gebhart/patrepeval huggingface dataset:
Functional Characterization of the Candidate Tumor Suppressor Gene <b> <i>NPRL2</i> </b>/<b> <i>G21</i> </b> Located in 3p21.3C (2004)

Initial analysis identified the NPRL2/G21 gene located in 3p21.3C, the lung cancer region, as a strong candidate tumor suppressor gene. Here we provide additional evidence of the tumor suppressor function of NPRL2/G21. The gene has highly conserved homologs/orthologs ranging from yeast to humans. The yeast ortholog, NPR2, shows three highly conserved regions with 32 to 36% identity over the whole length. By sequence analysis, the main product of NPRL2/G21 encodes a soluble protein that has a bipartite nuclear localization signal, a protein-binding domain, similarity to the MutS core domain, and a newly identified nitrogen permease regulator 2 domain with unknown function. The gene is highly expressed in many tissues. We report inactivating mutations in a variety of tumors and cancer cell lines, growth suppression of tumor cells with tet-controlled NPRL2/G21 transgenes on plastic Petri dishes, and suppression of tumor formation in SCID mice. Screening of 7 renal, 5 lung, and 7 cervical carcinoma cell lines showed homozygous deletions in the 3' end of NPRL2 in 2 renal, 3 lung, and 1 cervical (HeLa) cell line. Deletions in the 3' part of NPRL2 could result in improper splicing, leading to the loss of the 1.8 kb functional NPRL2 mRNA. We speculate that the NPRL2/G21 nuclear protein may be involved in mismatch repair, cell cycle checkpoint signaling, and activation of apoptotic pathway(s). The yeast NPR2 was shown to be a target of cisplatin, suggesting that the human NPRL2/G21 may play a similar role. At least two homozygous deletions of NPRL2/G21 were detected in 6 tumor biopsies from various locations and with microsatellite instability. This study, together with previously obtained results, indicates that NPRL2 is a multiple tumor suppressor gene.
Activation of a cryptic crystal protein gene of <i>Bacillus thuringiensis</i> subspecies <i>kurstaki</i> by gene fusion and determination of the crystal protein insecticidal specificity (1990)

DNA hybridization with the insecticidal crystal protein gene cryllA (formerly cryBl) of Bacillus thuringiensis supspecies kurstaki has shown that subspecies kurstaki contains a cryllA-related sequence in addition to the cryllA gene (Donovan et al., 1988a). We have cloned the cryllA-related sequence and have determined that the sequence, which has been designated cryllB, is 89% identical to the cryllA gene. Recombinant B. thuringiensis cells harbouring the cloned cryllB gene produced very little CryllB protein. A high level of production of the CryllB protein was achieved by fusing the regulatory region of the crylllA crystal protein gene to the cryllB gene. The CryllB protein was found to be highly toxic to Lymantria dispar, Heliothis virescens and Trichoplusia ni, and was not toxic to Aedes aegypti.
Web Service Discovery Using General-Purpose Search Engines (2007)

WSDL provides the potential for Web services to enrich consumers' lives. However, it has had only limited success in enterprise environments and even less in the mass market. Apart from the difficulties and high costs involved in current approaches, another reason is the low precision for Web Services discovery using the most widely known tool: search engines. Seeking for effective ways to change the situation, we conducted an experiment to examine better approaches of using general-purpose search engines to discover Web Services. We used nine different approaches for publishing Web Services and two groups of total 18 queries for retrieving them using Yahoo and Google search engines. The queries were fired to each search engine daily over a week and the top 100 search results returned from every search are collected and analyzed. The results show that for both search engines, embedding a WSDL specification in a Web page that provides semantic description of the service yield the best results.
Dysiherbaine:  A New Neurotoxic Amino Acid from the Micronesian Marine Sponge <i>Dysidea</i> <i>herbacea</i> (1997)

A new amino acid, dysiherbaine (1), was isolated from a Micronesian sponge Dysidea herbacea. The structure was determined by using FABMS, ESIMS, FABMS/CID/MS, and one- and two-dimensional NMR experiments of 1 and its dimethyl derivative 3 to be a novel diamino dicarboxylic acid, which consisted of a cis-fused hexahydrofuro[3,2-b]pyran ring substituted with a 3-[2-aminopropanoic acid] side chain. The relative configuration of the bicyclic portion of 1 was determined by 3JH,H analysis and difference NOE experiments, and that of the acyclic side chain was assigned by additional 2,3JC,H analysis, measured by hetero half-filtered TOCSY (HETLOC) and phase sensitive HMBC experiments. Systemic administration of 1 induced neurotoxic symptoms in mice which were reminiscent of neuroexcitatory amino acids such as domoic acid. Dysiherbaine inhibited bindings of [3H]-kainic acid (KA) and [3H]-1-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), but not [3H]CGS-19755, an N-methyl-d-asparatic acid (NMDA) receptor antagonist, on rat brain synaptic membranes, suggesting that 1 is a selective agonist of non-NMDA type glutamate receptors in the central nervous system.
Immediate and Ongoing Detection of Prions in the Blood of Hamsters and Deer following Oral, Nasal, or Blood Inoculations (2015)

Infectious prions traverse epithelial barriers to gain access to the circulatory system, yet the temporal parameters of transepithelial transport and persistence in the blood over time remain unknown. We used whole-blood real-time quaking-induced conversion (wbRT-QuIC) to analyze whole blood collected from transmissible spongiform encephalopathy (TSE)-inoculated deer and hamsters throughout the incubation period for the presence of common prion protein-conversion competent amyloid (PrPCCCA). We observed PrPC-CCA in the blood of TSE-inoculated hosts throughout the disease course from minutes postexposure to terminal disease.
Extrapolation and Correlation (EXTRACT): A New Method for Motion Compensation in MRI (2009)

A postprocessing technique is proposed for the correction of both translational and rotational motion artifacts in magnetic resonance imaging (MRI). The method consists of two steps: 1) k-space extrapolation to generate a motion-free reference, followed by 2) correlation with actual data to estimate motion. In this paper, two different extrapolation methods were investigated for the purpose of motion estimation: edge enhancement and finite-support solution. It was found that finite-support solution performs better near the k-space center, while the edge enhancement method is superior in the outer k-space regions. Therefore, a combination of the two methods was employed to generate a motion-free reference, whose correlations with the acquired data can subsequently determine the object motion. Motion compensation was demonstrated in simulation and in vivo MR experiments. The technique is shown to be robust against noise and various types of motion.
HeapMD (2006)

We present the design, implementation, and evaluation of HeapMD, a dynamic analysis tool that finds heap-based bugs using anomaly detection. HeapMD is based upon the observation that, in spite of the evolving nature of the heap, several of its properties remain stable. HeapMD uses this observation in a novel way: periodically, during the execution of the program, it computes a suite of metrics which are sensitive to the state of the heap. These metrics track heap behavior, and the stability of the heap reflects quantitatively in the values of these metrics. The "normal" ranges of stable metrics, obtained by running a program on multiple inputs, are then treated as indicators of correct behaviour, and are used in conjunction with an anomaly detector to find heap-based bugs. Using HeapMD, we were able to find 40 heap-based bugs, 31 of them previously unknown, in 5 large, commercial applications.
Cryo-Assisted Extrusion 3D Printing of Shape Memory Polymer-Graphene Composites (2022)

Abstract A cryo-system assisted extrusion 3D printing technique has been developed to fabricate Shape Memory Polymer Epoxy (SMPE) thermoset into a near-net shape. With a unique cryogenic sprayer assisted printing system, it is possible to 3D print &amp;amp;amp;amp;quot;pure&amp;amp;amp;amp;quot; thermoset polymer, otherwise which was limited to thermoplastic or highly functionalized co-polymeric thermoset systems. The temperature was maintained below 10oC during 3D printing, which enabled dimensionally accurate structures. Graphene Nanoplatelet (GNP) reinforced SMPE ink was synthesized to be compatible with cryo-assisted extrusion 3D printing of shape memory composites. The addition of a mere 0.1 wt.% GNP exhibited 15% faster shape recovery due to improved thermal conductivity. Also, GNP addition imparted a 30% improvement in the ultimate tensile strength and a 17% increase in 3D printed composites&amp;amp;amp;#39; elastic modulus. Dynamic mechanical testing showed that the addition of 0.1 wt.% GNP in SMPE increased the composite&amp;amp;amp;#39;s storage modulus by 365% and loss tangent by 66% compared to pure 3D printed SMPE, indicating enhanced damping characteristics. This study is the first to demonstrate a non-existent 3D printing technology for &#x93;pure thermoset&#x94; polymers with and without conductive graphene, that has the potential to develop an energy-efficient actuation system, passive thermal sensors, and self-deployable communication system structures.
Osteoclast Activated FoxP3+ CD8+ T-Cells Suppress Bone Resorption in vitro (2012)

We have determined that osteoclast-induced Tc(REG) can suppress osteoclast activity, forming a negative feedback system. As the CD8 T-cells are activated in the absence of inflammatory signals, these observations suggest that this regulatory loop may play a role in regulating skeletal homeostasis. Our results provide the first documentation of suppression of osteoclast activity by CD8 regulatory T-cells and thus, extend the purview of osteoimmunology.
Development of Monoclonal Antibodies and Immunoassays for Sensitive and Specific Detection of Shiga Toxin Stx2f (2013)

Novel mAbs specific to Stx2f were developed for the first time, providing new assets for the STEC community. Immunoassays with improved sensitivity and specificity will be useful for the detection of Stx2f present in food, environmental, and clinical samples.
Nonuniform quantization for compression of encrypted digital holograms (2005)

Compression and encryption/decryption are necessary for secure and effcient storage and transmission of image data. We present an optical encryption technique that takes advantage of both the massive parallelism inherent in optical systems and the flexibility offered by digital electronics. The encryption is performed using a phase mask and Fresnel propagation. We nonuniformly quantize the complex-valued encrypted hologram pixels using an artificial neural network. The in-line digital holograms of three-dimensional objects were created using phase-shift interferometry. With our lossy data compression technique we achieved good quality decryption and reconstruction from objects with a compression ratio of 32.
Tubing Buckling—The State of the Art (2006)

Abstract Almost unique in engineering analysis is the problem of tubing buckling in wellbores. In general, structures loaded above their critical load fail catastrophically. Yet, both tubing and drillstrings are commonly operated above the critical load. These tubing strings do not fail because the wellbore provides the necessary support for "post-buckling" equilibrium. The two fundamental questions about tubing buckling are: What is the critical load? What is the post-buckled configuration? The critical load tells us if the tubing will buckle. Euler solved the problem for "short" columns, but these results rarely have application in a wellbore, because the pipes are usually very long1. The first stability criterion which considered the stabilizing effect of weight on long pipes in inclined wellbores was developed by Paslay and Dawson2. The post-buckled configuration tells us about tubing movement, bending stresses, contact forces, and axial load distributions. The original buckling analysis by Lubinski and Woods3 proposed a helical configuration in a vertical wellbore, and used the method of virtual work to determine a specific constant pitch for that helix, as a function of the axial force and bending stiffness. These two works set the following themes for further analysis of tubing buckling: What is the critical buckling load in curved, three dimensional wellbores? How does torque affect the critical buckling load? How do tapered strings affect the critical buckling load? What is the buckling configuration in inclined wellbores? How do the boundary conditions affect the configuration? How do tapered strings buckle? How does torque affect the buckling configuration? What effect does friction play in tubing buckling? Many of these questions have been, at least, partly answered in the three decades since the original papers were published. This paper will examine the technical fundamentals of the tubing buckling problem, summarize the most useful new results from these papers, and discuss the remaining challenges in tubing buckling analysis.
Full-aperture, high-power semiconductor laser (1989)

A single quantum well laser with a 2-mm-wide aperture has exhibited low threshold current density and nearly 100% packing fraction. The lateral structure relies on epitaxial growth on a corrugated substrate to frustrate radiative lateral processes and it thus eliminates the need for isolation at least for incoherent operation. Threshold current densities are comparable to those for low-power devices, and slope efficiencies remain undiminished to our current limit where 10.7 W per facet is attained. The aperture size is limited only by our fixturing arrangement.
Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization (2020)

Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by FcεRI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and FcεRI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with FcεRI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.
Kevlar Functionalized Carbon Nanotubes for Next-Generation Composites (2010)

We report a sequential functionalization methodology for the covalent modification of multiwalled carbon nanotubes (MWNTs) with one and a half repeat units of the polymer poly-p-phenyleneterephthalamide (PPTA), Kevlar. Covalent attachment of PPTA monomer units, p-phenylenediamine (PDA) and terephthaloyl chloride (TPC), to the surface of MWNTs results in PPTA oligomer units forming an organic sheath around the nanotubes, PPTA-functionalized-MWNTs (PPTA-MWNTs). PPTA-MWNTs possess chemical functionality identical to that of PPTA, and thus provide nanoscale scaffolds which may be readily dispersed within a monomer solution and participate in the polymerization reaction to form a PPTA-MWNT/PPTA composite. We show that formation of PPTA in the presence of PPTA-MWNTs leads to a uniform dispersion of MWNTs within the polymer matrix, in contrast to aggregated masses of MWNTs in the case of pristine-MWNTs. The covalent attachment of oligomeric PPTA units to the surface of MWNTs represents the formation of a functional nanoscale building block which can be readily dispersed and integrated within the polymer PPTA to form a novel composite material. The implications of tuning the surface chemistries of carbon nanotubes (CNTs) to the chemistry of host polymer matrices are considered.
Development of Tl-based novel scintillators (2020)

Inorganic scintillators containing heavy Thallium-(Tl) in the host lattices are the novel emerging class discovered by our research group. In this class of scintillators, we studied elpasolites, ternary lanthanide halides, ternary metal halides and Tl-based hafnium/zirconium halides. These materials were synthesized by conventional melting, rotating melt direction and sublimation techniques. The single crystals were grown by conventional and modified two zones vertical Bridgman techniques and the phases were analyzed by differential scanning calorimetry and powder X-rays diffraction analysis. The emission properties studied at room temperature under X-rays irradiation shown to have efficient intrinsic and Ce<sup>3+</sup> or Eu<sup>2+</sup> dopant luminescence, mostly in the 370-530 nm range i.e compatible with the spectral sensitivity response of modern photosensors. The scintillation properties studied under γ-rays and α-particles irradiation shown to have good energy resolution, high light yield, faster timing response and good pulse shape discrimination. The heavy Tl ion give rise to high effective number and moderate densities to these scintillators, make them efficient for the detection of X- and γ-rays. With the modification of crystal growth furnaces, materials synthesis techniques, and purification procedure the scintillation performance of these scintillators improved significantly. The discovery and development for new Tl-based efficient scintillators and improvement in scintillation performance of the already discovered Tl-based scintillators are under investigation and will be reported in our future work.
The Origin of Periodontal Infections (1988)

Periodontal diseases are recognized as bacterial infections, and some forms are associated with specific organisms, such as Actinobacillus actinomycetemcomitans in juvenile periodontitis, and Bacteroides gingivalis and others in adult periodontitis. The source of the periodontal organisms, whether they are part of the indigenous or resident flora and overgrow to become opportunistic oral pathogens, or whether they are exogenous oral pathogens, is important to determine. The chain of periodontal infection, microbial agent(s) and their transmission, and host response are reviewed with respect to the role of A. actinomycetemcomitans in localized juvenile periodontitis and B. gingivalis in adult periodontitis. The present data lead us to hypothesize that some periodontal organisms may be exogenous pathogens. Prevention of periodontal diseases may be influenced by the knowledge of whether various forms are caused by opportunistic organisms or exogenous pathogens. If exogenous pathogens are responsible, prevention can be directed to intercepting transmission, thereby preventing colonization. On the other hand, if the organisms are opportunistic pathogens, prevention might be directed at interfering with initial acquisition of the flora earlier in life, as well as suppressing them to low levels consistent with health. For those exogenous periodontal infections, attempts at eradication and prevention of re-infection are likely to be effective. If the organisms are part of the indigenous flora, there is little hope of complete elimination of the organism. Criteria for distinguishing exogenous periodontal pathogens from opportunistic periodontal pathogens include the prediction that exogenous pathogens would be transient members of the oral flora associated with periodontal disease, likely to be comprised of one or a few clonal types, and intrinsically virulent. In contrast, opportunistic periodontal pathogens would likely be members of the indigenous flora and would overgrow. They would likely be comprised of many clonal types, and have an intrinsically low level of virulence.
Low-Loss Polarization-Insensitive Packaged WDM Monitor (1998)

Low-cost, high-performance wavelength division multiplexing (WDM) monitors and receivers are key components in WDM transmission and local area optical networks.
Rank-Modulation Rewrite Coding for Flash Memories (2015)

The current flash memory technology focuses on the cost minimization of its static storage capacity. However, the resulting approach supports a relatively small number of program-erase cycles. This technology is effective for consumer devices (e.g., smartphones and cameras) where the number of program-erase cycles is small. However, it is not economical for enterprise storage systems that require a large number of lifetime writes. The proposed approach in this paper for alleviating this problem consists of the efficient integration of two key ideas: 1) improving reliability and endurance by representing the information using relative values via the rank modulation scheme and 2) increasing the overall (lifetime) capacity of the flash device via rewriting codes, namely, performing multiple writes per cell before erasure. This paper presents a new coding scheme that combines rank-modulation with rewriting. The key benefits of the new scheme include: 1) the ability to store close to 2 bit per cell on each write with minimal impact on the lifetime of the memory and 2) efficient encoding and decoding algorithms that make use of capacity-achieving write-once-memory codes that were proposed recently.
An efficient source of single photons: a single quantum dot in a micropost microcavity (2003)

Summary form only given. We have studied the micropost microcavity modes using first-principles numerical simulation. These methods have reproduced the quality factors and lifetimes observed. We have also used these simulations to optimize the design of the microcavities. We have shown that there is the possibility of simultaneously obtaining very high quality factors and low mode volumes in this system, which should allow for the observation of novel physical effects.