gebhart/patrepeval huggingface dataset:
Process Implanting: A New Active Introspection Framework for Virtualization (2011)

Previous research on virtual machine introspection proposed "out-of-box" approach by moving out security tools from the guest operating system. However, compared to the traditional "in-the-box" approach, it remains a challenge to obtain a complete semantic view due to the semantic gap between the guest VM and the hyper visor. In this paper, we present Process Implanting, a new active VM introspection framework, to narrow the semantic gap by implanting a process from the host into the guest VM and executing it under the cover of an existing running process. With the protection and coordination from the hyper visor, the implanted process can run with a degree of stealthiest and exit gracefully without leaving negative impact on the guest operating system. We have designed and implemented a proof-of-concept prototype on KVM which leverages hardware virtualization. We also propose and demonstrate application scenarios for Process Implanting in the area of VM security.
The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms (2015)

Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters.
Solution Structure of a Calmodulin-Binding Domain in the Carboxy-Terminal Region of HIV Type 1 gp160 (2008)

The cytosolic domain of human immunodeficiency virus gp160 glycoprotein contains two calmodulin-binding regions. The role of these domains in modulating intracellular calmodulin signaling is of considerable interest in unraveling the mechanism whereby calmodulin regulates Fas-mediated apoptosis in HIV-infected cells. In this investigation we have employed 2D-NMR spectroscopy to determine the solution structure of the 30-residue calmodulin-binding domain corresponding to residues 826-855 of gp160. In solution, the gp160 (826-855) peptide exhibits a high degree of segmental flexibility. Within its conformational manifold, we have detected two separate flexible amphipathic helices involving residues 826-841 and 846-855 connected by a highly flexible type-II beta-turn at Pro-843 and Arg-844. The observed NOE pattern as well as the observation of long-range NOE contacts between the side chains of His-841 and Ile-846 are compatible with the presence of this turn in the conformational manifold of this peptide. This investigation focusing on the properties of the free peptide in solution paves the way for extending the investigations on the interaction of calmodulin with HIV-1 gp160.
Accuracy and Reliability of the Kinect Version 2 for Clinical Measurement of Motor Function (2016)

Given that this system is low-cost, portable and does not require any sensors to be attached to the body, it could provide numerous advantages when compared to established marker- or wearable sensor based system. The Kinect V2 has the potential to be used as a reliable and valid clinical measurement tool.
MysiRNA-Designer: A Workflow for Efficient siRNA Design (2011)

The design of small interfering RNA (siRNA) is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based) desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.
Plasma Ouabain-Like Factor During Acute and Chronic Changes in Sodium Balance in Essential Hypertension (2001)

An ouabain-like factor has been implicated repeatedly in salt-sensitive hypertension as a natriuretic agent. However, the response of plasma ouabain-like factor to acute and chronic variation of body sodium is unclear. We studied 138 patients with essential hypertension who underwent an acute volume expansion/contraction maneuver (2 days) and 20 patients who entered a blind randomized crossover design involving chronically controlled sodium intake and depletion (170 to 70 mmol/d; 2 weeks each period). In both studies, plasma levels of ouabain-like factor were higher during sodium depletion (acute: 338.8+/-17.4 and 402.7+/-22.8 pmol/L for baseline and low sodium, respectively, P<0.01; chronic: 320.4+/-32.0 versus 481.0+/-48.1 pmol/L, P=0.01). No significant change in plasma ouabain-like factor was observed after a 2-hour saline infusion (333.4+/-23.9 pmol/L) or controlled sodium (402.1+/-34.9 pmol/L). When patients were divided into salt-sensitive or salt-resistant groups, no differences in plasma ouabain-like factor were observed in the 2 groups at baseline or in response to the 2 protocols: salt resistant (n=69, 340.1+/-25.9 pmol/L) versus salt sensitive (n=69, 337.4+/-23.6 pmol/L) and chronic salt resistant (n=11, 336.0+/-53.2) versus salt sensitive (n=9, 301.1+/-331.4 pmol/L). However, circulating ouabain-like factor was increased by sodium depletion in both groups. These results demonstrate that circulating ouabain-like factor is raised specifically by maneuvers that promote the loss of body sodium. Acute expansion of body fluids with isotonic saline is not a stimulus to plasma ouabain-like factor. Moreover, basal levels of plasma ouabain-like factor do not differ among patients with salt-sensitive or salt-resistant hypertension. Taken together, these new results suggest that ouabain-like factor is involved in the adaptation of humans to sodium depletion and argue against the hypothesis that ouabain-like factor is a natriuretic hormone.
The NRF2-KEAP1 Pathway Is an Early Responsive Gene Network in Arsenic Exposed Lymphoblastoid Cells (2014)

Inorganic arsenic (iAs), a major environmental contaminant, has risen as an important health problem worldwide. More detailed identification of the molecular mechanisms associated with iAs exposure would help to establish better strategies for prevention and treatment. Although chronic iAs exposures have been previously studied there is little to no information regarding the early events of exposure to iAs. To better characterize the early mechanisms of iAs exposure we conducted gene expression studies using sublethal doses of iAs at two different time-points. The major transcripts differentially regulated at 2 hrs of iAs exposure included antioxidants, detoxificants and chaperones. Moreover, after 12 hrs of exposure many of the down-regulated genes were associated with DNA replication and S phase cell cycle progression. Interestingly, the most affected biological pathway by both 2 or 12 hrs of iAs exposure were the Nrf2-Keap1 pathway, represented by the highly up-regulated HMOX1 transcript, which is transcriptionally regulated by the transcription factor Nrf2. Additional Nrf2 targets included SQSTM1 and ABCB6, which were not previously associated with acute iAs exposure. Signalling pathways such as interferon, B cell receptor and AhR route were also responsive to acute iAs exposure. Since HMOX1 expression increased early (20 min) and was responsive to low iAs concentrations (0.1 µM), this gene could be a suitable early biomarker for iAs exposure. In addition, the novel Nrf2 targets SQSTM1 and ABCB6 could play an important and previously unrecognized role in cellular protection against iAs.
Beyond the lock icon: real-time detection of phishing websites using public key certificates (2015)

We propose a machine-learning approach to detect phishing websites using features from their X.509 public key certificates. We show that its efficacy extends beyond HTTPS-enabled sites. Our solution enables immediate local identification of phishing sites. As such, this serves as an important complement to the existing server-based anti-phishing mechanisms which predominately use blacklists. Blacklisting suffers from several inherent drawbacks in terms of correctness, timeliness, and completeness. Due to the potentially significant lag prior to site blacklisting, there is a window of opportunity for attackers. Other local client-side phishing detection approaches also exist, but primarily rely on page content or URLs, which are arguably easier to manipulate by attackers. We illustrate that our certificate-based approach greatly increases the difficulty of masquerading undetected for phishers, with single millisecond delays for users. We further show that this approach works not only against HTTPS-enabled phishing attacks, but also detects HTTP phishing attacks with port 443 enabled.
Molecular characterization of a somatically mutated anti-DNA antibody bearing two systemic lupus erythematosus-related idiotypes. (1990)

We report the molecular characterization of 2A4, an IgG, DNA-binding antibody bearing the 3I and F4 idiotypes which are associated with anti-DNA antibodies in serum of patients with systemic lupus erythematosus (SLE). The antibody is produced by an EBV-transformed B cell line derived from a patient with multiple myeloma whose myeloma protein is also an IgG, 3I-reactive, F4-reactive, DNA-binding immunoglobulin, although the 2A4 antibody does not itself represent the myeloma protein. The 2A4 heavy chain is encoded by a VH4 gene, a D-D gene fusion and the JH6 gene; the light chain is derived from a Vk1 gene and the Jk2 gene. This is the first human antibody shown to have a CDR3 encoded by a D-D fusion. DNA sequence analysis of the 2A4 VH gene together with a Southern blot of genomic DNA probed with a 2A4 VH-specific oligonucleotide strongly suggest it to be somatically mutated. The data provide evidence that human autoantibodies can be products of somatically mutated genes and suggest that the 2A4 antibody may reflect the selective pressure of antigen.
Modulation of cardiac tissue electrophysiological properties with light-sensitive proteins (2014)

The results of this proof-of-concept study highlight the unique potential of optogenetics for future biological pacemaking and resynchronization therapy applications and for the development of novel anti-arrhythmic strategies.
Photodissociation of CO2− in water clusters via Renner-Teller and conical interactions (2007)

The photochemistry of mass selected CO(2) (-)(H2O)(m), m=2-40 cluster anions is investigated using 266 nm photofragment spectroscopy and theoretical calculations. Similar to the previous 355 nm experiment [Habteyes et al., Chem. Phys. Lett. 424, 268 (2006)], the fragmentation at 266 nm yields two types of anionic products: O(-)(H2O)(m-k) (core-dissociation products) and CO(2) (-)(H2O)(m-k) (solvent-evaporation products). Despite the same product types, different electronic transitions and dissociation mechanisms are implicated at 355 and 266 nm. The 355 nm dissociation is initiated by excitation to the first excited electronic state of the CO(2) (-) cluster core, the 1 (2)B(1)(2A") state, and proceeds via a glancing Renner-Teller intersection with the ground electronic state at a linear geometry. The 266 nm dissociation involves the second excited electronic state of CO(2) (-), the 2 (2)A(1)(2A') state, which exhibits a conical intersection with the 3 (2)B(2)(A') state at a bent geometry. The asymptotic O(-) based products are believed to be formed via this 3 (2)B(2)(A') state. By analyzing the fragmentation results, the bond dissociation energy of CO(2) (-) to O(-)+CO in hydrated clusters (m> or =20) is estimated as 2.49 eV, compared to 3.46 eV for bare CO(2) (-). The enthalpy of evaporation of one water molecule from asymptotically large CO(2) (-)(H(2)O)(m) clusters is determined to be 0.466+/-0.001 eV (45.0+/-0.1 kJ/mol). This result compares very favorably with the heat of evaporation of bulk water, 0.456 eV (43.98 kJ/mol).
Development of a Navigation System Using Smartphone and Bluetooth Technologies to Help the Visually Impaired Navigate Work Zones Safely (2014)

According to statistics from the Federal Highway Administration (FHWA), each year approximately 17% of all work zone fatalities are pedestrians. People who are visually impaired often encounter physical and information barriers that limit their accessibility and mobility. A survey was conducted among 10 visually impaired participants as a starting point to understand their challenges and what types of information are helpful in providing bypass or routing instructions to them around work zones. The survey results were incorporated into development of guiding documents in determining information elements that are essential and useful for providing routing instructions to the visually impaired around work zones. Building on our previous efforts to provide geometry and signal timing to the visually impaired at signalized intersections, a smartphone-based navigation system was developed and integrated with navigational audible information to alert pedestrians at decision points prior to their arrival at a work zone. The recommended message elements from survey results were implemented in a smartphone app that uses GPS and Bluetooth technologies to determine a user’s location. When a work zone is detected, the smartphone will vibrate to alert users and the app will then announce a corresponding audible message to users. The visually impaired users can perform a single tap on the smartphone to repeat the messages, if needed. Functionality testing and system validation of the smartphone app were performed by attaching four Bluetooth beacons to light posts near a construction site in St. Paul, MN. Additional research is needed to conduct experiments with visually impaired users and evaluate system reliability and usefulness.
Chemical Vapor Deposition of TiSi Nanowires on C54 TiSi<sub>2</sub> Thin Film: An Amorphous Titanium Silicide Interlayer Assisted Nanowire Growth (2009)

A C54-TiSi2 film was grown on a Si substrate at 1073 K by low pressure chemical vapor deposition (LPCVD) employing titanium subchlorides TiClx(g), generated by reacting between TiCl4(g) and Ti(s) at 1173 K, as the Ti source. Growth of titanium silicide (TiSi) nanowires (NWs; diameter 30−80 nm, length several micrometers) on a C54-TiSi2 film was observed. Growth direction of the NWs was determined to be along the [010] axis. An amorphous titanium silicide interlayer was observed between the NWs and the C54-TiSi2 film. This interlayer, probably existing as a quasi-liquid thin film during the growth, appears to be the key factor to assist the NW development. Field emission properties, turn-on field Eo and field enhancement factor β, of the vertically grown TiSi NWs were determined to be 5.25 V μm−1 and 876, respectively.
The role of iron in anthracycline cardiotoxicity (2014)

The clinical use of the antitumor anthracycline Doxorubicin is limited by the risk of severe cardiotoxicity. The mechanisms underlying anthracycline-dependent cardiotoxicity are multiple and remain uncompletely understood, but many observations indicate that interactions with cellular iron metabolism are important. Convincing evidence showing that iron plays a role in Doxorubicin cardiotoxicity is provided by the protecting efficacy of iron chelation in patients and experimental models, and studies showing that iron overload exacerbates the cardiotoxic effects of the drug, but the underlying molecular mechanisms remain to be completely characterized. Since anthracyclines generate reactive oxygen species, increased iron-catalyzed formation of free radicals appears an obvious explanation for the aggravating role of iron in Doxorubicin cardiotoxicity, but antioxidants did not offer protection in clinical settings. Moreover, how the interaction between reactive oxygen species and iron damages heart cells exposed to Doxorubicin is still unclear. This review discusses the pathogenic role of the disruption of iron homeostasis in Doxorubicin-mediated cardiotoxicity in the context of current and future pharmacologic approaches to cardioprotection.
Contribution of Leydig and Sertoli Cells to Testosterone Production in Mouse Fetal Testes (2012)

Testosterone is a final product of androgenic hormone biosynthesis, and Leydig cells are known to be the primary source of androgens. In the mammalian testis, two distinct populations of Leydig cells, the fetal and the adult Leydig cells, develop sequentially, and these two cell types differ both morphologically and functionally. It is well known that the adult Leydig cells maintain male reproductive function by producing testosterone. However, it has been controversial whether fetal Leydig cells can produce testosterone, and the synthetic pathway of testosterone in the fetal testis is not fully understood. In the present study, we generated transgenic mice in which enhanced green fluorescence protein was expressed under the control of a fetal Leydig cell-specific enhancer of the Ad4BP/SF-1 (Nr5a1) gene. The transgene construct was prepared by mutating the LIM homeodomain transcription factor (LHX9)-binding sequence in the promoter, which abolished promoter activity in the undifferentiated testicular cells. These transgenic mice were used to collect highly pure fetal Leydig cells. Gene expression and steroidogenic enzyme activities in the fetal Leydig cells as well as in the fetal Sertoli cells and adult Leydig cells were analyzed. Our results revealed that the fetal Leydig cells synthesize only androstenedione because they lack expression of Hsd17b3, and fetal Sertoli cells convert androstenedione to testosterone, whereas adult Leydig cells synthesize testosterone by themselves. The current study demonstrated that both Leydig and Sertoli cells are required for testosterone synthesis in the mouse fetal testis.
A theoretical analysis and experimental confirmation of the optimally loaded and overdriven RF power amplifier (1967)

Although the conventional Class B approach to RF amplifier design yields high output power and reasonable collector efficiency (78.5 percent at maximum output power), neither the power nor the efficiency are optimum, and both are dependent on RF drive level. This paper presents an analysis of appropriately selected collector voltage and current waveforms which determine the load impedance at the fundamental and harmonically related frequencies; these conditions define the ClassB "optimum efficiency" case with 100 percent collector efficiency and 1.27 times the conventional Class B value of output power. If the RF drive level is increased, and the collector voltage and current waveforms are appropriately selected so that the amplifier is overdriven, a different load impedance is determined; these conditions define the "optimum power" case with 1.46 times the conventional Class B value of output power and 88 percent collector efficiency. The "optimum power" case has the added advantage that the output power and collector efficiency are essentially constant over a predetermined range of drive level. Finally, the theory is verified by the construction and testing of a UHF power amplifier having a power output of 46 watts and an over-all dc to RF conversion efficiency of 65 percent with a 1 dB for 10.5- dB insensitivity of output power to RF drive.
Deep eye fixation map learning for calibration-free eye gaze tracking (2016)

The existing eye trackers typically require an explicit personal calibration procedure to estimate subject-dependent eye parameters. Despite efforts in simplifying the calibration process, such a calibration process remains unnatural and bothersome, in particular for users of personal and mobile devices. To alleviate this problem, we introduce a technique that can eliminate explicit personal calibration. Based on combining a new calibration procedure with the eye fixation prediction, the proposed method performs implicit personal calibration without active participation or even knowledge of the user. Specifically, different from traditional deterministic calibration procedure that minimizes the differences between the predicted eye gazes and the actual eye gazes, we introduce a stochastic calibration procedure that minimizes the differences between the probability distribution of the predicted eye gaze and the distribution of the actual eye gaze. Furthermore, instead of using saliency map to approximate eye fixation distribution, we propose to use a regression based deep convolutional neural network (RCNN) that specifically learns image features to predict eye fixation. By combining the distribution based calibration with the deep fixation prediction procedure, personal eye parameters can be estimated without explicit user collaboration. We apply the proposed method to both 2D regression-based and 3D model-based eye gaze tracking methods. Experimental results show that the proposed method outperforms other implicit calibration methods and achieve comparable results to those that use traditional explicit calibration methods.
Perforated Diode Fabrication for Neutron Detection (2006)

Excessive leakage current in perforated pin diodes was identified and addressed through simple changes in processing techniques. The first pulse height spectra from a perforated diode operated as a radiation detector is reported. Also, methods to load <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> LiF neutron absorbing material into deep perforations are reported.