gebhart/patrepeval huggingface dataset:
Enhancement of plasmid DNA immunogenicity with linear polyethylenimine (2012)

The utility of plasmid DNA as an immunogen has been limited by its weak immunogenicity. In the present study, we evaluated the ability of a family of linear polyethylenimine (PEI) polymers, complexed to plasmid DNA, to augment DNA expression in vivo and to enhance antigen-specific adaptive immune responses. We showed that four of five structurally different PEIs that we evaluated increased in vivo DNA expression 20- to 400-fold, and enhanced DNA-induced epitope-specific CD8⁺ T-cell responses 10- to 25-fold in BALB/c and C57BL/6J mice respectively, when delivered intravenously. Functional studies of the PEI-DNA-induced CD8⁺ T-cell responses demonstrated that formulation of DNA with PEI was associated with increased numbers of cells secreting type I cytokines. In addition, PEI-DNA complexes improved antigen-specific T(H) 1-helper cell and humoral responses. Most importantly, the PEI-DNA complexes elicited memory cellular responses, capable of rapid expansion and accelerated clearance of a lethal dose of recombinant Listeria monocytogenes. Lastly, we identified physical properties of PEI-DNA complexes that are associated with enhanced DNA-elicited immunogenicity. These findings demonstrate that PEI polymers can play an important role in the development of DNA-based vaccines in the setting of infectious disease prevention and cancer therapy.
Modeling and percept of transcorneal electrical stimulation in humans (2010)

Retinal activation via transcorneal electrical stimulation (TcES) in normal humans was investigated by comparing subject perception, model predictions, and brain activation patterns. The preferential location of retinal stimulation was predicted from 3-D admittance modeling. Visual cortex activation was measured using positron emission tomography (PET) and (18)F-fluorodeoxyglucose (FDG). Two different corneal electrodes were investigated: DTL-Plus and ERG-Jet. Modeling results predicted preferential stimulation of the peripheral, inferior, nasal retina during right eye TcES using DTL-Plus, but more extensive activation of peripheral, nasal hemiretina using ERG-Jet. The results from human FDG PET study using both corneal electrodes showed areas of visual cortex activation that consistently corresponded with the reported phosphene percept and modeling predictions. ERG-Jet was able to generate brighter phosphene percept than DTL-Plus and elicited retinotopically mapped primary visual cortex activation. This study demonstrates that admittance modeling and PET imaging consistently predict the perceived location of electrically elicited phosphenes produced during TcES.
The role of electron diffraction in zeolite structure determination (2006)

Because electron diffraction can sample individual microcrystals, it is clear that this single crystal method can facilitate, in at least two ways, structure determination for inorganic materials, such as zeolites, that are preferentially microcrystalline. First, in a qualitative application, three-dimensional tilts of individual small crystals, to map the reciprocal lattice, greatly facilitates unit cell and space group determination when powder diffraction indexing programs fail. If incoherent multiple scattering leads to violation of systematic absences, these absences can be restored by collection of precession diffraction patterns based on the Vincent-Midgley method [1], as demonstrated recently [2]. The second, quantitative application, i. e. ab initio structure determination from electron diffraction intensity data, also seems to be feasible. In the auspicious case of thin layered zeolite crystals in the MWW framework, the three-dimensional structure was determined by direct methods based on maximum entropy and likelihood [3], the only difficulty arising from the ’missing cone’ of structural information imposed by the goniometric tilt limit. Possible methods for restoration of the missing information, although approximately provided by phase and amplitude prediction (Sayre equation), include alternate crystallization of the desired crystal projection by appropriate structure directing agents, or, simply, by sectioning the desired view of the structure in available samples. Multiple scattering perturbations include both n-beam dynamical and secondary scattering; collection of precession data greatly reduces the latter influence [2], facilitating ab initio analyses via direct methods (e. g. tests on LTA, ITQ-1, ITQ-7, ZSM-10, MOR, MCM-68), while systematic dynamical diffraction is still observed (even at 300 kV). Improved collection of intensity data via imaging plates, exploiting a much greater linear response to intensity, is also recommended. One other, largely unexplored, possibility is to collect zero loss electron diffraction intensities in electron microscopes with in-line ’omega’ energy filters. Generally, for unknown zeolite structures, electron diffraction analyses have been carried out in parallel with the usual powder determinations, not only to provide needed symmetry information but also to detect structural details of important zones, e. g. the location of porous channels to guide the powder determination; in some cases, the crystal structure would not have been solved without this electron crystallographic information. Whether or not true ab initio electron crystallography can ever exist as an independent structural tool for zeolites remains a question to be answered by ongoing research.
Conversation as Action Under Uncertainty (2013)

Conversations abound with uncertainties of various kinds. Treating conversation as inference and decision making under uncertainty, we propose a task independent, multimodal architecture for supporting robust continuous spoken dialog called Quartet. We introduce four interdependent levels of analysis, and describe representations, inference procedures, and decision strategies for managing uncertainties within and between the levels. We highlight the approach by reviewing interactions between a user and two spoken dialog systems developed using the Quartet architecture: Presenter, a prototype system for navigating Microsoft PowerPoint presentations, and the Bayesian Receptionist, a prototype system for dealing with tasks typically handled by front desk receptionists at the Microsoft corporate campus. 1
A Dynactin Subunit with a Highly Conserved Cysteine-rich Motif Interacts Directly with Arp1 (2000)

Dynactin is a multisubunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. Using a dynein affinity column, the previously uncharacterized p62 subunit of dynactin was isolated and microsequenced. Two peptide sequences were used to clone human cDNAs encoding p62. Sequence analysis of the predicted human polypeptide of 53 kDa revealed a highly conserved pattern of eleven cysteine residues, eight of which fit the consensus sequence for a Zn(2+)-binding RING domain. We have characterized p62 as an integral component of 20 S dynactin by biochemical and immunocytochemical methods. Affinity chromatography experiments demonstrate that p62 binds directly to the Arp1 subunit of dynactin. Immunocytochemistry with antibodies to p62 demonstrates that this polypeptide has a punctate cytoplasmic distribution as well as centrosomal distribution typical of dynactin. In transfected cells, overexpression of p62 did not disrupt microtubule organization or the integrity of the Golgi but did cause both cytosolic and nuclear distribution of the protein, suggesting that this polypeptide may be targeted to the nucleus at very high expression levels.
Image Selection in Photo Albums (2018)

The selection of the best photos in personal albums is a task that is often faced by photographers. This task can become laborious when the photo collection is large and it contains multiple similar photos. Recent advances on image aesthetics and photo importance evaluation has led to the creation of different metrics for automatically assessing a given image. However, these metrics are intended for the independent assessment of an image, without considering the possible context implicitly present within photo albums. In this work, we perform a user study for assessing how users select photos when provided with a complete photo album---a task that better reflects how users may review their personal photos and collections. Using the data provided by our study, we evaluate how existing state-of-the-art photo assessment methods perform relative to user selection, focusing in particular on deep learning based approaches. Finally, we explore a recent framework for adapting independent image scores to collections and evaluate in which scenarios such an adaptation can prove beneficial.
A contemporary review of clade-specific virological differences in monkeypox viruses (2023)

Although zoonosis has been historically linked to emergence events in humans, epidemiological analyses of more recent outbreaks have identified increasing frequencies of human-to-human transmission. Furthermore, viral transmission during the 2022 global human mpox outbreak, caused by a recently identified MPXV subclade, has relied exclusively on human-to-human contact with no known zoonotic link.
Study of Poly-SiGe Structural Properties for Modularly Integrated MEMS (2006)

Approaches to improve the strain gradient of low-temperature- deposited LPCVD poly-SiGe for MEMS inertial sensor applications are investigated. Correlation between the strain gradient and film microstructure is found, and the effects of film deposition conditions on film microstructure are studied. Boron-doped poly-SiGe films generally have vertically oriented grains, either conical or columnar in shape. Films with small strain gradient usually have columnar grain structure with low defect density. The best strain gradient achieved is 1.1×10-6 µm-1 for a 3.5 µm thick film deposited at 410ºC, with a worst- case variation across a 150 mm-diameter wafer of 1.6×10-5 µm- 1. The uniformity of films deposited in a batch LPCVD reactor can be improved by increasing the deposited film thickness, using a proper seeding layer, and/or depositing the film in muliple layers. Post-deposition annealing and argon implantation can be used to tune the strain gradient so that lower strain gradient can be achieved with proper deposition and annealing/implantation combinations.
Symbolic Analysis of Concurrent Programs with Polymorphism (2010)

The current trend of multi-core and multi-processor computing is causing a paradigm shift from inherently sequential to highly concurrent and parallel applications. Certain thread interleavings, data input values, or combinations of both often cause errors in the system. Systematic verification techniques such as explicit state model checking and symbolic execution are extensively used to detect errors in such systems [7, 9]. Explicit state model checking enumerates possible thread schedules and input data values of a program in order to check for errors [3, 9]. To partially mitigate the state space explosion from data input values, symbolic execution techniques substitute data input values with symbolic values [5, 7, 6]. Explicit state model checking and symbolic execution techniques used in conjunction with exhaustive search techniques such as depth-first search are unable to detect errors in medium to large-sized concurrent programs because the number of behaviors caused by data and thread non-determinism is extremely large. We present an overview of abstraction-guided symbolic execution for concurrent programs that detects errors manifested by a combination of thread schedules and data values [8]. The technique generates a set of key program locations relevant in testing the reachability of the target locations. The symbolic execution is then guided along these locations in an attempt to generate a feasible execution path to the error state. This allows the execution to focus in parts of the behavior space more likely to contain an error.
Genome Sequence of the Swine Pathogen Streptococcus suis Serotype 2 Strain S735 (2012)

Streptococcus suis is a major swine pathogen responsible for significant, worldwide economic losses in the swine industry, in addition to being an emerging zoonotic agent. Strains of serotype 2 are the most commonly associated with infections causing meningitis, endocarditis, and septicemia. Here we present the genome sequence of S. suis serotype 2 strain S735.
MicroRNA Profiles Discriminate among Colon Cancer Metastasis (2014)

MicroRNAs are being exploited for diagnosis, prognosis and monitoring of cancer and other diseases. Their high tissue specificity and critical role in oncogenesis provide new biomarkers for the diagnosis and classification of cancer as well as predicting patients' outcomes. MicroRNAs signatures have been identified for many human tumors, including colorectal cancer (CRC). In most cases, metastatic disease is difficult to predict and to prevent with adequate therapies. The aim of our study was to identify a microRNA signature for metastatic CRC that could predict and differentiate metastatic target organ localization. Normal and cancer tissues of three different groups of CRC patients were analyzed. RNA microarray and TaqMan Array analysis were performed on 66 Italian patients with or without lymph nodes and/or liver recurrences. Data obtained with the two assays were analyzed separately and then intersected to identify a primary CRC metastatic signature. Five differentially expressed microRNAs (hsa-miR-21, -103, -93, -31 and -566) were validated by qRT-PCR on a second group of 16 American metastatic patients. In situ hybridization was performed on the 16 American patients as well as on three distinct commercial tissues microarray (TMA) containing normal adjacent colon, the primary adenocarcinoma, normal and metastatic lymph nodes and liver. Hsa-miRNA-21, -93, and -103 upregulation together with hsa-miR-566 downregulation defined the CRC metastatic signature, while in situ hybridization data identified a lymphonodal invasion profile. We provided the first microRNAs signature that could discriminate between colorectal recurrences to lymph nodes and liver and between colorectal liver metastasis and primary hepatic tumor.
An Active Magnetic Damper Concept for Stabilization of Gas Bearings in High-Speed Permanent-Magnet Machines (2013)

The successful application of ultrahigh-speed electrical-drive systems in industrial products is currently limited by lacking high-speed bearing technologies permitting high reliability and long lifetime. Promising bearing technologies for high rotational speeds are contactless bearing concepts such as active magnetic bearings or gas bearings. While magnetic bearings usually are major electromechanical systems with substantial complexity, gas bearings allow compact realizations with high load capacity and stiffness; however, poor dynamic stability has been limiting their use at high rotational speeds. Following a hybrid bearing approach with an aerodynamic gas bearing for load support, a small-sized active magnetic damper concept is proposed to enable the stable high-speed operation of the gas bearing with a minimum of additional complexity and costs. As for the effective stabilization of the gas bearing, a high-quality displacement measurement is essential, and a new eddy-current-based rotor-displacement self-sensing concept employing an auxiliary signal injection and rotor displacement measurement circuit is presented. A hardware implementation of the proposed concept is shown providing high-resolution measurement signals.
Surface expression of squamous cell carcinoma antigen (SCCA) can be increased by the preS1(21–47) sequence of hepatitis B virus (2004)

A variant of the serpin squamous cell carcinoma antigen (SCCA) has been identified as a hepatitis B virus binding protein and high expression of SCCA has recently been found in hepatocarcinoma. Since HBV is involved in liver carcinogenesis, experiments were carried out to examine the effect of HBV preS1 envelope protein on SCCA expression. Surface and intracellular staining for SCCA was assessed by FACS analysis. Preincubation of HepG2 cells and primary human hepatocytes with preS1 protein or with preS1(21-47) tetrameric peptide significantly increased the surface expression of SCCA, without modification of its overall cellular burden, suggesting a surface redistribution of the serpin. An increase in HBV binding and internalization was observed after pre-incubation of the cells with preS1 preparations, compared to cells preincubated with medium alone. Pretreatment of cells with DMSO, while not influencing SCCA basal expression, was responsible for an increase in the efficiency of HBV internalization and this effect was additive to that obtained after incubation with preS1 preparations. In conclusion, the HBV preS1(21-47) sequence is able to induce overexpression of SCCA at the cell surface facilitating virus internalization, while the increased efficiency of HBV entry following DMSO addition is not mediated by SCCA.
Incentivizing Platform–User Interactions for Crowdsensing (2020)

For effective crowdsensing, it is essential to incentivize the interactions of participants and platforms. Existing approaches do not tailor users’ bidding to their preferences, i.e., personalized bidding (PB). To meet this need, we design an incentive mechanism, called Picasso, that achieves not only the expressiveness and description efficiency of PB for users, but also minimal social cost, computational efficiency, and strategy proof for platform owners. This design is, however, challenging due to the intrinsic conflicting goals of the platform owner and users. To handle these conflicts, Picasso represents bids in a novel 3-D expression space by orchestrating three logical operations to balance among expressiveness, computational complexity, and description efficiency. Moreover, we equivalently decompose and recombine the complex task dependencies of bids originated from the expressiveness of PB, thus achieving a constant-factor approximation of optimal task allocation with strategy proof in polynomial time. These properties of Picasso are proven theoretically. In addition to a detailed simulation study, our trace-driven evaluations show that, compared to existing approaches, Picasso can enable each user to bid <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$9.7\times $ </tex-math></inline-formula> more tasks, on average, and decrease the description length by 74%, thus encouraging more users’ participation. Picasso also reduces the platform owner’s payment by more than 61%, hence yielding a win–win solution for incentivizing platform–user interactions.
Role of kerogen in the origin and evolution of nickel and vanadyl geoporphyrins (1987)

The role of petroleum source rock kerogen in the origin and evolution of the geoporphyrins was investigated by measuring the Ni and V content of four oil shale kerogens and comparing the Ni(II) and VO(II) porphyrins in the bitumen of two oil shales with the Ni(II) and VO(II) porphyrins generated from the associated kerogens during simulated catagenesis. A method for determining the organically-bound Ni and V content of kerogen by instrumental neutron activation analysis (INAA) was used to measure the Ni and V content of four oil shale kerogens Green River (Colorado); New Albany (Clark County, IN); Sunbury (Powell County, KY); Woodford (Carter County, OK). Sequential pyrolysis at temperatures ranging from 100-450/sup 0/C generated organically-bound Ni and V complexes from the New Albany and Woodford kerogens (determined by INAA), including Ni(II) and VO(II) porphyrins (determined by uv-visible spectrometry and high performance liquid chromatography). Nickel and vanadyl porphyrins are associated with the kerogen in a similar manner providing direct evidence that kerogen is involved in the geochemical evolution of both metalloporphyrins. The Ni(II) and VO(II) porphyrins in New Albany shale bitumen-I and kerogen pyrolysates were investigated using liquid chromatography, thin-layer chromatography, and electron impact-mass spectrometry. Alternate porphyrin series are generated formmore » the kerogen, but the mineral matrix may also be involved in their formation and association in source rocks.« less
Coherent Multiscale Image Processing Using Dual-Tree Quaternion Wavelets (2008)

The dual-tree quaternion wavelet transform (QWT) is a new multiscale analysis tool for geometric image features. The QWT is a near shift-invariant tight frame representation whose coefficients sport a magnitude and three phases: two phases encode local image shifts while the third contains image texture information. The QWT is based on an alternative theory for the 2-D Hilbert transform and can be computed using a dual-tree filter bank with linear computational complexity. To demonstrate the properties of the QWT's coherent magnitude/phase representation, we develop an efficient and accurate procedure for estimating the local geometrical structure of an image. We also develop a new multiscale algorithm for estimating the disparity between a pair of images that is promising for image registration and flow estimation applications. The algorithm features multiscale phase unwrapping, linear complexity, and sub-pixel estimation accuracy.
Data for: Texture diversity in melon (Cucumis melo L.): Sensory and physical assessments (2019)

Raw data on melon quality