gebhart/patrepeval huggingface dataset:
Simian virus 40 DNA replication in vitro: specificity of initiation and evidence for bidirectional replication. (1985)

We recently described a soluble cell-free system derived from monkey cells that is capable of replicating exogenous plasmid DNA molecules containing the simian virus 40 (SV40) origin of replication (J.J. Li, and T.J. Kelly, Proc. Natl. Acad. Sci. U.S.A. 81:6973-6977, 1984). Replication in the system is completely dependent upon the addition of the SV40 large T antigen. In this report we describe additional properties of the in vitro replication reaction. Extracts prepared from cells of several nonsimian species were tested for the ability to support origin-dependent replication in the presence of T antigen. The activities of extracts derived from human cell lines HeLa and 293 were approximately the same as those of monkey cell extracts. Chinese hamster ovary cell extracts also supported SV40 DNA replication in vitro, but the extent of replication was approximately 1% of that observed with human or monkey cell extracts. No replication activity was detectable in extracts derived from BALB/3T3 mouse cells. The ability of these extracts to support replication in vitro closely parallels the ability of the same cells to support replication in vivo. We also examined the ability of various DNA molecules containing sequences homologous to the SV40 origin to serve as templates in the cell-free system. Plasmids containing the origins of human papovaviruses BKV and JCV replicated with an efficiency 10 to 20% of that of plasmids containing the SV40 origin. Plasmids containing Alu repeat sequences (BLUR8) did not support detectable DNA replication in vitro. Circular DNA molecules were found to be the best templates for DNA replication in the cell-free system; however, linear DNA molecules containing the SV40 origin also replicated to a significant extent (10 to 20% of circular molecules). Finally, electron microscopy of replication intermediates demonstrated that the initiation of DNA synthesis in vivo takes place at a unique site corresponding to the in vivo origin and that replication is bidirectional. These findings provide further evidence that replication in the cell-free system faithfully mimics SV40 DNA replication in vivo.
Impairment of nucleoid segregation and cell division at high osmolarity in a strain of<i>Escherichia coli</i>overproducing the chaperone DnaK (1993)

Escherichia coli strain WM1390, which overproduces 20-fold the chaperone protein DnaK, was able to grow exponentially without apparent abnormality in 300 mosM medium. In contrast, it showed both aberrant nucleoid segregation and strong inhibition of septation when shifted to high osmolarity. These impairments could not be accounted for by a bacteriocidal effect of the high DnaK content. Rather, the DnaK content appeared to promote faster growth than that of the parent C600, at least at high osmolarity in the presence of the osmoprotectant glycine betaine.
Chromatin structure implicated in activation of HIV-1 gene expression by ultraviolet light. (1990)

We have investigated the effects of different DNA-damaging agents on HIV-1 gene expression. We find that agents that produce "bulky" DNA lesions, similar to those induced by ultraviolet light (UV), all dramatically increase HIV-1 gene expression, whereas agents that produce primarily base damage and DNA breakage, such as ionizing radiation, have little or no effect. We show that these effects are independent of DNA synthesis per se and do not require DNA nucleotide excision repair. The drug novobiocin effectively prevents the UV activation process, consistent with the idea that a change in DNA chromatin structure may be required. We suggest that a transient decondensation of chromatin structure, an early step in DNA nucleotide excision repair but not in base excision repair, may be the triggering mechanism. The decondensation may allow the transcriptional machinery better access to the HIV-1 promoter region, thereby increasing gene expression.
Architectural Supports to Protect OS Kernels from Code-Injection Attacks and Their Applications (2017)

The kernel code injection is a common behavior of kernel-compromising attacks where the attackers aim to gain their goals by manipulating an OS kernel. Several security mechanisms have been proposed to mitigate such threats, but they all suffer from non-negligible performance overhead. This article introduces a hardware reference monitor, called Kargos, which can detect the kernel code injection attacks with nearly zero performance cost. Kargos monitors the behaviors of an OS kernel from outside the CPU through the standard bus interconnect and debug interface available with most major microprocessors. By watching the execution traces and memory access events in the monitored target system, Kargos uncovers attempts to execute malicious code with the kernel privilege. On top of this, we also applied the architectural supports for Kargos to the detection of ROP attacks. KS-Stack is the hardware component that builds and maintains the shadow stacks using the existing supports to detect this ROP attacks. According to our experiments, Kargos detected all the kernel code injection attacks that we tested, yet just increasing the computational loads on the target CPU by less than 1% on average. The performance overhead of the KS-Stack was also less than 1%.
The Effect of Interleukin 4 (BSF-1) on Infection of Peripheral Blood Monocyte-Derived Macrophages with HIV-1 (1990)

The effects of various cytokines were examined in an in vitro model of human immunodeficiency virus type 1 (HIV-1) infection of human peripheral blood monocyte-derived macrophages (MDM). Monocytes were obtained from blood of normal donors by Ficoll/hypaque gradient centrifugation and adherence. These cells were allowed to mature in the presence of varying concentrations of cytokines. After five days in culture, cells were harvested, counted, and inoculated with S5G7, an HTLV-IIIB subclone. The cells were replated in the presence of the same concentrations of cytokines. Culture supernatants were sampled over 28 days for p24 antigen (Ag) as measured by Ag capture assay. In repeat experiments, the following observations were made: 1. MDM from some donors could be infected only in the presence of tumor necrosis factor-alpha (TNF-alpha), granulocyte/macrophage colony-stimulating factor (GM-CSF) or interleukin 4 (IL-4); 2. The effect of GM-CSF was variable; TNF alpha also enhanced HIV replication above controls; 3. IL-4 was the most potent enhancer of HIV-1 replication in MDM of the cytokines tested, inducing p24 Ag levels 75-230 times those seen in control cultures run simultaneously. This effect was dose dependent. Ag production was not observed until Day 14 postinfection in most experiments. Multinucleated giant cell formation was observed only in the presence of IL-4.
NF-κB-to-AP-1 Switch: A Mechanism Regulating Transition From Endothelial Barrier Injury to Repair in Endotoxemic Mice (2014)

Endothelial barrier disruption is a hallmark of multiple organ injury (MOI). However, mechanisms governing the restoration of endothelial barrier function are poorly understood. Here, we uncovered an NF-κB-to-AP-1 switch that regulates the transition from barrier injury to repair following endotoxemic MOI. Endothelial NF-κB mediates barrier repair by inhibiting endothelial cell (EC) apoptosis. Blockade of endothelial NF-κB pathway activated the activator protein (AP)-1 pathway (NF-κB-to-AP-1 switch), which compensated for the anti-apoptotic and barrier-repair functions of NF-κB. The NF-κB-to-AP-1 switch occurred at 24 hours (injury to repair transition phase), but not at 48 hours (repair phase) post-LPS, and required an inflammatory signal within the endothelium. In the absence of an inflammatory signal, the NF-κB-to-AP-1 switch failed, resulting in enhanced EC apoptosis, augmented endothelial permeability, and impeded transition from barrier injury to recovery. The NF-κB-to-AP-1 switch is a protective mechanism to ensure timely transition from endothelial barrier injury to repair, accelerating barrier restoration following MOI.
Specifying abstract data types by restriction (1978)

Restrictions are one instance of mathematically-based relationships between types that can be used to simplify program specifications. Restriction of an abstract data type provides a theoretical justification for the concept of a hidden function that appears in some current specification methodologies. The use of type restrictions to simplify formal specifications is illustrated by the example of traversible stacks.
Finderlists, Computer-Generated, for Bilingual Dictionaries (1992)

This paper discusses keyword finderlists for bilingual dictionaries, focussing on their structure and a system for computer-generating them. We examine the concept of finderlist and discuss techniques for specifying finderlist headwords. We develop a typology of finderlist format and argue for the merits of a particular type. A description is presented of an automated system which transforms dictionary glosses according to a set of associated rules to produce a keyword finderlist. Finally we address a number of computer-related lexicographical issues, including data representation and strategies for computer-aided lexicography.
Phase imaging and synthetic aperture super-resolution via total internal reflection microscopy (2018)

Total internal reflection microscopy is mainly used in its fluorescence mode and is the reference technique to image fluorescent proteins in the vicinity of cell membranes. Here, we show that this technique can easily become a phase microscope by simply detecting the coherent signal resulting from the interference between the field scattered by the probed sample and the total internal reflection. Moreover, combining several illumination angles permits generating synthetic aperture reconstructions with improved resolutions compared to standard label-free microscopy techniques.
Automotive radar interference test (2017)

Fully automated vehicles are currently under research and development and will become reality in the near future. Key enabling sensors in this area are automotive radars, which currently support driving comfort and crash prevention. These radars operate in the 24 GHz and 76-81 GHz bands as of today and occupy the spectrum heavily. Hence automotive radar sensors require immunity to interference of some other automotive radar sensors. This paper presents methods to verify interference mitigation techniques using very wide band arbitrary RF signals in high frequency mmWave domain. It shows measurements that the noise floor increases in between 10 dB to 25 dB depending on the interference signal level and waveform. Without interference cancellation objects with low radar cross sections, like pedestrians, would most likely go undetected.
Efficient Luminescence from Perovskite Quantum Dot Solids (2015)

Nanocrystals of CsPbX3 perovskites are promising materials for light-emitting optoelectronics because of their colloidal stability, optically tunable bandgap, bright photoluminescence, and excellent photoluminescence quantum yield. Despite their promise, nanocrystal-only films of CsPbX3 perovskites have not yet been fabricated; instead, highly insulating polymers have been relied upon to compensate for nanocrystals' unstable surfaces. We develop solution chemistry that enables single-step casting of perovskite nanocrystal films and overcomes problems in both perovskite quantum dot purification and film fabrication. Centrifugally cast films retain bright photoluminescence and achieve dense and homogeneous morphologies. The new materials offer a platform for optoelectronic applications of perovskite quantum dot solids.
Prolonged application of pressure in transluminal coronary angioplasty (1984)

We investigated the morphologic structure and fluid content of atherosclerotic specimens of fresh human postmortem artery segments before and after application of a pressure of 5 atmospheres simulated by a weight of 5 kg per 1 cm2. After applying pressure in nonorganized atheromata, we noticed a marked reduction in thickness while in fibrotic atheromata we observed only smaller differences in thickness. Reduction in fluid content was significantly more pronounced in nonorganized atheromatous tissue. Reduction in thickness was closely related to reduction in weight (i e, fluid content). The time of pressure application necessary to achieve the optimal result averaged 60 sec. The conclusions drawn from these experiments were incorporated into clinical application of coronary angioplasty. Prolonged balloon inflation was applied to the last 400 out of a total of 600 coronary angioplasty procedures, performed between October 1977 and October 1983. Stenoses not sufficiently responsive to balloon inflation periods of 5-10 sec were exposed to periods of 60 sec (30-120 sec). The number of "non dilatable" stenoses was 15% with the standard short pressure procedure, but only 5% with the prolonged pressure application. No serious complications related to prolonged pressure application were observed. Thus, from experimental data and clinical experience the application of longer pressure periods appears justified and beneficial.
The Essential Role of Clathrin-mediated Endocytosis in the Infectious Entry of Human Enterovirus 71 (2010)

Little is currently known about the infectious entry process of human enterovirus 71 (HEV71) into host cells, which may represent potential anti-viral targeting sites. In this study a targeted small-interfering RNA (siRNA) screening platform assay was established and validated to identify and profile key cellular genes involved in processes of endocytosis, cytoskeletal dynamics, and endosomal trafficking essential for HEV71 infection. Screen evaluation was conducted via the expression of well characterized dominant-negative mutants, bioimaging studies (double-labeled immunofluorescence assays, transmission electron microscopy analysis), secondary siRNA-based dosage dependence studies, and drug inhibition assays. The infectious entry of HEV71 into rhabdomyosarcoma cells was shown to be significantly inhibited by siRNAs targeting genes associated with clathrin-mediated endocytosis (CME) that include AP2A1, ARRB1, CLTC, CLTCL1, SYNJ1, ARPC5, PAK1, ROCK1, and WASF1. The functional role of CME was verified by the observation of strong co-localization between HEV71 particles and clathrin as well as dose-dependent inhibition of HEV71 infection upon siRNA knockdown of CME-associated genes. HEV71 entry by CME was further confirmed via inhibition by dominant-negative EPS15 mutants and treatment of CME drug inhibitors, with more than 80% inhibition observed at 20 μm chlorpromazine. Furthermore, HEV71 infection was shown to be sensitive to the disruption of human genes in regulating early to late endosomal trafficking as well as endosomal acidic pH. The identification of clathrin-mediated endocytosis as the entry pathway for HEV71 infection of susceptible host cells contributes to a better understanding of HEV71 pathogenesis and enables future development of anti-viral strategies against HEV71 infection.
Maintenance of Murine Embryonic Stem Cells' Self-Renewal and Pluripotency with Increase in Proliferation Rate by a Bovine Granulosa Cell Line-Conditioned Medium (2010)

Murine embryonic stem cells (mESCs) are pluripotent cells that can be propagated in an undifferentiated state in continuous culture on a feeder layer or without feeders in the presence of leukemia inhibitory factor (LIF). Although there has been a great advance since their establishment, ESC culture is still complex and expensive. Therefore, finding culture conditions that maintain the self-renewal of ESCs, preventing their differentiation and promoting their proliferation, is still an area of great interest. In this work, we studied the effects of the conditioned medium from a bovine granulosa cell line (BGC-CM) on the maintenance of self-renewal and pluripotency of mESCs. We found that this medium is able to maintain mESCs' self-renewal while preserving its critical properties without LIF addition. mESCs cultured in BGC-CM expressed the stem cell markers Oct4, Sox2, Nanog, SSEA-1, Klf4, Rex1, and ECAT1. Moreover, mESCs cultured in BGC-CM gave rise to embryoid bodies and teratomas that differentiated effectively to diverse cell populations from endoderm, mesoderm, and ectoderm. Further, we found that mESCs cultured in BGC-CM have an increased proliferation rate compared with cells grown in the mESC standard culture medium supplemented with LIF. These findings may provide a powerful tool to culture mESCs for long periods of time with high proliferation rate while preserving its basic characteristics, contributing to the application of these cells to assess potential tissue engineering and cellular therapy applications.
Nanostructured Materials Generated by High-Intensity Ultrasound:  Sonochemical Synthesis and Catalytic Studies (1996)

The sonochemical decomposition of volatile organometallic compounds produces high surface area solids that consist of agglomerates of nanometer clusters. For iron pentacarbonyl and tricarbonylnitrosylcobalt, nanostructured metals and alloys are formed; for molybdenum hexacarbonyl, the metal carbide is produced. These sonochemically produced nanostructured solids are active heterogeneous catalysts for hydrocarbon re-forming and CO hydrogenation. The sonochemical synthesis, characterization, and catalytic studies will be discussed in this review.
Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis. (1995)

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.
Enhanced Bacterial Protein Expression During Auto-Induction Obtained by Alteration of Lac Repressor Dosage and Medium Composition (2007)

The auto-induction method of protein expression in E. coli is based on diauxic growth resulting from dynamic function of lac operon regulatory elements (lacO and LacI) in mixtures of glucose, glycerol, and lactose. The results show that successful execution of auto-induction is strongly dependent on the plasmid promoter and repressor construction, on the oxygenation state of the culture, and on the composition of the auto-induction medium. Thus expression hosts expressing high levels of LacI during aerobic growth exhibit reduced ability to effectively complete the auto-induction process. Manipulation of the promoter to decrease the expression of LacI altered the preference for lactose consumption in a manner that led to increased protein expression and partially relieved the sensitivity of the auto-induction process to the oxygenation state of the culture. Factorial design methods were used to optimize the chemically defined growth medium used for expression of two model proteins, Photinus luciferase and enhanced green fluorescent protein, including variations for production of both unlabeled and selenomethionine-labeled samples. The optimization included studies of the expression from T7 and T7-lacI promoter plasmids and from T5 phage promoter plasmids expressing two levels of LacI. Upon the basis of the analysis of over 500 independent expression results, combinations of optimized expression media and expression plasmids that gave protein yields of greater than 1000 mug/mL of expression culture were identified.
Microwave Drying of Corn III. Constant Power, Intermittent Operation (1992)

In drying corn, intermittent microwave operation reduced energy loss through flowing air, and the energy requirement was lower than when similar levels of microwave power were applied continuously. Time for drying increased with intermittent operation, but the total duration of power application was less than for comparable drying in the continuous mode. Substantial reductions in energy loss were thereby achieved. Dried corn quality under the drying conditions studied did not meet seed certification standards; however, the data indicate that it may be possible to obtain seed quality corn using a 5/15 min duty cycle at 0.50 W/g absorbed power.
New Front To Back-side 3D Interconnects Based High Aspect Ratio Through Silicon Vias (2008)

This paper describes a new front to back-side metallization process for 3D interconnect applications that require high aspect ratio through silicon vias (TSVs). A new bottom-up copper electroplating process is used to achieve a high aspect ratio vias of 15. First, a local sealing method is used in order to attain 80% of the vias filling with copper. Then a 're-fill' process is used for complete feedthrough metallization. By optimizing the process steps, cross-Kelvin structures based TSVs are implemented on both sides of the wafer and connected together without the need of a chemical mechanical polishing step. A very low Kelvin resistance (25m¿) is measured indicating that the process presented here is suitable for advanced 3D interconnects that requires fast signal transmission.
Conventional vs. newer antipsychotics in elderly patients. (1999)

Elderly patients with schizophrenia and dementia patients with agitation are frequently candidates for antipsychotic treatment. Conventional neuroleptics have relatively little effect on negative symptoms and may cause considerable side effects, especially in elderly patients. The authors have found a 29% cumulative annual incidence of tardive dyskinesia (TD) in middle-aged and elderly outpatients treated with relatively low doses of conventional neuroleptics Newer antipsychotics are less likely to cause extrapyramidal symptoms and may be associated with a lower risk of TD. They are generally effective for both positive and negative symptoms and may also improve some aspects of cognition, but these drugs have their own side effects. Dosing requirements for elderly patients tend to be much lower than those for younger adults.
Gang scheduling performance on a cluster of non-dedicated workstations (2003)

Clusters of workstations have emerged as a cost effective solution to the high performance computing problem. To take advantage of any opportunities, however, effective scheduling techniques are necessary that enable parallel applications to dynamically share workstations with their owners. In this paper a special type of parallel applications called gangs are considered. Gangs are jobs that consist of a number of interacting tasks scheduled to run simultaneously on separate and distinct processors. A simulation model is used to address performance issues associated with gang scheduling on a non-dedicated workstation cluster for various workloads. Simulated results indicate that the relative performance of the gang scheduling policies that we examine depends on the workload characteristics.