gebhart/patrepeval huggingface dataset:
Jamming in hard sphere and disk packings (2004)

Hard-particle packings have provided a rich source of outstanding theoretical problems and served as useful starting points to model the structure of granular media, liquids, living cells, glasses, and random media. The nature of “jammed” hard-particle packings is a current subject of keen interest. Elsewhere, we introduced rigorous and efficient linear-programming algorithms to assess whether a hard-sphere packing is locally, collectively, or strictly jammed, as defined by Torquato and Stillinger [J. Phys. Chem. B 105, 11849 (2001)]. One algorithm applies to ideal packings in which particles form perfect contacts. Another algorithm treats the case of jamming in packings with significant interparticle gaps. We have applied these algorithms to test jamming categories of ordered lattices as well as random packings of circular disks and spheres under periodic boundary conditions. The random packings were produced computationally with a variety of packing generation algorithms, all of which should, in principle, produce at least collectively jammed packings. Our results highlight the importance of jamming categories in characterizing particle packings. One important and interesting conclusion is that the amorphous monodisperse sphere packings with density φ≈0.64 were for practical purposes strictly jammed in three dimensions, but in two dimensions the monodisperse disk packings at previously reported “random close packed” densities of φ≈0.83 were not even collectively jammed. On the other hand, amorphous bidisperse disk packings with density of φ≈0.84 were virtually strictly jammed. This clearly demonstrates one cannot judge “stability” in packings based solely on local criteria. Numerous interactive visualization models are provided on the authors’ webpage.
Interface Strengthening Mechanisms in Polymeric Fiber Reinforced Cementitious Composites (1994)

Peer Reviewed
Nuclear factor-kB is involved in the catecholaminergic suppression of immunocompetent cells (2000)

Nuclear factor-kB is involved in the catecholaminergic suppression of immunocompetent cells
Cognitive repeaters for flexible mobile data traffic offloading (2013)

We investigate the performance of cognitive amplify-and-forward (AF) repeaters in a dense urban environment. The benefit of repeaters is twofold. First, repeaters can compensate penetration losses and serve as wireless backhauling technology to bring high data rates into shielded environments. Second, a cognitive repeater can utilize very flexible different frequency bands and adopt its wireless link to the current frequency reuse plan. In this paper, we propose a new cognitive repeater concept which utilizes multiband signal offloading. Therefore, a cognitive repeater is implemented as a real-time hardware prototype in an amplify-and-forward (AF) relay and deployed in a real LTE-A testbed. The system performance is evaluated by various measurement trials within shielded indoor hotspot environments. It is shown, that cognitive repeaters can take advantage of the signal shielding to the outside and beneficially improve system performance for indoor user hotspots.
Inactivated Mycoplasma pneumoniae vaccine. Evaluation in volunteers. (1967)

The protective effect of an experimental, inactivated Mycoplasma pneumoniae vaccine was evaluated by first injecting volunteers with vaccine and then infecting them with the organism. The vaccine induced the development of growth-inhibiting antibody in ten of 19 volunteers who initially lacked this antibody. Following experimental challenge with M pneumoniae, only one of these ten men who responded to the vaccine became ill, whereas, respiratory tract disease developed in seven of nine men who failed to respond to the vaccine and in ten of 13 volunteers in the control group who lacked the antibody. The most severe clinical illnesses developed in the men who failed to respond to the vaccine. These findings suggest that the vaccine had a protective effect in those men who developed antibody, while those who failed to develop antibody may have been sensitized.
Exactly realizable bounds on the trapping constant and permeability of porous media (2004)

Sandstone, granular media, bone, wood, and cell membranes are just a few examples of porous media that abound in Nature and in synthetic situations. Two important effective properties of fluid-saturated porous media that have been extensively studied are the trapping constant γ and scalar fluid permeability k. Exact expressions for the “void” bounds on γ and k for coated-spheres and coated-cylinders models of porous media are derived. In certain instances, the bounds are shown to be optimal, i.e., the void bounds coincide with the corresponding exact solutions of γ and k for these coated-inclusions models. In the optimal cases, we obtain exact expressions for the relevant length scale that arises in the void bounds, which depends on a two-point correlation function that characterizes the porous medium. By contrast, optimal bounds on the effective conductivity and elastic moduli of composite media have long been known.
Inkjet printing of pixel arrays: droplet formation and pattern uniformity of a non-aqueous ink with tunable viscosity (2023)

Abstract Inkjet printing is a rapid and material-efficient process that is suitable for the fabrication of large-area microarrays from a range of optoelectronic materials. In order to ensure stable droplet formation and a uniform print image with very smooth surfaces, however, the ink properties such as viscosity and surface tension have to be precisely adjusted. In this study, a non-aqueous ink formulation is proposed whose viscosity can be conveniently adjusted by controlling the mixing ratio of propylene carbonate (PC) as the low-viscosity solvent and propylene glycol (PG) as the high-viscosity solvent. Using a combination of advanced imaging techniques, we show that raising the PG content from 20% to 80% increased the viscosity of the ink from 3.36 cP to 26.70 cP, resulting in stable droplet formation and a more evenly printed image. At a spacing of 5 dots/pixel, the roughness value decreased dramatically, from root mean square (RMS): 11.28 (20% PG) to RMS: 0.09 (80% PG). Alternatively, more homogeneous patterns (albeit with a rough surface) were also produced with the low-viscosity ink (20% PG) when a conditioned substrate with low surface energy and selective liquid repellency was used. With this we present a simple but effective strategy to improve droplet formation while obtaining highly uniform pixel arrays. The knowledge gained will be particularly useful for inkjet printing of pixel-patterned color conversion layers in devices such as organic light-emitting diodes (LEDs) and micro-LED displays.
Molecular targets for rapid identification of Brucella spp (2006)

Although not all of the differentiating genes identified were transcribed under steady state conditions, a group of genes sufficient to discriminate unambiguously between B. suis, B. melitensis, and B. abortus was identified. We present an overview of these genomic differences and the use of these features to discriminate among a number of Brucella biovars.
Dominant Role of N-Type Ca 2+ Channels in Evoked Release of Norepinephrine from Sympathetic Neurons (1988)

Multiple types of calcium channels have been found in neurons, but uncertainty remains about which ones are involved in stimulus-secretion coupling. Two types of calcium channels in rat sympathetic neurons were described, and their relative importance in controlling norepinephrine release was analyzed. N-type and L-type calcium channels differed in voltage dependence, unitary barium conductance, and pharmacology. Nitrendipine inhibited activity of L-type channels but not N-type channels. Potassium-evoked norepinephrine release was markedly reduced by cadmium and the conesnail peptide toxin omega-Conus geographus toxin VIA, agents that block both N- and L-type channels, but was little affected by nitrendipine at concentrations that strongly reduce calcium influx, as measured by fura-2. Thus N-type calcium channels play a dominant role in the depolarization-evoked release of norepinephrine.
Characterization of Cytomegalovirus Disease in Solid Organ Transplant Recipients by Markers of Inflammation in Plasma (2013)

Our findings illustrate the complex interaction between cytomegalovirus and the immune system, involving a wide range of inflammatory mediators that could be associated to disease manifestations in cytomegalovirus related disease.
Apoptosis in Cerebellar Granule Neurones: Involvement of Interleukin‐1β Converting Enzyme‐Like Proteases (1997)

Proteases of the interleukin-1 beta converting enzyme (ICE) family have been implicated as mediators of apoptosis in several cell types. Here we report the ability of peptide inhibitors of ICE-like proteases to inhibit apoptosis of cultured cerebellar granule neurones caused by reduction of extracellular K+ levels and by the broad-spectrum protein kinase inhibitor staurosporine. Unlike apoptosis induced by K+ deprivation, staurosporine-induced neuronal death does not require new protein synthesis. The ICE-like protease inhibitor benzyloxycarbonyl-Val-Ala-Asp (O-methyl)fluoromethyl ketone (zVAD-fmk) was found to be extremely effective at preventing staurosporine-induced death of cerebellar granule neurones and yet was completely ineffective in preventing K+ deprivation-induced death. Staurosporine induced cleavage of the 116-kDa poly (ADP-ribose) polymerase enzyme, a substrate of ICE-like proteases, to the 85-kDa product, and this cleavage was also blocked by zVAD. By comparison, K+ deprivation led to the disappearance of the 116-kDa protein, with no detectable increase in level of the 85-kDa cleavage product. Taken together, these results imply the existence of divergent ICE-like protease pathways in a CNS model of neuronal apoptosis.
Channel Mobility Improvement in 4H-SiC MOSFETs Using a Combination of Surface Counter-Doping and NO Annealing (2015)

Lateral MOSFET devices with a thin surface counter-doped layer using Sb and As with and without NO passivation have been fabricated and characterized. The results demonstrate that Sb and As counter-dope the interface without significant trap passivation while in combination with NO there is a superposition of both trap passivation and counter-doping related performance enhancement. In addition, by varying the counter doping level, a universal mobility characteristics of NO passivated devices has been identified.
A proposed framework for cerebral venous congestion (2021)

This framework is the first clinically structured description of venous pathologies resulting in intracranial venous and cerebrospinal fluid hypertension. Our proposed system highlights unique clinical symptoms and features critical for appropriate diagnostic work-up and potential treatment. This novel schema allows clinicians effectively to approach cases of intracranial hypertension secondary to venous etiologies, and furthermore provides a framework by which researchers can better understand this developing area of cerebrovascular disease.
Optical Frequency Transfer via 920 km Fiber Link with 10−19 Relative Accuracy (2012)

Optical frequency transfer via a 920 km fiber link has been investigated. Active noise compensation enables the transfer of a stable optical frequency with a stability of 3.8 × 10−14 at 1 s reaching 4 × 10−18 after 104 s and an accuracy of 3.6 × 10−19.
The Anti-Apoptotic Role of Berberine in Preimplantation Embryo In Vitro Development through Regulation of miRNA-21 (2015)

Traditional Chinese medicinal herbs containing berberine have been historically used to prevent miscarriage. Here, we investigated whether the anti-apoptotic effects of berberine on pre-implantation embryonic development are regulated by miRNA-21. Mouse pronuclear embryos were cultured in medium with or without berberine, and some were then microinjected with a miRNA-21 inhibitor. The in vitro developmental rates of 2- and 4-cell embryos and blastocysts, blastocyst cell numbers, apoptotic rates, and apoptotic cell numbers were measured in each group. Furthermore, we examined the transcription levels of miRNA-21 and its target genes (caspase-3, PTEN, and Bcl-2) and their translation levels. Comparisons were made with in vivo-developed and untreated embryos. We found that berberine significantly increased the developmental rates and cell numbers of mouse blastocysts and decreased apoptotic cell rates in vitro. Berberine also significantly increased miRNA-21 and Bcl-2 transcription levels and significantly decreased caspase-3 and PTEN transcription levels. In embryos treated with a miRNA-21 inhibitor, the results followed the opposite trend; PTEN and caspase-3 transcription levels increased significantly, while the transcription level of Bcl-2 decreased significantly. Additionally, berberine treatment significantly increased the Bcl-2 protein level and significantly decreased the caspase-3 and PTEN protein levels in blastocysts, but there were no significant differences observed in the levels of these proteins in 2- and 4-cell embryos. This study revealed that miRNA-21 is important for pre-implantation embryonic development, especially blastocyst development in vitro. Berberine elevates miRNA-21 expression, decreases PTEN and caspase-3 levels, increases Bcl-2 levels, and exerts anti-apoptotic and pro-growth effects.
Diffusion plasma chemical vapour deposition yielding freestanding individual single-walled carbon nanotubes on a silicon-based flat substrate (2006)

Isolated freestanding single-walled carbon nanotubes (SWNTs) have been successfully produced on silicon-based flat substrates using diffusion plasma-enhanced chemical vapour deposition. The quantitative effects of plasma parameters, such as ion density and sheath electric field, on the growth and tube alignments of freestanding SWNTs are discussed on the basis of Langmuir probe measurements and simple calculations.
Computational staining of pathology images to study tumor microenvironment in lung cancer (2019)

ABSTRACT The spatial organization of different types of cells in tumor tissues reveals important information about the tumor microenvironment (TME). In order to facilitate the study of cellular spatial organization and interactions, we developed a comprehensive nuclei segmentation and classification tool to characterize the TME from standard Hematoxylin and Eosin (H&amp;E)-stained pathology images. This tool can computationally “stain” different types of cell nuclei in H&amp;E pathology images to facilitate pathologists in analyzing the TME. A Mask Regional-Convolutional Neural Network (Mask-RCNN) model was developed to segment the nuclei of tumor, stromal, lymphocyte, macrophage, karyorrhexis and red blood cells in lung adenocarcinoma (ADC). Using this tool, we identified and classified cell nuclei and extracted 48 cell spatial organization-related features that characterize the TME. Using these features, we developed a prognostic model from the National Lung Screening Trial dataset, and independently validated the model in The Cancer Genome Atlas (TCGA) lung ADC dataset, in which the predicted high-risk group showed significantly worse survival than the low-risk group (pv= 0.001), with a hazard ratio of 2.23 [1.37-3.65] after adjusting for clinical variables. Furthermore, the image-derived TME features were significantly correlated with the gene expression of biological pathways. For example, transcription activation of both the T-cell receptor (TCR) and Programmed cell death protein 1 (PD1) pathways was positively correlated with the density of detected lymphocytes in tumor tissues, while expression of the extracellular matrix organization pathway was positively correlated with the density of stromal cells. This study developed a deep learning-based analysis tool to dissect the TME from tumor tissue images. Using this tool, we demonstrated that the spatial organization of different cell types is predictive of patient survival and associated with the gene expression of biological pathways. Although developed from the pathology images of lung ADC, this model can be adapted into other types of cancers.
Costal Cartilage Autografts to Simulated Degenerative Intervertebral Discs in the Rat (2006)

Costal cartilage transplantation may rehydrate degenerated intervertebral discs and might serve as a promising model for understanding and perhaps modifying this complex degenerative disease.
A Whole-Genome Association Study of Major Determinants for Host Control of HIV-1 (2007)

Understanding why some people establish and maintain effective control of HIV-1 and others do not is a priority in the effort to develop new treatments for HIV/AIDS. Using a whole-genome association strategy, we identified polymorphisms that explain nearly 15% of the variation among individuals in viral load during the asymptomatic set-point period of infection. One of these is found within an endogenous retroviral element and is associated with major histocompatibility allele human leukocyte antigen (HLA)-B*5701, whereas a second is located near the HLA-C gene. An additional analysis of the time to HIV disease progression implicated two genes, one of which encodes an RNA polymerase I subunit. These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents.
Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction. (2014)

International audience
Regioselective Organocadmium Alkylations of Substituted Quinones (2001)

A series of substituted quinones was alkylated with diethylcadmium. Regiochemistry of addition shifted from quinol formation to conjugate addition as a function of the steric and electronic effects of the substituents.
The role of medicine donations in the global programme for the elimination of lymphatic filariasis (2020)

World Health Assembly Resolution 50.29, adopted in 1997, committed the World Health Organization (WHO) and its member states to eliminate lymphatic filariasis (LF) as a public health problem. In 2000, to support this ambitious goal and the health ministries in the >70 LF-endemic countries, the Global Programme to Eliminate Lymphatic Filariasis (GPELF) was created. The resulting WHO elimination strategy consists of two main components: to stop the spread of infection by interrupting transmission and to alleviate the suffering of affected populations (by controlling morbidity). The GPELF has brought together a broad global partnership of public and private actors, including three pharmaceutical companies with headquarters in three different continents. The medicine donations programmes from GlaxoSmithKline, MSD (trade name of Merck & Co., Kenilworth, NJ, USA) and Eisai have enabled significant achievements during the first 20 y of the GPELF and are positioned to provide essential contributions to the GPELF's goals for the next decade. As we celebrate the progress towards LF elimination during the GPELF's first 20 y, this article reflects on the factors that led to the creation of the three donation programmes, the contributions these programmes have made and some lessons learned along the way. We close by emphasizing our continued commitments to LF elimination and perspectives on the next decade.
CNN-based Classification of Degraded Images (2020)

Classification of degraded images is very important in practice because images are usually degraded by compression, noise, blurring, etc. Nevertheless, most of the research in image classification only focuses on clean images without any degradation. Some papers have already proposed deep convolutional neural networks composed of an image restoration network and a classification network to classify degraded images. This paper proposes an alternative approach in which we use a degraded image and an additional degradation parameter for classification. The proposed classification network has two inputs which are the degraded image and the degradation parameter. The estimation network of degradation parameters is also incorporated if degradation parameters of degraded images are unknown. The experimental results showed that the proposed method outperforms a straightforward approach where the classification network is trained with degraded images only.
Combination therapy of androgen-independent prostate cancer using a prostate restricted replicative adenovirus and a replication-defective adenovirus encoding human endostatin-angiostatin fusion gene (2006)

Although prostate-restricted replicative adenovirus has exhibited significant antitumor efficacy in preclinical studies, it is necessary to develop more potent adenoviruses for prostate cancer gene therapy. We evaluated the synergistic killing effect of prostate-restricted replicative adenovirus and AdEndoAngio, a replication-defective adenovirus expressing the endostatin-angiostatin fusion protein (EndoAngio). When coadministered with AdEndoAngio, prostate-restricted replicative adenovirus significantly elevated EndoAngio expression, suggesting that AdEndoAngio coreplicates with prostate-restricted replicative adenovirus. Conditioned medium from prostate cancer cells infected by prostate-restricted replicative adenovirus plus AdEndoAngio inhibited the growth, tubular network formation, and migration of human umbilical vein endothelial cells better than conditioned medium from prostate cancer cells infected by AdEndoAngio alone. Furthermore, in vivo animal studies showed that the coadministration of prostate-restricted replicative adenovirus plus AdEndoAngio resulted in the complete regression of seven out of eight treated androgen-independent CWR22rv tumors, with a tumor nodule maintaining a small size for 14 weeks. The residual single tumor exhibited extreme pathologic features together with more endostatin-reactive antibody-labeled tumor cells and fewer CD31-reactive antibody-labeled capillaries than the AdEndoAngio-treated tumors. These results show that combination therapy using prostate-restricted replicative adenovirus together with antiangiogenic therapy has more potent antitumor effects and advantages than single prostate-restricted replicative adenovirus and deserves more extensive investigation.
Radioimmunoassay of the Group-specific Antigen in Detection of Avian Leukosis Virus Infection (1974)

Summary The major group-specific antigen (gs-a) of avian leukoviruses was detected by radioimmunoassay in extracellular medium of all embryonic cultures prepared from infected chickens. Embryos of birds not carrying an avian leukosis virus infection and of chickens from a leukosis-free flock could thus clearly be distinguished from infected ones. Release of group-specific antigen into the extracellular medium was independent of subgroup or strain of avian leukosis or Rous sarcoma virus. The radioimmunoassay of the group-specific antigen seems to be well suited to complement the COFAL (complement fixation avian leukosis) and RIF (resistance inducing factor) tests in the detection of leukosis virus in infected material.