gebhart/patrepeval huggingface dataset:
p16INK4a Expression and Immunologic Aging in Chronic HIV Infection (2016)

Chronic HIV infection is characterized by increased immune activation and immunosenescence. p16 INK4a (p16) is a member of the cyclin-dependent kinase antagonist family that inhibits cellular proliferation, and its protein expression increases during normal chronological aging. However, some infectious diseases can increase the expression of this anti-proliferative protein, potentially accelerating immunological aging and dysfunction. In order to investigate the immunological aging in HIV patients, p16 protein expression was evaluated by flow cytometry, in T cell subsets in a cohort of chronically HIV-infected patients on and off ART as well as age-matched healthy controls. Results showed that untreated HIV-infected subjects exhibited increased per-cell p16 protein expression that was discordant with chronological aging. ART restored p16 protein expression to levels comparable with HIV-negative subjects in the CD4 compartment, but not in CD8 T cells, which can be an indicative of an irreversible activation/exhaustion status on these cells. Additionally, the frequency of activated CD4+ and CD8+ T cells was positively correlated with p16 expression in CD4+ and CD8+ T cells in untreated subjects. In contrast to healthy controls, untreated HIV-infected individuals had increased p16 levels within the effector memory (TEM) subset, indicating a possible role for this marker in impaired clonal expansion during antiviral effector function. Taken together, these data demonstrate that chronic HIV infection is associated with elevated expression of the cellular aging marker p16 in T cells. ART restored normal p16 levels in the CD4+ T cell compartment, indicating that use of therapy can be of fundamental importance to normal cell cycling and maintaining immune homeostasis.
Maximum mutual information vector quantization (2002)

A method is proposed for designing a maximum mutual information (MMI) vector quantizer, for applications in which quantization is used to extract a set of discrete features for use in classification.
Comparison of multiple vaccine vectors in a single heterologous prime-boost trial (2020)

The prevention of infectious disease via prophylactic immunization is a mainstay of global public health efforts. Vaccine design would be facilitated by a better understanding of the type and durability of immune responses generated by different vaccine vectors. We report here the results of a comparative immunogenicity trial of six different vaccine vectors expressing the same insert antigen, cowpox virus B5 (CPXV-B5). Of those vectors tested, recombinant adenovirus (rAd5) was the most immunogenic, inducing the highest titer anti-B5 antibodies and conferring protection from sublethal vaccinia virus challenge in mice after a single immunization. We tested select heterologous prime-boost combinations and identified recombinant vesicular stomatitis virus (rVSV) and recombinant Venezuelan equine encephalitis virus replicons (VRP) as the most synergistic regimen. Comparative data such as those presented here are critical to efforts to generate protective vaccines for emerging infectious diseases as well as for biothreat agents.
Figure S1 from Genetic Variants of <i>VEGFA</i> and <i>FLT4</i> Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib (2023)

&lt;p&gt;Study schematic for patients genotyped in this study.&lt;/p&gt;
Performance evaluation of FIR sensor systems applied to pedestrian detection (2010)

Besides resolution, an important performance parameter of a FIR camera is the sensitivity. It depends on the sensitivity of the detector array itself and the characteristics of the optic. The effects of the optic are considerably driven by the f-number, with high values resulting in decreased sensitivity, but providing the possibility for simple lens design and cheaper production costs. In this contribution 4 different sensor setups with different optics are evaluated for their impact on the performance of trained pedestrian classifiers. To overcome the expensive and time consuming process of ground truth generation for multiple sensors, an approach for reusing available high sensitivity reference data is presented. Classifiers are trained on specially transformed reference data with characteristics of sensors with degraded sensitivity. For the evaluation of the classifiers, data of real world road scenarios is collected simultaneously with the target sensors mounted in parallel in a test vehicle, following a detailed script for recording a pedestrian scene test catalogue. This allows for a direct analysis and comparison of the different sensors and their impact on the detection performance.
Improving the knowledge of integration of medical devices in bone : a comparison of 3D STμCT data to histomorphometrical data obtained on cut and ground sections (2007)

Improving the knowledge of integration of medical devices in bone : a comparison of 3D STμCT data to histomorphometrical data obtained on cut and ground sections
Quantum dot assisted tracking of the intracellular protein Cyclin E in Xenopus laevis embryos (2015)

These studies provide "proof-of-concept" for this approach by tracking QD-tagged Cyclin E within cells of developing embryos, before and during an important developmental period, the midblastula transition. Importantly, we show that the attachment of QD to Cyclin E did not disrupt its proper intracellular distribution prior to and during the midblastula transition. The fate of the QD after cyclin E degradation following the midblastula transition remains unknown.
Surface Passivation of Nanoporous TiO2 via Atomic Layer Deposition of ZrO2 for Solid-State Dye-Sensitized Solar Cell Applications (2009)

We report here the utilization of atomic layer deposition to passivate surface trap states in mesoporous TiO2 nanoparticles for solid-state dye-sensitized solar cells based on 2,2′,7,7′-tetrakis(N,N-di-p-methoxyphenylamine)-9,9′-spirobifluorene (spiro-OMeTAD). By depositing ZrO2 films with angstrom-level precision, coating the mesoporous TiO2 produces over a two-fold enhancement in short-circuit current density, as compared to a control device. Impedance spectroscopy measurements provide evidence that the ZrO2 coating reduces recombination losses at the TiO2/spiro-OMeTAD interface and passivates localized surface states. Low-frequency negative capacitances, frequently observed in nanocomposite solar cells, have been associated with the surface-state mediated charge transfer from TiO2 to the spiro-OMeTAD.
A Single-Stage, Single-Inductor, 6-Input 9-Output Multi-Modal Energy Harvesting Power Management IC for 100µW-120MW Battery-Powered IoT Edge Nodes (2018)

A 25MHz switching, event driven, 6-input and 9-output single inductor Energy-Harvesting PMIC (EHPMIC) with multi-modal harvesting capability from DC & AC sources delivers up to 120mW with a peak efficiency of 81.7% and only 120µW control power overhead. The high-frequency, high-bandwidth design optimally trades off EHPMIC conversion efficiency with inductor/capacitor size & transient response speed to enable the fast power state transitions demanded by the SoC in a compact IoT edge node, thus minimizing the overall platform size & energy consumption.
The p38 MAPK pathway inhibits tristetraprolin‐directed decay of interleukin‐10 and pro‐inflammatory mediator mRNAs in murine macrophages (2009)

p38 mitogen-activated protein kinase (MAPK) stabilises pro-inflammatory mediator mRNAs by inhibiting AU-rich element (ARE)-mediated decay. We show that in bone-marrow derived murine macrophages tristetraprolin (TTP) is necessary for the p38 MAPK-sensitive decay of several pro-inflammatory mRNAs, including cyclooxygenase-2 and the novel targets interleukin (IL)-6, and IL-1alpha. TTP(-/-) macrophages also strongly overexpress IL-10, an anti-inflammatory cytokine that constrains the production of the IL-6 despite its disregulation at the post-transcriptional level. TTP directly controls IL-10 mRNA stability, which is increased and insensitive to inhibition of p38 MAPK in TTP(-/-) macrophages. Furthermore, TTP enhances deadenylation of an IL-10 3'-untranslated region RNA in vitro.
Automated Generation and Selection of Interpretable Features for Enterprise Security (2018)

We present an effective machine learning method for malicious activity detection in enterprise security logs. Our method involves feature engineering, or generating new features by applying operators on features of the raw data. We generate DNF formulas from raw features, extract Boolean functions from them, and leverage Fourier analysis to generate new parity features and rank them based on their highest Fourier coefficients. We demonstrate on real enterprise data sets that the engineered features enhance the performance of a wide range of classifiers and clustering algorithms. As compared to classification of raw data features, the engineered features achieve up to 50.6% improvement in malicious recall, while sacrificing no more than 0.47% in accuracy. We also observe better isolation of malicious clusters, when performing clustering on engineered features. In general, a small number of engineered features achieve higher performance than raw data features according to our metrics of interest. Our feature engineering method also retains interpretability, an important consideration in cyber security applications.
Nanoparticle‐Enabled Dual Modulation of Phagocytic Signals to Improve Macrophage‐Mediated Cancer Immunotherapy (2020)

Activation of the phagocytosis of macrophages to tumor cells is an attractive strategy for cancer immunotherapy, but the effectiveness is limited by the fact that many tumor cells express an increased level of anti-phagocytic signals (e.g., CD47 molecules) on their surface. To promote phagocytosis of macrophages, a pro-phagocytic nanoparticle (SNPA<sub>CALR&aCD47</sub> ) that concurrently carries CD47 antibody (aCD47) and a pro-phagocytic molecule calreticulin (CALR) is constructed to simultaneously modulate the phagocytic signals of macrophages. SNPA<sub>CALR&aCD47</sub> can achieve targeted delivery to tumor cells by specifically binding to the cell-surface CD47 and block the CD47-SIRPα pathway to inhibit the "don't eat me" signal. Tumor cell-targeted delivery increases the exposure of recombinant CALR on the cell surface and stimulates an "eat me" signal. Simultaneous modulation of the two signals enhances the phagocytosis of 4T1 tumor cells by macrophages, which leads to significantly improved anti-tumor efficacy in vivo. The findings demonstrate that the concurrent blockade of anti-phagocytic signals and activation of pro-phagocytic signals can be effective in macrophage-mediated cancer immunotherapy.
Can traditional programming bridge the Ninja performance gap for parallel computing applications? (2012)

Current processor trends of integrating more cores with wider SIMD units, along with a deeper and complex memory hierarchy, have made it increasingly more challenging to extract performance from applications. It is believed by some that traditional approaches to programming do not apply to these modern processors and hence radical new languages must be discovered. In this paper, we question this thinking and offer evidence in support of traditional programming methods and the performance-vs-programming effort effectiveness of common multi-core processors and upcoming many-core architectures in delivering significant speedup, and close-to-optimal performance for commonly used parallel computing workloads. We first quantify the extent of the " Ninja gap ", which is the performance gap between naively written C/C++ code that is parallelism unaware (often serial) and best-optimized code on modern multi-/many-core processors. Using a set of representative throughput computing benchmarks, we show that there is an average Ninja gap of 24X (up to 53X ) for a recent 6-core Intel® Core™ i7 X980 Westmere CPU, and that this gap if left unaddressed will inevitably increase. We show how a set of well-known algorithmic changes coupled with advancements in modern compiler technology can bring down the Ninja gap to an average of just 1.3X . These changes typically require low programming effort, as compared to the very high effort in producing Ninja code. We also discuss hardware support for programmability that can reduce the impact of these changes and even further increase programmer productivity. We show equally encouraging results for the upcoming Intel® Many Integrated Core architecture (Intel® MIC) which has more cores and wider SIMD. We thus demonstrate that we can contain the otherwise uncontrolled growth of the Ninja gap and offer a more stable and predictable performance growth over future architectures, offering strong evidence that radical language changes are not required.
A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data (2005)

Transcriptional regulation is one of the most important means of gene regulation. Uncovering transcriptional regulatory networks helps us to understand the complex cellular process. In this paper, we describe a statistical approach for constructing transcriptional regulatory networks using data of gene expression, promoter sequence, and transcription factor binding sites. Our simulation studies show that the overall and false positive error rates in the estimated transcriptional regulatory networks are expected to be small if the systematic noise in the constructed feature matrix is small. Our analysis based on 658 microarray experiments on yeast gene expression programs and 46 transcription factors suggests that the method is capable of identifying significant transcriptional regulatory interactions and uncovering the corresponding regulatory network structures.
Genetic deletion of an instability motif in the Tristetraprolin (TTP) transcript increases TTP mRNA stability and protein expression and provides protection against inflammatory diseases (2015)

Objective Tristetraprolin (TTP) is an mRNA binding protein that binds to AU‐rich elements (AREs) in the 3′‐untranslated regions (3′UTR) of specific mRNAs, such as tumor necrosis factor (TNF) mRNA, and increases their rates of deadenylation and turnover. TTP mRNA also contains AREs within its own 3′UTR that are partly responsible for its own instability. The objective of this study was to test the hypothesis that increased TTP mRNA stability, and the resulting increased TTP protein expression, may provide protection against inflammatory diseases. Results Using knock‐in technology, a novel TTP mouse line (TTPΔARE) was generated in which 136 bases in the 3′UTR AU‐rich region of TTP mRNA were deleted. TTPΔARE mice developed and reproduced normally, and exhibited no phenotypic or histopathological abnormalities. TTP mRNA stability was found to be significantly enhanced in bone marrow‐derived macrophages (BMDMs) and mouse embryonic fibroblasts (MEFs) isolated from TTPΔARE mice. Moreover, TTP protein expression was increased in unstimulated and LPS‐stimulated BMDMs, and in various mouse tissues. In addition, LPS‐induced expression of TTP target mRNAs, particularly TNF and Il‐1β mRNAs, was significantly reduced in TTPΔARE BMDMs. TTPΔARE mice exhibited reduced skin inflammation in an experimental model of psoriasis, and were completely protected from collagen antibody‐induced arthritis. Conclusions Our data demonstrate that modestly increased levels of TTP in mouse cells and tissues are protective against certain inflammatory disease models. These data may have implications for the development of therapeutic strategies to target chronic inflammatory diseases via enhancing TTP expression.
Heterologous Expression of the Pathogen-Specific LIC11711 Gene in the Saprophyte L. biflexa Increases Bacterial Binding to Laminin and Plasminogen (2020)

Leptospirosis is a febrile disease and the etiological agents are pathogenic bacteria of the genus <i>Leptospira</i>. The leptospiral virulence mechanisms are not fully understood and the application of genetic tools is still limited, despite advances in molecular biology techniques. The leptospiral recombinant protein LIC11711 has shown interaction with several host components, indicating a potential function in virulence. This study describes a system for heterologous expression of the <i>L. interrogans</i> gene <i>lic11711</i> using the saprophyte <i>L. biflexa</i> serovar Patoc as a surrogate, aiming to investigate its possible activity in bacterial virulence. Heterologous expression of LIC11711 was performed using the pMaOri vector under regulation of the <i>lipL32</i> promoter. The protein was found mainly on the leptospiral outer surface, confirming its location. The <i>lipL32</i> promoter enhanced the expression of LIC11711 in <i>L. biflexa</i> compared to the pathogenic strain, indicating that this strategy may be used to overexpress low-copy proteins. The presence of LIC11711 enhanced the capacity of <i>L. biflexa</i> to adhere to laminin (Lam) and plasminogen (Plg)/plasmin (Pla) in vitro, suggesting the involvement of this protein in bacterial pathogenesis. We show for the first time that the expression of LIC11711 protein of <i>L. interrogans</i> confers a virulence-associated phenotype on <i>L. biflexa</i>, pointing out possible mechanisms used by pathogenic leptospires.
High resolution ADC system (1997)

We have developed and verified experimentally a novel high-resolution superconducting ADC architecture based on phase modulation/demodulation principle and implemented in RSFQ logic. We have demonstrated an ADC chip providing full implementation of this architecture, including on-chip decimation filter and multiple-channel synchronizer. We have also developed a digital ADC evaluation system consisting of an interface electronics block converting the low-voltage ADC output to standard TTL form at multi-MHz sampling rate, and a computerized test station performing data acquisition, processing and display in real time. Using this system we have demonstrated that for low-frequency (kHz) signals our ADC chips possess linearity in excess of 16 bits with Spur-Free Dynamic Range over 108 dB, which is an important benchmark for any high-resolution ADC technology.
Independent drive of integrated multicolor (RGBY) micro-LED array using regularly arrayed InGaN based nanocolumns (2017)

We demonstrate monolithic integration of blue-, green-, yellow-, and red-emitting micro light emitting diodes (LEDs) and their independent drive using matrix wiring electrodes. The four-color (RGBY) micro-LEDs are prepared on the same template by using regularly arrayed InGaN based nanocolumns with different column diameters and periods via selective area growth.
Thallium Bromide Gamma-Ray Spectrometers and Pixel Arrays (2020)

Thallium bromide (TlBr) is a compound semiconductor with a band gap of 2.68 eV making it ideal for room temperature radiation detection. The high atomic numbers, 81 and 35, and the high density of 7.56 g/cm3 give it excellent gamma-ray stopping power. TlBr is a cubic material that melts congruently at a relatively low temperature (~ 480 C). These properties make it relatively easy to grow good quality crystals with high yield. As a result of improvements in the purification of TlBr mobility-lifetime product of electrons, µτe, is now on the order of 10-2 cm2/V, which is similar to that of CZT. High µτe enables the fabrication of thicker detectors with good charge collection and energy resolution. The properties of TlBr make it ideal for use in room temperature gamma radiation operation [Smith 2013]. Single carrier devices such as small pixel arrays [O'Neal 2018a] and Frisch collar devices [Hitomi, et al.2013] which were developed for CZT can also been applied to TlBr. For example, better than 1% FWHM at 662 keV has been obtained for single pixel events with small (e.g. 3 x 3 pixels, 1-mm pitch, 5-mm thick) arrays.
A wireless multi-drop IPT security camera system (2009)

This paper presents the design of an IPT security camera system with the integration of a secure wireless communication scheme. Two innovative circuits known as an LCL tuning circuit and a multi-phase interleaving system have been applied to the design of the IPT pick-up circuit. A wireless local area network (WLAN) using 802.11 g protocol has been chosen to realise the high bandwidth communication scheme which supports multiple cameras to operate simultaneously to form a multi-drop configuration. An experimental prototype has been built to verify the proposed concept.
12-watt single-mode Yb<sup>3+</sup>-doped phosphate fiber laser (2006)

We report the first continuous-wave Yb <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> +-doped phosphate fiber laser. 12 W of diffraction-limited, 1.06-mum power was generated from a 71-cm length of double-clad fiber with 34 W of absorbed pump power.
The Relation Between Coloring and Bleaching with Lithium in Tungsten Oxide Based Electrochromic Devices: Step Current Analysis (1997)

An analysis of Li‐intercalation and deintercalation in a tungsten‐oxide based electrochromic device is presented. An hysteresis between intercalation and deintercalation has been separately observed in both the built‐in potential and the optical efficiency of the devices. This hysteresis is explained by a two‐phase model in which intercalation occurs as the parallel, equipotential filling of the two phases, but where a deintercalation barrier associated with one of the phases imposes the observed asymmetry. An equivalent circuit model is given, allowing for the prediction of the deintercalation behavior from the intercalation behavior with a single adjustable parameter (representing the deintercalation barrier). The observed data are well‐explained by the circuit model; using a single adjustable parameter, an accurate description of the deintercalation behavior may be obtained from the data on intercalation.
In-plane optical anisotropy in self-assembled Ge quantum dots induced by interfacial chemical bonds (2007)

In-plane optical anisotropy has been observed in self-assembled Ge quantum dots (QDs). It is found that the photoluminescence (PL) spectrum polarized along [110] exhibits different features compared to that corresponding to [11¯0]. Besides, the polarized PL spectrum is able to reveal a detailed fine structure much more pronounced than that in the unpolarized spectrum. It is shown that the observed optical anisotropy is a result of the inherent property of the type-II band alignment of Ge QDs embedded in Si matrix. The light emission arises from the recombination of electrons and holes across the interface, and it thus reflects the anisotropic nature of the interfacial chemical bonds.
Luminescent Silicon Nanocrystals as Downconverters for Photovoltaic and Lighting Applications (2016)

Nanocrystals offer new functionalities for optoelectronics. Ensemble and single-dot measurements of chemically-synthesized silicon nanocrystals revealed high quantum yield, narrow homogeneous linewidth, and large Stokes shift, confirming application feasibility for these non-toxic and abundant material nanoparticles.
Experimental transfusion of variant CJD-infected blood reveals previously uncharacterised prion disorder in mice and macaque (2017)

Exposure of human populations to bovine spongiform encephalopathy through contaminated food has resulted in <250 cases of variant Creutzfeldt-Jakob disease (vCJD). However, more than 99% of vCJD infections could have remained silent suggesting a long-term risk of secondary transmission particularly through blood. Here, we present experimental evidence that transfusion in mice and non-human primates of blood products from symptomatic and non-symptomatic infected donors induces not only vCJD, but also a different class of neurological impairments. These impairments can all be retransmitted to mice with a pathognomonic accumulation of abnormal prion protein, thus expanding the spectrum of known prion diseases. Our findings suggest that the intravenous route promotes propagation of masked prion variants according to different mechanisms involved in peripheral replication.