gebhart/patrepeval huggingface dataset:
Digital photogrammetry and TLS data fusion applied to Cultural Heritage 3D modeling. (2006)

A great number of papers have been so far published about the comparison and the integration between terrestrial laser scanning and digital photogrammetry, as surveying and 3D modeling techniques. Though most of the works report about their application to Cultural Heritage, achieved results have shown that these two technologies can supplement each other in creating high-quality 3D recordings and presentations: laser scanning can produce the dense 3D point-cloud data that is required to create high-resolution geometric models, while digital photogrammetry is more suited to produce high-resolution textured 3D models representing just the main object structure. It should be noted however that in many cases, fusion or integration of both surveying techniques is regarded only as the application of digital images onto the laser scanning-based 3D model and/or the production of orthophotos.\nIt is well known that for complex architectures, no modeling technique by itself can efficiently and quickly provide a complete and detailed 3D model: a hibryd approach is required. In the view of an insight investigation on this topic, this paper reports on the study of merging digital photogrammetry and laser scanning to produce a unique detailed 3D model of a complex historical building. The basic shapes (e.g. walls and other main structures) were determined by image-based methods using a 7Mpixel digital camera while fine details or more complex shapes were surveyed with a TOF laser scanner. Adopted data collection procedures and modeling issues, related to the integration of the different datasets, will be discussed. A final textured 3D model and virtual flights over the historical building will be also presented.
Antroquinonol D, Isolated from <i>Antrodia camphorata</i>, with DNA Demethylation and Anticancer Potential (2014)

DNA methyltransferase 1 (DNMT1) catalyzes DNA methylation and is overexpressed in various human diseases, including cancer. A rational approach to preventing tumorigenesis involves the use of pharmacologic inhibitors of DNA methylation; these inhibitors should reactivate tumor suppressor genes (TSGs) in tumor cells and restore tumor suppressor pathways. Antroquinonol D (3-demethoxyl antroquinonol), a new DNMT1 inhibitor, was isolated from Antrodia camphorata and identified using nuclear magnetic resonance. Antroquinonol D inhibited the growth of MCF7, T47D, and MDA-MB-231 breast cancer cells without harming normal MCF10A and IMR-90 cells. The SRB assay showed that the 50% growth inhibition (GI50) in MCF7, T47D, and MDA-MB-231 breast cancer cells following treatment with antroquinonol D was 8.01, 3.57, and 25.08 μM, respectively. d-Antroquinonol also inhibited the migratory ability of MDA-MB-231 breast cancer cells in wound healing and Transwell assays. In addition, antroquinonol D inhibited DNMT1 activity, as assessed by the DNMT1 methyltransferase activity assay. As the cofactor SAM level increased, the inhibitory effects of d-antroquinonol on DNMT1 gradually decreased. An enzyme activity assay and molecular modeling revealed that antroquinonol D is bound to the catalytic domain of DNMT1 and competes for the same binding pocket in the DNMT1 enzyme as the cofactor SAM, but does not compete for the binding pocket in the DNMT3B enzyme. An Illumina Methylation 450 K array-based assay and real-time PCR assay revealed that antroquinonol D decreased the methylation status and reactivated the expression of multiple TSGs in MDA-MB-231 breast cancer cells. In conclusion, we showed that antroquinonol D induces DNA demethylation and the recovery of multiple tumor suppressor genes, while inhibiting breast cancer growth and migration potential.
Antibodies against the Majority Subunit (PilA) of the Type IV Pilus of Nontypeable Haemophilus influenzae Disperse Moraxella catarrhalis from a Dual-Species Biofilm (2018)

Otitis media (OM) is often polymicrobial, with nontypeable <i>Haemophilus influenzae</i> (NTHI) and <i>Moraxella catarrhalis</i> (Mcat) frequently cocultured from clinical specimens. Bacterial biofilms in the middle ear contribute to the chronicity and recurrence of OM; therefore, strategies to disrupt biofilms are needed. We have focused our vaccine development efforts on the majority subunit of NTHI type IV pili, PilA. Antibodies against a recombinant, soluble form of PilA (rsPilA) both disrupt and prevent the formation of NTHI biofilms <i>in vitro.</i> Moreover, immunization with rsPilA prevents and resolves NTHI-induced experimental OM. Here, we show that antibodies against rsPilA also prevent and disrupt polymicrobial biofilms. Dual-species biofilms formed by NTHI and Mcat at temperatures that mimic the human nasopharynx (34°C) or middle ear (37°C) were exposed to antiserum against either rsPilA or the OMP P5 adhesin of NTHI. NTHI+Mcat biofilm formation was significantly inhibited by antiserum directed against both adhesin proteins at either temperature. However, only anti-rsPilA disrupted NTHI+Mcat preestablished biofilms at either temperature and actively dispersed both NTHI and Mcat via interspecies quorum signaling. Newly released NTHI and Mcat were significantly more susceptible to killing by antibiotics. Taken together, these results revealed new opportunities for treatment of biofilm-associated diseases via a strategy that combines vaccine-induced antibody-mediated biofilm dispersal with traditional antibiotics, at a significantly reduced dosage to exploit the newly released, antibiotic-sensitive phenotype. Combined, our data strongly support the utility of rsPilA both as a preventative and as a therapeutic vaccine antigen for polymicrobial OM due to NTHI and Mcat.<b>IMPORTANCE</b> Middle ear infections (or otitis media [OM]) are highly prevalent among children worldwide and present a tremendous socioeconomic challenge for health care systems. More importantly, this disease diminishes the quality of life of young children. OM is often chronic and recurrent, due to the presence of highly antibiotic-resistant communities of bacteria (called biofilms) that persist within the middle ear space. To combat these recalcitrant infections, new and powerful biofilm-directed approaches are needed. Here, we describe the ability to disrupt a biofilm formed by the two most common bacteria that cause chronic and recurrent OM in children, via an approach that combines the power of vaccines with that of traditional antibiotics. An outcome of this strategy is that antibiotics can more easily kill the bacteria that our vaccine-induced antibodies have released from the biofilm. We believe that this approach holds great promise for both the prevention and treatment of OM.
Efficient dynamic dispatching with type slicing (2007)

A fundamental problem in the implementation of object-oriented languages is that of a frugal implementation of dynamic dispatching, that is, a small footprint data structure that supports quick response to runtime dispatching queries of the following format: which method should be executed in response to a certain message sent to a given object. Previous theoretical algorithms for this problem tend to be impractical due to their conceptual complexity and large hidden constants. In contrast, successful practical heuristics lack theoretical support. The contribution of this article is in a novel type slicing technique, which results in two dispatching schemes: TS and CT d . We make the case for these schemes both practically and theoretically. The empirical findings on a corpus of 35 hierarchies totaling some 64 thousand types from eight different languages, demonstrate improvement over previous results in terms of the space required for the representation, and the time required for computing it. The theoretical analysis is with respect to ι, the best possible compression factor of the dispatching matrix. The results are expressed as a function of a parameter κ, which can be thought of as a metric of the complexity of the topology of a multiple inheritance hierarchy. In single inheritance hierarchies κ = 1, but although κ can be in the order of the size of the hierarchy, it is typically a small constant in actual use of inheritance; in our corpus, the median value of κ is 5, while its average is 6.4. The TS scheme generalizes the famous interval containment technique to multiple inheritance. TS achieves a compression factor of ι/κ, that is, our generalization comes with an increase to the space requirement by a small factor of κ. The pay is in the dispatching time, which is no longer constant as in a naive matrix implementation, but logarithmic in the number of different method implementations. In practice, dispatching uses one indirect branch and, on average, only 2.5 binary branches. The CT schemes are a sequence of algorithms CT 1 , CT 2 , CT 3 , …, where CT d uses d memory dereferencing operations during dispatch, and achieves a compression factor of 1/ d ι 1−1/ d in a single inheritance setting. A generalization of these algorithms to a multiple inheritance setting, increases the space by a factor of (2κ) 1−1/ d . This trade-off represents the first bounds on the compression ratio of constant-time dispatching algorithms. We also present an incremental variant of the CT d suited for languages such as Java.
An Immunoglobulin Superfamily-Like Domain Unique to the <i>Yersinia pseudotuberculosis</i> Invasin Protein Is Required for Stimulation of Bacterial Uptake via Integrin Receptors (2000)

ABSTRACT The binding of the Yersinia pseudotuberculosis and Yersinia enterocolitica invasin proteins to β 1 integrin receptors allows internalization of these organisms by cultured cells. The C-terminal 192-residue superdomain of the Y. pseudotuberculosis invasin is necessary and sufficient for integrin recognition, while a region located outside, and N-terminal to, this superdomain strongly enhances the efficiency of bacterial uptake. Within the enhancer region is a domain called D2 that allows invasin-invasin interaction. To investigate the role of the enhancer region, bacterial cell binding and entry mediated by the Y. pseudotuberculosis invasin protein (invasin pstb ) was compared to that of Y. enterocolitica invasin (invasin ent ), which lacks the D2 self-association domain. Invasin ent was shown to be unable to promote self-interaction, using the DNA binding domain of λ repressor as a reporter. Furthermore, two genetically engineered in-frame deletion mutations that removed D2 from invasin pstb were significantly less proficient than wild-type invasin pstb at promoting uptake, although the amount of surface-exposed invasin as well as the cell binding capacity of the recombinant Escherichia coli strains remained similar. Competitive uptake assays showed that E. coli cells expressing invasin pstb had a significant advantage in the internalization process versus either E. coli cells expressing invasin ent or the invasin pstb derivatives deleted for D2, further demonstrating the importance of invasin self-interaction for the efficiency of invasin-mediated uptake.
Self-Organized Liquid Phase and Co-Crystallization of Rod-Like Polymers Hydrogen-Bonded to Amphiphilic Molecules (1999)

The application of self-organization to rod-like polymers to form ordered nanoscale structures is not straightforward because such polymers are often infusible and poorly soluble. A concept is introduced—involving the stoichiometric protonation of a π-conjugated electroactive rod-like polymer by a sulfonic acid to give a polymeric salt, which in turn is complexed with an alkylphenol to produce a self-organized nanoscale structure—that has many implications for new processing routes and controlled nanoscale structures of rigid rod-like polymers, in particular electroactive polymers.
Laser annealing of doped semiconductors for ultra-shallow junctions: Systems for thermal processes in the ms range (2005)

For future 65 nm and smaller nodes, thermal anneal processes in the ms range or shorter are required. Using laboratory laser systems, encouraging results have been achieved, which demonstrate the feasibility of the process.
Resolvin D1 prevents smoking-induced emphysema and promotes lung tissue regeneration (2016)

RvD1 attenuated smoking-induced emphysema in vivo by reducing inflammation and promoting tissue regeneration. This result suggests that RvD1 may be useful in the prevention and treatment of emphysema.
Continued Production of Drug-Sensitive Human Immunodeficiency Virus Type 1 in Children on Combination Antiretroviral Therapy Who Have Undetectable Viral Loads (2003)

Highly active antiretroviral therapy (HAART) can suppress plasma human immunodeficiency virus type 1 (HIV-1) levels to below the detection limit of ultrasensitive clinical assays. However, HIV-1 persists in cellular reservoirs, and in adults, persistent low-level viremia is detected with more sensitive assays. The nature of this viremia is poorly understood, and it is unclear whether viremia persists in children on HAART, particularly those who start therapy shortly after birth. We therefore developed a reverse transcriptase PCR (RT-PCR) assay that allows genotyping of HIV-1 protease even when viremia is present at levels as low as 5 copies of HIV-1 RNA/ml. We demonstrated that viremia persists in children with plasma virus levels below the limit of detection of clinical assays. Viremia was detected even in children who began HAART in early infancy and maintained such strong suppression of viremia that HIV-1-specific antibody responses were absent or minimal. The low-level plasma virus lacked protease inhibitor resistance mutations despite the frequent use of nelfinavir, which has a low mutational barrier to resistance. Protease sequences resembled those of viruses in the latent reservoir in resting CD4(+) T cells. Thus, in most children on HAART with clinically undetectable viremia, there is continued virus production without evolution of resistance in the protease gene.
An intelligent RFID system (2011)

RFID tags are miniscule microchips, which continue to get smaller and cheaper every day. This paper introduces IPURSE, an intelligent system built on a mobile platform which keeps track of items a user carries in their purse/handbag and also alerts the user when any item is missing from the purse/handbag. IPURSE is a unique project that brings the RFID and NFC technologies together into a single system by 'cleverly' monitoring, reminding and alerting users about their missing items based on the current weather, reminder messages and daily items usually carried by the user. We discuss the methods, equipments and technologies used to successfully implement such an application. It includes the design evolution and technical design of the system, followed by a working prototype and experimentation. The pros and cons of the application are also discussed towards the end of this paper.
Towards Automatic Support for Augmenting Concept Maps with Documents (2006)

Abstract. Concept mapping has been used extensively in educational settings as a learning and teaching tool and, more recently, as a knowledge elicitation tool to capture expert knowledge for preservation purposes. In these contexts, electronic concept maps annotated with supplementary multi-media resources can provide a rich source of information. Unfortunately, it can be challenging for users to identify the right resources to attach, especially when dealing with large resource collections. This paper presents ongoing research on methods for easing the annotation task by automatically searching a document library for relevant documents and suggesting them as potential associations for concepts in a map. The paper begins by discussing how concept map structure can be exploited to automatically generate queries to a database of indexed documents, to search for documents to link to the concepts in a map. It then presents methods for indexing documents to improve the search results. The methods for generating queries and indexing documents have been evaluated using two pre-existing expert knowledge models, with encouraging results. 1
A robot arm/hand teleoperation system with telepresence and shared control (2006)

This paper describes a master-slave teleoperation system which is developed to evaluate the effectiveness of teleopresence in telerobotics applications. The operator wears a dataglove augmented with an arm-grounded force feedback device to control the dexterous hand and utilizes a spaceball to control robot arm. Contact forces measured by the finger sensors can be feedback to the operator and visual telepresence systems collect the remote operation scenes and display to the operator by a stereo helmet. A primitive autonomous grasp system based on parallel joint torque/position control is developed. The experimental results show that this teleoperation system is intuitive and productive and the primitive autonomous grasp is feasible and efficient
ROUND TRIP DELAY TIME AS A LINEAR FUNCTION OF DISTANCE BETWEEN THE SENSOR NODES IN WIRELESS SENSOR NETWORK (2012)

In a dense wireless sensor networks with portable sensor nodes identification of sensor node location, distance of particular sensor node from some reference node and fault detection are the great challenging issues. Round trip delay (RTD) time measurement technique is an easy way to obtain the information regarding above issues in WSN. But round trip delay measurement is affected by various parameters of wireless sensor network. As the sensor nodes are placed randomly in network, sensor node distance has more impact on this time measurement. So it is necessary to study the relationship between the round trip delay time and Sensor node distance. To prove this relationship the other parameters affecting round trip delay time like speed, data transfer rate, number of sensor nodes in RTD path and other request handled by intermediate nodes are either made constant or disabled. A wireless sensor node hardware designed for this purpose consists of microcontroller (ATMEGA 16L) and ZigBee (XBEE S2) wireless communication module. For configuring the ZigBee module of each sensor nodes in round trip delay path X-CTU software is used. After configuring the all sensor nodes the entire network is simulated in real time by using Dock light V1.9 software. The graph plotted between round trip delay time and sensor node distance proves a linear relationship between it.
All‐trans retinoic acid attenuates ultraviolet radiation‐induced down‐regulation of aquaporin‐3 and water permeability in human keratinocytes (2007)

One of the major characteristics of human skin photoaging induced by ultraviolet (UV) radiation is the dehydration of the skin. Water movement across plasma membrane occurs via diffusion through lipid bilayer and via aquaporins (AQPs). We find that UV induces aquaporin-3 (AQP3) down-regulation in human skin keratinocytes. MEK/ERK inhibitors PD98059 and U0126 inhibit UV-induced down-regulation of AQP3. Antioxidant N-acetyl-L-cysteine or NAC blocks UV-induced MEK/ERK activation and down-regulation of AQP3. All-trans retinoic acid or atRA, while alone inducing AQP3 expression, attenuates UV-induced down-regulation of AQP3 and water permeability. Using special inhibitors, we find that activation of EGFR and inhibition on ERK activation are involved in atRA's protective effects against UV-induced AQP3 down-regulation. Using specific AQP3's water transport inhibitors and siRNA knockdown, we observe that AQP3 is involved in cell migration and in vitro wound healing. UV-induced AQP3 down-regulation results in reduced water permeability, decreased cell migration, and delayed wound healing, which are attenuated by atRA pretreatment. We conclude that atRA protects against UV-induced down-regulation AQP3 and decrease in water permeability, reduction in cell migration and delayed in vitro wound healing via trans-activation of EGFR and inhibition on ROS-mediated MEK/ERK pathway. This novel finding provides evidence to support possible involvement of AQP3 in UV induced skin dehydration.
Laboratory Astrophysics Needs of the Herschel Space Observatory (2002)

Most antipsychotic medications produce motoric side effects, including parkinsonism and tardive dyskinesia (TD). Correlates of these behaviors in rats (catalepsy and vacuous chewing movements, respectively) were used as a model to assess the usefulness of chronic naloxone administration in symptom reduction. Previous studies have suggested that increased neurotransmission in the endogenous opioid system modulates neuroleptic-induced motoric side effects. Rats were treated with haloperidol decanoate or vehicle for 27 weeks, and withdrawn for 30 weeks. Subsequently, naloxone (0.5 to 2.0 mg/kg SC twice daily) was given for 5 weeks. Long-term haloperidol treatment produced a syndrome of vacuous chewing movements (VCMs) that persisted during the drug withdrawal period. Catalepsy developed rapidly and also persisted. Naloxone treatment had little effect on VCMs but increased catalepsy scores in both haloperidol and vehicle treated groups. Naloxone reduced rearing and grooming in haloperidol rats while increasing these measures in vehicle treated rats. The results indicate that neuroleptic-induced motoric side effects are not reversed by naloxone in rats. Furthermore, they suggest that increased opioid neurotransmission may not underlie the expression of VCMs. This does not rule out the possibility that endogenous opioid system may be involved in the development of VCMs. To the extent that this animal model is valid, naloxone may not be effective in treating TD and neuroleptic-induced parkinsonism in humans.
Directional Light Extinction and Emission in a Metasurface of Tilted Plasmonic Nanopillars (2015)

Plasmonic optical antennas and metamaterials with an ability to boost light-matter interactions for particular incidence or emission angles could find widespread use in solar harvesting, biophotonics, and in improving photon source performance at optical frequencies. However, directional plasmonic structures have generally large footprints or require complicated geometries and costly nanofabrication technologies. Here, we present a directional metasurface realized by breaking the out-of-plane symmetry of its individual elements: tilted subwavelength plasmonic gold nanopillars. Directionality is caused by the complex charge oscillation induced in each individual nanopillar, which essentially acts as a tilted dipole above a dielectric interface. The metasurface is homogeneous over a macroscopic area and it is fabricated by a combination of facile colloidal lithography and off-normal metal deposition. Fluorescence excitation and emission from dye molecules deposited on the metasurface is enhanced in specific directions determined by the tilt angle of the nanopillars. We envisage that these directional metasurfaces can be used as cost-effective substrates for surface-enhanced spectroscopies and a variety of nanophotonic applications.
DCSE, an interactive tool for sequence alignment and secondary structure research (1993)

DCSE provides a user-friendly package for the creation and editing of sequence alignments. The program runs on different platforms, including microcomputers and workstations. Apart from available hardware, the program is not limited in the size of the alignment it can handle. It deviates more from classical text editors than other available sequence editors because it uses a different approach towards editing. It shifts characters or entire blocks of aligned characters, rather than inserting or deleting gaps in the sequences. Alignment of a new sequence to an existing alignment is partly automated. Although DCSE can be used on protein sequence alignments, it is especially targeted at the examination of RNA. The secondary structure for every sequence can be incorporated easily in the alignment. DCSE also has extensive built-in support for finding and checking secondary structure elements. A sophisticated system of markers allows notation of special positions in an alignment. This system can be used to store information such as the position of hidden breaks, introns and tertiary structure interactions.