diseases. However, it remains unclear whether loquat leaf extract can protect myoblasts from oxidative damage. To investigate the protective effect of loquat leaf ethanol extract (LE) against hydrogen peroxide (H2O2)-induced oxidative stress in C2C12 murine myoblasts and the effect of LE on cellular differentiation in C2C12 cells. LE inhibited H2O2-induced cytotoxicity and reduced both the expression level of γ-H2AX and reactive oxygen species formation. LE also inhibited H2O2-induced apoptosis, which resulted in the upregulation of B-cell lymphoma 2 and pro-caspase-3 and inhibition of poly(ADP-ribose) polymerase cleavage, and the dysfunction of mitochondria under H2O2-induced oxidative stress, which inhibited the release of cytochrome c from mitochondria to the cytoplasm. Moreover, LE upregulated p-AMP-activated protein kinase (AMPK), p-nuclear factor erythroid 2-related factor 2 (Nrf2), and heme oxygenase-1 (HO-1) and downregulated Kelch-like ECH-associated protein 1 in H2O2-treated C2C12 cells. In addition, LE promoted the differentiation of C2C12 cells into myotubes and increased the expression levels of myogenic proteins, myogenic differentiation 1 (MyoD) and myogenin. These findings suggest that LE may be a promising therapeutic candidate for treating oxidative stress-mediated myoblast injury and enhancing cellular differentiation of C2C12 murine myoblasts into myotubes.
Distance-Based Probability Model for Octree Coding (2018)

We present a context-driven method to encode nodes of an octree, which is typically used to encode the point-cloud geometry. Instead of using one bit per node of the tree, the context allows for deriving probabilities for that node based on distances of the actual voxel to the voxels in a reference point cloud. Accurate probabilities of the node state allow for the use of an arithmetic coder to reduce the bit rate. Results point to potentially large reductions in rate if there is a good model from which to derive the context, i.e., one can get large reductions if the reference-cloud geometry is close enough to the one being encoded.
Microelectrical Mechanical Systems in Surgery and Medicine (2002)

Salzberg, Arnold D MD; Bloom, Matthew B MD; Mourlas, Nicolas J PhD; Krummel, Thomas M MD Author Information
A peptide antagonist of chemokine receptor CXCR4 reduces tumor metastasis in a murine orthotopic model of human prostate cancer (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

2162 

Prostate cancer is the second most common form of cancer in America and a leading cause of cancer-related deaths in men. The cure rate declines dramatically once the cancer metastasizes from the prostate glands to distant sites in the body. The main target for prostate cancer metastasis is bone. Prostate cancer cells are also commonly found in other organs surrounding the prostate area including the seminal vesicle, lymph nodes in the groin area and the rectum. Reports in the literature indicate that the expression of the chemokine receptor CXCR4 by prostate cancer correlates to their metastatic potential. CXCR4 is the receptor for the chemokine CXCL12, also known as stromal cell-derived factor-1 (SDF-1). The expression of SDF-1 is especially high in the bone marrow and is related to hematopoiesis. Cancer cells expressing CXCR4 home in to SDF-1 in the bone marrow and other specific organs. We have synthesized a number of analogs of SDF-1 using rational based drug design and some of these analogs have been shown to be antagonists of CXCR4. The lead compound of these synthetic antagonists, known as CTCE-9908, was tested in a murine orthotopic model of human prostate cancer (PC-3) for its ability to reduce metastases. Before initiation of in vivo studies, PC-3-GFP cells were mounted on poly-L-lysine-coated slides and stained with an anti-CXCR4 antibody. Varying degrees of CXCR4 expression was observed in all PC-3-GFP cells. For in vivo studies, two 1mm3 fragments of viable PC-3-GFP tumors harvested from the subcutaneous maintenance site of nude mice were sutured between two ventral lobes of the prostate in nude mice. Three days after tumor implantation, daily CTCE-9908 injections at a dose of 25 mg/kg/day IP or SC was initiated. Control mice received injections of vehicle. Mice were sacrificed after 4 weeks of treatment or when moribund. The fluorescent tumor pattern was then imaged. Analyses showed that the total area of metastasis was reduced from 370mm2 to 160mm2 for IP, and 130mm2 for SC. Reductions of 58% and 64%, respectively. This is consistent with findings of metastasis inhibition in other models including osteosarcoma, melanoma, and lung carcinoma. Further studies are in progress to determine optimal dose, scheduling, and combination with current therapies in this model. A phase I study has shown safety in healthy adults. A phase Ib/II study is expected to be initiated this year. The results to date suggest that the continued study of CTCE-9908 against a variety of metastatic tumor types is warranted.
Parameter Optimization for Applying the Prepulse Gap Paradigm to Humans (2013)

The optimal stimulus should be composed of the 1 kHz pulse noise without Hanning window. The intensity of the background noise should be 20 dB HL and the location of the gap should be 20 msec prior to the pulse noise. It seems that with these optimized parameters we could expect a 78.0% inhibition of N1-P2 amplitude in normal subjects without tinnitus.
Impact of the Physicochemical Composition and Microbial Diversity in Apple Juice Fermentation Process: A Review (2020)

Fermented apple beverages are produced all over the world with diverse characteristics associated with each country. Despite the diversifications, cider producers are confronted with similar issues and risks. The nature of the raw material, also known as the fermentation medium, plays a key role in fermentation. A well-defined composition of apples is, therefore, required to produce cider with good quality. In addition, ferment and its metabolism are important factors in the fermentation process. The producers of cider and other alcoholic beverages are looking in general for novel yeast strains or for the use of native strains to produce "authentic" and diversified beverages that are distinct from each other, and that attract more and more consumers. Research articles on cider production are infrequent compared to wine production, especially on the impact of the chemical composition and microbial diversity of apples on fermentation. Even though the processing of fermented beverages is close in terms of microbial interactions and production, the study of the specific properties of apples and the production challenges of cider production is advantageous and meaningful for cider producers. This review summarizes the current knowledge on apple composition and the impact of the must composition on fermentation and yeast growth. In addition, the microbial diversity of cider, activities, and its influence on fermentation are reviewed.
Sputtered platinum cluster growth in porous carbon: A grazing incidence small angle X-ray scattering study (2009)

International audience
Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation (2015)

Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject-specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole-brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available state-of-the art approaches.