gebhart/patrepeval huggingface dataset:
Roles of Cyclic Diguanylate in the Regulation of Bacterial Pathogenesis (2007)

Cyclic diguanylate (c-di-GMP) is a bacterial second messenger of growing recognition involved in the regulation of a number of complex physiological processes. This review describes the biosynthesis and hydrolysis of c-di-GMP and several mechanisms of regulation of c-di-GMP metabolism. The contribution of c-di-GMP to regulating biofilm formation and motility, processes that affect pathogenesis of many bacteria, is described, as is c-di-GMP regulation of virulence gene expression. Finally, ways in which c-di-GMP may mediate these regulatory effects are proposed.
The ballistic nano-transistor (2003)

We have achieved extremely high drive current performance and ballistic (T>0.8) transport using ultra-thin (<2 nm) gate oxides in sub-30 nm effective channel length nMOSFETs. The peak drive performance in an nMOSFET was observed at t/sub ox//spl ap/1.3 nm for a 1.5 V power supply voltage with T/sub n//spl ap/0.7, while the peak performance in a pMOSFET was observed at t/sub ox//spl ap/1.5 nm for a -1.5 V supply with T/sub p//spl ap/0.5. Since the carrier scattering in the channel is due predominately to interface roughness, reducing the transverse surface field, either by reducing the gate voltage or by increasing the oxide thickness, can be used to improve the transmittance T/sub n//spl rarr/0.85, T/sub p//spl rarr/0.6, while diminishing the drive current.
Noninvasive early detection of brain edema in mice by near-infrared light scattering (2005)

Brain edema accounts for significant morbidity and mortality in many neurologic conditions such as head trauma, stroke, meningitis, and brain tumor. The water channel aquaporin-4 (AQP4) has been found to be an important determinant of brain water accumulation and clearance of excess brain water. We report the development of a noninvasive near-infrared (NIR) light-scattering method to compare the early kinetics of brain swelling in normal and AQP4-deficient mice. Brain tissue was illuminated through the intact skull with NIR light at 850 nm, and steady-state scattered light intensity was monitored at an angle of 90 degrees at a position on the skull approximately 10 mm from the illuminated site. NIR light scattering reversibly increased with brain swelling (DeltaI/Io approximately 25% per 1% increase in brain water content), but was insensitive to changes in cerebral blood flow, blood oxygenation, or blood flow-related changes in intracranial pressure (ICP). DeltaI/Io increased approximately linearly with brain water content as measured by wet-to-dry weight ratios. Acute water intoxication (intraperitoneal water, 20% body weight) produced a gradual increase in DeltaI/Io of 12 +/- 4% in wild-type mice at 5 min, much greater than that of 2 +/- 1% in AQP4-null mice. Correlation of the NIR signal with ICP showed that increased DeltaI/Io preceded measurable increases in ICP, indicating the ability of the NIR method to detect early brain edema before ICP elevation. NIR light scattering provides a simple noninvasive method to monitor brain edema in mice, with potential clinical applications.
Warping virtual space for low-cost haptic feedback (2013)

With the introduction of the Nintendo Wii, Playstation Move, and Microsoft Kinect, gaming and virtual reality technologies have begun to merge. These technologies have enabled low-cost, more-natural interaction with games and virtual environments (VEs). However, the sense of touch is usually missing. Interacting with virtual objects often means holding a hand in the air, which can be tiring if done for long. I present a technique to turn simple objects into haptic surfaces for virtual objects, extending earlier work on Redirected Touching [Kohli et al. 2012].
Antibodies specific for left-handed Z-DNA. (1981)

We prepared a brominated poly(dG-dC).poly(dG-dC) which forms a stable Z-DNA helix under physiological salt conditions. Rabbits and mice were immunized with brominated and unbrominated poly(dG-dC).poly(dG-dC) complexed with methylated bovine serum albumin. Antibodies specific for Z-DNA were produced. These antibodies were found not only in the sera of animals immunized with the low-salt stabilized Z-DNA [Br-poly(dG-dC).poly(dG-dC)] but also in sera from animals immunized with the unbrominated B-DNA form of the polymer. From this it is inferred that the unbrominated poly(dG-dC).poly(dG-dC) was partially converted to Z-DNA by its combination with the basic protein methylated bovine serum albumin. In addition to specific anti-Z-DNA antibody populations, two other interesting types of antibody populations were found. One of these reacted with both the Z and B forms of poly(dG-dC).poly(dG-dC). This antibody may be converting the polymer from the B-DNA to the Z-DNA form. The other type of antibody was specific for a B form of poly(dG-dC).poly(dG-dC) and did not react at all with the Z form. The antibodies raised to Z-DNA were shown to be highly specific for Z-DNA and did not react with B-DNA, RNA, DNA.RNA hybrids, or a number of other polynucleotides. This specificity for Z-DNA will make possible their use as reagents for determining the presence of Z-DNA in biological systems. Sera of autoimmune lupus mice were also shown to have a considerable amount of naturally occurring anti-Z-DNA antibody activity.
Rat liver alcohol dehydrogenase of class III (1988)

The amino acid sequence of alcohol dehydrogenase of class III from rat liver (the enzyme ADH-2) has been determined. This type of structure is quite different from those of both the class I and the class II alcohol dehydrogenases. The rat class III structure differs from the rat and human class I structures by 133-138 residues (exact value depending on species and isozyme type); and from that of human class II by 132 residues. In contrast, the rat/human species difference within the class III enzymes is only 21 residues. The protein was carboxymethylated with iodo[2(14)C]acetate, and cleaved with CNBr and proteolytic enzymes. Peptides purified by exclusion chromatography and reverse-phase high-performance liquid chromatography were analyzed by degradation with a gas-phase sequencer and with the manual 4-N,N-dimethylaminoazobenzene-4'-isothiocyanate double-coupling method. The protein chain has 373 residues with a blocked N terminus. No evidence was obtained for heterogeneity. The rat ADH-2 enzyme of class III contains an insertion of Cys at position 60 in relation to the class I enzymes, while the latter alcohol dehydrogenase in rat (ADH-3) has another Cys insertion (at position 111) relative to ADH-2. The structure deduced explains the characteristic differences of the class III alcohol dehydrogenase in relation to the other classes of alcohol dehydrogenase, including a high absorbance, an anodic electrophoretic mobility and special kinetic properties. The main amino acid substitutions are found in the catalytic domain and in the subunit interacting segments of the coenzyme-binding domain, the latter explaining the lack of hybrid dimers between subunits of different classes. Several substitutions provide an enlarged and more hydrophilic substrate-binding pocket, which appears compatible with a higher water content in the pocket and hence could possibly explain the higher Km for all substrates as compared with the corresponding values for the class I enzymes. Finally the class III structure supports evolutionary relationships suggesting that the three classes constitute clearly separate enzymes within the group of mammalian zinc-containing alcohol dehydrogenases.
Role of recombination activating genes in the generation of antigen receptor diversity and beyond (2012)

V(D)J recombination is the process by which antibody and T-cell receptor diversity is attained. During this process, antigen receptor gene segments are cleaved and rejoined by non-homologous DNA end joining for the generation of combinatorial diversity. The major players of the initial process of cleavage are the proteins known as RAG1 (recombination activating gene 1) and RAG2. In this review, we discuss the physiological function of RAGs as a sequence-specific nuclease and its pathological role as a structure-specific nuclease. The first part of the review discusses the basic mechanism of V(D)J recombination, and the last part focuses on how the RAG complex functions as a sequence-specific and structure-specific nuclease. It also deals with the off-target cleavage of RAGs and its implications in genomic instability.
Quantitative histology analysis of the ovarian tumour microenvironment (2015)

Concerted efforts in genomic studies examining RNA transcription and DNA methylation patterns have revealed profound insights in prognostic ovarian cancer subtypes. On the other hand, abundant histology slides have been generated to date, yet their uses remain very limited and largely qualitative. Our goal is to develop automated histology analysis as an alternative subtyping technology for ovarian cancer that is cost-efficient and does not rely on DNA quality. We developed an automated system for scoring primary tumour sections of 91 late-stage ovarian cancer to identify single cells. We demonstrated high accuracy of our system based on expert pathologists' scores (cancer = 97.1%, stromal = 89.1%) as well as compared to immunohistochemistry scoring (correlation = 0.87). The percentage of stromal cells in all cells is significantly associated with poor overall survival after controlling for clinical parameters including debulking status and age (multivariate analysis p = 0.0021, HR = 2.54, CI = 1.40-4.60) and progression-free survival (multivariate analysis p = 0.022, HR = 1.75, CI = 1.09-2.82). We demonstrate how automated image analysis enables objective quantification of microenvironmental composition of ovarian tumours. Our analysis reveals a strong effect of the tumour microenvironment on ovarian cancer progression and highlights the potential of therapeutic interventions that target the stromal compartment or cancer-stroma signalling in the stroma-high, late-stage ovarian cancer subset.
The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function (2007)

Our data presents the first direct observation that a mammalian non-coding antisense molecule can positively influence the abundance of a cis-transcribed mRNA under physiological abundance conditions. While our analysis implies a possible human specific and dsRNA-mediated mechanism for stabilizing the expression of svPINK1, it also points to a broader genomic strategy for regulating a human disease locus and increases the complexity through which alterations in the regulation of the PINK1 locus could occur.
Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy (2015)

The use of adeno-associated virus (AAV) as a gene therapy vector has been approved recently for clinical use and has demonstrated efficacy in a growing number of clinical trials. However, the safety of AAV as a vector has been challenged by a single study that documented hepatocellular carcinoma (HCC) after AAV gene delivery in mice. Most studies have not noted genotoxicity following AAV-mediated gene delivery; therefore, the possibility that there is an association between AAV and HCC is controversial. Here, we performed a comprehensive study of HCC in a large number of mice following therapeutic AAV gene delivery. Using a sensitive high-throughput integration site-capture technique and global expressional analysis, we found that AAV integration into the RNA imprinted and accumulated in nucleus (Rian) locus, and the resulting overexpression of proximal microRNAs and retrotransposon-like 1 (Rtl1) were associated with HCC. In addition, we demonstrated that the AAV vector dose, enhancer/promoter selection, and the timing of gene delivery are all critical factors for determining HCC incidence after AAV gene delivery. Together, our results define aspects of AAV-mediated gene therapy that influence genotoxicity and suggest that these features should be considered for design of both safer AAV vectors and gene therapy studies.
[Characterization of Echinococcus granulosus and Echinococcus multilocularis by DNA probe]. (1993)

Cloned DNA fragments pHD5, pSM889 and pEG18 have been used as DNA probes in the restriction endonuclease analysis and southern blot hybridization to characterize E. granulosus and E. multilocularis protoscolices from China. Southern blot hybridization method is sensitive, specific and has the advantage in identification over microscopic examination. The authors deem that it can be used in the base-line epidemiological survey and surveillance of hydatid disease to provide data for hydatid disease control.
Microwave Protocols for Paraffin Microtechnique and In Situ Localization in Plants (1998)

: We have developed a microwave protocol for a paraffin-embedding microtechnique of the shoot apical meristem of Zea mays and have successfully applied this protocol to other plant tissues. This protocol decreases the time required for all aspects of microtechnique tissue processing, including fixation (24 hr to 15 min), dehydration (73 hr to 10 min), and infiltration (96 hr to 3 hr). Additionally, the time required to adhere paraffin ribbons to gelatin-coated slides and for the Johanson's safranin O, fast green FCF staining protocol has been significantly decreased. Using this technique, the quality of tissue preservation and subsequent in situ localization of knotted mRNA was increased by using microwaves.
<title>Status of BMDO/IST lasercom advanced technology demonstration</title> (1994)

Laser communications between satellites, high flying aircraft (such as JSTARS), and the ground offer the potential to transfer extremely high amounts of information faster and with a much smaller package than is possible using current radio frequency and microwave technologies. This can be especially important in downlinking time sensitive satellite reconnaissance information because the satellite stays within range of a ground station or aircraft for only a few minutes. A capability to downlink from a satellite to an aircraft can provide all weather performance, and multiple data transfers for every satellite orbit. Over the last few years, SDIO (now BMDO) has funded a number of technology efforts through the US Army Space and Strategic Defense Command reducing the risks associated with laser communications. This paper describes one of these efforts which is now being carried forward to an Advanced Technology Demonstration at ThermoTrex Corporation. The program will lead to the demonstration of high data rate communications of 270 MBPS (Mega Bits Per Second) to 1.08 GBPS (Giga Bits Per Second) between high altitude aircraft and possibly between a satellite and the ground. The Laser Communications Terminals incorporate Atomic Line Filter technology for background light rejection during acquisition, reactionless Roto-Lok offset cable drive gimbals for fast slewing and high accuracy pointing, and direct digital modulation of semiconductor diode lasers detected with low noise avalanche photodiodes. We present designs and preliminary performance results for both a simplified terminal appropriate for a near term satellite-to-ground data transfer experiment, and a full capability terminal appropriate for ground, aircraft, or satellite operations.
A novel method for in-line process monitoring by measuring the gray level values of SEM images (2005)

A novel semiconductor wafer metrology method for in-line process monitoring of the production wafer is proposed in this paper. A new electron beam (e-beam) system, eProfile, is developed to implement this methodology. By taking high-resolution scanning electron microscope (SEM) images on one or multiple specified locations on each die or some sampled dies and collecting gray level value (GLV) information at the locations of interest in these images, one can get the process signature across wafer very quickly. It can help to shorten the process development cycle and also can be used to monitor process in a wafer production line to prevent a process go out of specification or catch process excursions.
The posttranslational processing of ras p21 is critical for its stimulation of yeast adenylate cyclase. (1992)

Mammalian ras genes substitute for the yeast RAS gene, and their products activate adenylate cyclase in yeast cells, although the direct target protein of mammalian ras p21s remains to be identified. ras p21s undergo posttranslational processing, including prenylation, proteolysis, methylation, and palmitoylation, at their C-terminal regions. We have previously reported that the posttranslational processing of Ki-ras p21 is essential for its interaction with one of its GDP/GTP exchange proteins named smg GDS. In this investigation, we have studied whether the posttranslational processing of Ki- and Ha-ras p21s is critical for their stimulation of yeast adenylate cyclase in a cell-free system. We show that the posttranslationally fully processed Ki- and Ha-ras p21s activate yeast adenylate cyclase far more effectively than do the unprocessed proteins. The previous and present results suggest that the posttranslational processing of ras p21s is important for their interaction not only with smg GDS but also with the target protein.
Small Increases in the Level of Sox2 Trigger the Differentiation of Mouse Embryonic Stem Cells (2008)

Previous studies have demonstrated that the transcription factor Sox2 is essential during the early stages of development. Furthermore, decreasing the expression of Sox2 severely interferes with the self-renewal and pluripotency of embryonic stem (ES) cells. Other studies have shown that Sox2, in conjunction with the transcription factor Oct-3/4, stimulates its own transcription as well as the expression of a growing list of genes (Sox2:Oct-3/4 target genes) that require the cooperative action of Sox2 and Oct-3/4. Remarkably, recent studies have shown that overexpression of Sox2 decreases expression of its own gene, as well as four other Sox2:Oct-3/4 target genes (Oct-3/4, Nanog, Fgf-4, and Utf1). This finding led to the prediction that overexpression of Sox2 in ES cells would trigger their differentiation. In the current study, we initially engineered mouse ES cells for inducible overexpression of Sox2. Using this model system, we demonstrate that small increases (twofold or less) in Sox2 protein trigger the differentiation of ES cells into cells that exhibit markers for a wide range of differentiated cell types, including neuroectoderm, mesoderm, and trophectoderm but not endoderm. We also demonstrate that elevating the levels of Sox2 quickly downregulates several developmentally regulated genes, including Nanog, and a newly identified Sox2:Oct-3/4 target gene, Lefty1. Together, these data argue that the self-renewal of ES cells requires that Sox2 levels be maintained within narrow limits. Thus, Sox2 appears to function as a molecular rheostat that controls the expression of a critical set of embryonic genes, as well as the self-renewal and differentiation of ES cells.
Evolution of multiprotocol label switching (1998)

Multiprotocol label switching (MPLS) is rapidly emerging as an Internet Engineering Task Force (IETF) standard intended to enhance the speed, scalability, and service provisioning capabilities in the Internet. MPLS uses the technique of packet forwarding based on labels, to enable the implementation of a simpler high-performance packet forwarding engine. This also decouples packet forwarding from routing, facilitating the provision of varied routing services independent of the packet forwarding paradigm. The authors track the evolution of this technology in relation to other existing technologies. Then an overview of the MPLS architecture and design is provided. In addition, some of the work that was a precursor to MPLS is discussed, as well as related issues and debates.
Production and Characterization of Nano-Aluminum and its Effect in Solid Propellant Combustion (2007)

Nano-aluminum particles were produced by the electrical wire explosion method at this laboratory. The size and shape of the particles were measured using a transmission electron microscope (TEM). Aluminum wires are exploded by application of high voltage, to yield particles of size around 40 nm. The X-ray diffraction (XRD) results also confirm that the powder formed by the above process as aluminum with an average size of 42 nm. Previous studies on ultrafine-aluminum applied to solid propellants have tested a particle size not less than about 100 nm. The thermal characteristics were analyzed using thermo gravimetric and differential thermal analyses (TG-DTA). The composition of the material was characterized by energy dispersive angle X-ray (EDAX) analysis. The low pressure deflagration limit (LPDL) tests were carried out for dry-pressed pellets of the nanoaluminum or normal aluminum with ammonium perchlorate (AP). Sandwich burning tests of the nano-aluminum and normal aluminum added to the middle lamina of binder were also carried out. It showed that the addition of nano-aluminum marginally increased the burning rate at elevated pressures and higher lamina thicknesses. Composite propellant formulations were developed out with a bimodal size distribution of AP particles, with the baseline non-aluminized formulations exhibiting plateau burning rate trends. Burning rate studies of the non-aluminized, nano-aluminized, and normal aluminized propellants were carried out. It was found that the burning rate of the nano-aluminized propellants increased by 100% compared to normal aluminized propellants. In the nano-aluminized propellants, the plateau effects in the burning rate of the corresponding non-aluminized propellants in the intermediate pressure range were removed, but significantly low pressure-exponents were observed at elevated pressures. The results point out that the nearly complete combustion of nano-aluminum near the propellant burning surface actually controls the propellant burning rate. The nano-aluminum combustion is diffusion-limited at elevated pressures, and hence, results in significantly low pressure-exponents of burning rate in that pressure range.
Homology-directed repair is a major double-strand break repair pathway in mammalian cells (1998)

Mammalian cells have been presumed to repair potentially lethal chromosomal double-strand breaks (DSBs) in large part by processes that do not require homology to the break site. This contrasts with Saccharomyces cerevisiae where the major DSB repair pathway is homologous recombination. Recently, it has been determined that DSBs in genomic DNA in mammalian cells can stimulate homologous recombination as much as 3 or 4 orders of magnitude, suggesting that homology-directed repair may play an important role in the repair of chromosomal breaks. To determine whether mammalian cells use recombinational repair at a significant level, we have analyzed the spectrum of repair events at a defined chromosomal break by using direct physical analysis of repair products. When an endonuclease-generated DSB is introduced into one of two direct repeats, homologous repair is found to account for 30-50% of observed repair events. Both noncrossover and deletional homologous repair products are detected, at approximately a 1:3 ratio. These results demonstrate the importance of homologous recombination in the repair of DSBs in mammalian cells. In the remaining observed repair events, DSBs are repaired by nonhomologous processes. The nonhomologous repair events generally result in small deletions or insertions at the break site, although a small fraction of events result in larger chromosomal rearrangements. Interestingly, in two insertions, GT repeats were integrated at one of the broken chromosome ends, suggesting that DSB repair can contribute to the spread of microsatellite sequences in mammalian genomes.