gebhart/patrepeval huggingface dataset:
Matrix Metalloproteinases in Cerebral Hypoxia-Ischemia (2009)

Matrix metalloproteinase enzymes (MMPs) have been implicated in the pathogenesis of cerebral ischemia (stroke) and neurodegenerative diseases. Until recently, however, the mechanism of activation of MMPs in these disorders remained unclear. Following a hypoxic-ischemic insult, we identified a novel posttranslational modification (PTM) of MMPs involving S-nitrosylation (transfer of an NO group to a critical cysteine thiol) that is responsible for their activation (1). During cerebral ischemia/reperfusion in vivo, MMP-9 colocalizes with neuronal nitric oxide synthase (nNOS). In vitro, we showed that NO generated by nNOS activates the proform of MMP-9, forming S-nitrosylated MMP-9 (or SNOMMP-9), which induces neuronal apoptosis. Both in vitro and in vivo mass spectrometry identified the activated, stable derivative of MMP-9 as a sulfinic or sulfonic acid, whose formation was triggered by S-nitrosylation following nitrosa-tive and oxidative stress. These findings suggest the existence of an extracellular proteolysis pathway to neuronal cell death in which S-nitrosylation leads to activation of MMPs, and further oxidation results in stable PTM to a sulfinic or sulfonic acid derivative with pathological activity. Our group and others have shown that aberrant proteolytic activity of MMPs, especially MMP-9, contributes directly to neuronal injury, apoptosis, and brain damage after acute cerebral ischemia (1–4). We further investigated potential mechanisms for this toxic effect. We found that activated MMP-9 degrades the extracellular matrix (ECM) component laminin and that this degradation induces neuronal apoptosis in a model of transient focal cerebral ischemia in mice. We determined that the highly specific, mechanism-based, MMP-2/9 inhibitor, SB-3CT, blocks MMP-9 activity, including downstream laminin cleavage, thus rescuing neurons from apoptosis (5). We thus concluded that MMP-9 is a potential drug target in acute cerebral ischemia and that SB-3CT derivatives may have significant therapeutic potential in acute stroke patients. Importantly, however, as Eng Lo and colleagues (6) have recently shown, long-term activity of MMPs may be necessary for recovery from ischemic damage, so it appears that only short-term therapy with an MMP antagonist should be entertained in future clinical trials.
Does continuous visual feedback aid debugging in direct-manipulation programming systems? (1997)

Continuous visual feedback is becoming a common feature in direct-manipulation programming systems of all klndsfrom demonstrational macro builders to spreadsheet packages to visual programming languages featuring direct manipulation. But does continuous visual feedback actually help in the domain of programming?
DİNDARLIK VE ÖZNEL İYİ OLUŞ: ULUSLARARASI BİR BAKIŞ (2019)

Dinin bireylerin ve toplumlarin oznel iyi olusunu (OIO) artirip artirmadigi sikca tartisilmaktadirlar. Insanlarin buyuk bir cogunlugunun  dinin gunluk yasamlarinda onemli oldugunu belirttigi dikkate alindiginda bu konu ozellikle goze carpmaktadir. Ancak, bazi evrimciler dinin uyum sagladigi, ahlak ve sosyal uyumu besledigi, her ikisinin de iyi olusu tesvik ettigi sonucuna varmislardir. Bununla birlikte,  dinin aciya neden olabilecegi de ileri surulmustur. Bu makalede dindarligin ve OIO'nun farkli sosyal baglamlarda iliskili olup olmadigini belirlemek icin son on yilda yayinlanmis dindarlik ve OIO hakkindaki calismalari gozden gecirilmektedir. Oncelikle dindarlik ve oznel iyi olusun tanimi yapilmakta ve sanayilesmis Batili uluslardan elde edilen dindarlik ve OIO hakkindaki bulgular tartisilmaktadir. Dindarlik ve OIO arasindaki iliskiye dair uluslararasi calismalarin rapor edildigi calismada dindarlik-OIO iliskisinde baglamsal konulari ele alinmakta ve son bolumde, gelecekteki arastirmalarin ele alabilecegi mevcut literaturdeki bosluklari belirtilmektedir.
Dynamic QoS Management for Interactive Multimedia in Integrated 4G/5G Networks (2021)

INTRODUCTION: Emerging interactive multimedia applications such as VR have some key requirements that communication medium must full fill in order to have a smooth interactive experience. These requirements include higher uplink and downlink throughput requirement, low latency, and consistent throug
Large-area semi-transparent light-sensitive nanocrystal skins (2012)

We report a large-area, semi-transparent, light-sensitive nanocrystal skin (LS-NS) platform consisting of single monolayer colloidal nanocrystals. LS-NS devices, which were fabricated over areas up to 48 cm(2) using spray-coating and several cm-squares using dip-coating, are operated on the principle of photogenerated potential buildup, unlike the conventional charge collection. Implementing proof-of-concept devices using CdTe nanocrystals with ligand removal, we observed a substantial sensitivity enhancement factor of ~73%, accompanied with a 3-fold faster response time (<100 ms). With fully sealed nanocrystal monolayers, LS-NS is found to be highly stable under ambient conditions, promising for low-cost large-area UV/visible sensing in windows and facades of smart buildings.
Scale and the Gaze of a Machine (2020)

Scale suffuses the work we do and, recently, has us considering an aspect of scale best suited to those with ethnographic training. We've been asked to help with scaling up one of the latest blockbusters in high tech – deep learning. Advances in deep learning have enabled technology to be programmed to not only see who we are by using facial ID systems and hear what we say by using natural language systems; machines are now even programmed to recognize what we do with vision‐based activity recognition. However, machines often define the objects of their gaze at the wrong scale. Rather than “look for” people or objects, with deep learning, machines typically look for patterns at the smallest scale possible. In multiple projects, we've found that insights from anthropology are needed to inform both the scale and uses of these systems.
<i>In vitro</i> and <i>in vivo</i> pharmacology of YNT-X, a novel small-molecule orexin type 2 receptor agonist (2019)

Orexin, a neuropeptide produced by neurons in the lateral hypothalamus, regulates sleep and wakefulness. Orexin deficiency causes narcolepsy-cataplexy characterized by excessive sleepiness and cataplexy, a sudden loss of muscle tone triggered by emotion.
ChemInform Abstract: Prenylated Xanthonoids from Calophyllum apetalum. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Low power ASIC transmitter for UWB-IR radio communication and positioning (2010)

This paper describes a low power Ultra-Wideband Impulse Radio (UWB-IR) Application Specific Integrated Circuit (ASIC) transmitter implemented in UMC 0.18 μm. This transmitter has been designed for low data rate communication applications and indoor positioning systems. It is powered by 1.8 V and its current consumption is 20 mA during pulse transmission and lower than 45 μA the rest of the time. This leads to an average power for the transmitter of less than 85 μW for a 288-pulse burst at a burst repetition rate of 1 Hz. The center frequency and bandwidth of the pulse generated by this transmitter are compliant with the current international regulations (FCC/ECC).
Optical Triggering of 12 kV 1 cm<sup>2</sup> 4H-SiC Thyristors (2013)

We report on switch-on of 12 kV, 1cm2 optically triggered 4H-SiC thyristor fabricated by CREE Inc., to Imax=270 А with current rise time of ~ 3 s. Temperature dependence of holding current Ih in this thyristor has been experimentally studied in the temperature range from 300 to 425 K. It is shown that measurements of Ih temperature dependence under condition of optical switch-on at small anode bias and large load resistance reveal the existence of a ”weak point” within the optical window. This point is characterized by a much smaller critical charge than that within the remaining part of the window.
Lensless hyperspectral spectromicroscopy with a tabletop extreme-ultraviolet source (2016)

We demonstrate hyperspectral coherent imaging in the EUV spectral region for the first time, without the need for hardware-based wavelength separation. This new scheme of spectromicroscopy is the most efficient use of EUV photons for imaging because there is no energy loss from mirrors or monochromatizing optics. An EUV spectral comb from a tabletop high-harmonic source, centered at a wavelength of 30nm, illuminates the sample and the scattered light is collected on a pixel-array detector. Using a lensless imaging technique known as ptychographical information multiplexing, we simultaneously retrieve images of the spectral response of the sample at each individual harmonic. We show that the retrieved spectral amplitude and phase agrees with theoretical predictions. This work demonstrates the power of coherent EUV beams for rapid material identification with nanometer-scale resolution.
A seamless coordinator switching (SCS) scheme for wireless personal area network (2003)

In the emerging wireless personal area networks (WPANs), one of the active devices in a piconet is designated as a coordinator, which plays a critical roles, e.g., to provide the basic timing for operation of the piconet and manage the QoS requirements/power saving modes. To warrant maintenance of the coordinating function under some unpredictable situations such as sudden power-off or fast movement of a coordinator, it must be seamlessly switched. This paper proposes a new SCS (seamless coordinator switching) scheme to maintain the piconet by selecting a coordinator in the subsequent superframe without incurring the re-initialization overhead.
Label-Free Specific Detection of Femtomolar Cardiac Troponin Using an Integrated Nanoslit Array Fluidic Diode (2014)

We demonstrate here for the first time the utility of an integrated nanofluidic diode for detecting and quantifying physiologically relevant macromolecules. Troponin T, a key human cardiac protein biomarker, was selectively and rapidly detected free of labels for concentrations down to 10 fg/mL (∼ 0.3 fM) in buffer as well as 10 pg/mL (∼ 300 fM) in untreated human serum. This ultrasensitive detection arises from monolithic integration of a unique nanofluidic diode structure that is highly robust and amenable to site-specific surface modification. The structure features a planar nanoslit array where each nanoslit is defined at a nominal width of 70 nm over a micrometer-scale silicon trench without the use of high-resolution patterning techniques. Through vapor deposition, a glass layer is placed at a nonuniform thickness, tapering the trench profile upward and contributing to the triangular nanoslit structure. This asymmetric profile is essential for ionic current rectification noted here at various pH values, ionic strengths, and captured target species, which modulate the surface-charge density within the sensitive region of the nanoslit. The nanoslit, unlike nanopores, offers only 1D confinement, which appears to be adequate for reasonable rectification. The measurements are found in quantitative agreement with the diode simulations for the first time based on a pH- and salt-dependent surface-charge model.
Progression-free and overall survival in ovarian cancer patients treated with CVac, a mucin 1 dendritic cell therapy in a randomized phase 2 trial (2016)

NCT01068509. Study Initiation Date (first patient screened): 20 July 2010. Study Completion Date (last patient observation): 20 August 2013, the last patient observation for progression-free survival; 29 April 2015, the last patient was documented regarding overall survival.
High-Throughput Low-Latency Encoder and Decoder for a Class of Generalized Reed–Solomon Codes for Short-Reach Optical Communications (2019)

Forward error correction is imperative in most communication systems. Applications like short-reach optical communications have a limited power and area occupation budget for encoder and decoder implementation. In this brief, we propose high-throughput low-latency Reed Solomon (RS) encoder and decoder architectures, compatible with a recently proposed class of generalized RS codes. The architectures are synthesized in TSMC 65 nm CMOS technology, showing a significant performance improvement with moderate hardware cost and power consumption. Throughput is increased by ×11.5 for the encoder, with respect to a conventional architecture, while the latency is reduced by ×10.3. These improvements respectively amount to ×14.7 and ×7.5 for the decoder.
On Detecting Manifestation of Adversary Characteristics (2018)

Adversaries are conducting attack campaigns with increasing levels of sophistication. Additionally, with the prevalence of out-of-the-box toolkits that simplify attack operations during different stages of an attack campaign, multiple new adversaries and attack groups have appeared over the past decade. Characterizing the behavior and the modus operandi of different adversaries is critical in identifying the appropriate security maneuver to detect and mitigate the impact of an ongoing attack. To this end, in this paper, we study two characteristics of an adversary: Risk-averseness and Experience level. Risk-averse adversaries are more cautious during their campaign while fledgling adversaries do not wait to develop adequate expertise and knowledge before launching attack campaigns. One manifestation of these characteristics is through the adversary's choice and usage of attack tools. To detect these characteristics, we present multi-level machine learning (ML) models that use network data generated while under attack by different attack tools and usage patterns. In particular, for risk-averseness, we considered different configurations for scanning tools and trained the models in a testbed environment. The resulting model was used to predict the cautiousness of different red teams that participated in the Cyber Shield ‘16 exercise. The predictions matched the expected behavior of the red teams. For Experience level, we considered publicly-available remote access tools and usage patterns. We developed a Markov model to simulate usage patterns of attackers with different levels of expertise and through experiments on CyberVAN, we showed that the ML model has a high accuracy.
Integrated Microwave Photonic Filter on a Hybrid Silicon Platform (2010)

A hybrid silicon photonic integrated filter is proposed and demonstrated with a novel structure. This filter incorporates a ring resonator in one arm of a Mach-Zehnder interferometer making it possible to obtain a programmable filter response. The optical filter consists of a 5-mm-long delay loop made of low-loss silicon waveguides with integrated thermal modulators resulting in a 0.164-nm free spectral range with absolute phase tunability and gain elements that allow for the tuning of the filter factor. The microwave response of this integrated filter is measured and display tunability of 20 GHz.
Opportunities and challenges in mRNA-LNP vaccine design (2023)

“Future research should focus on how much of the mRNA-LNP dose drains into lymph nodes and spreads systemically, which immune cell types are involved in the uptake, translation, and presentation of the mRNA-encoded antigens, and which cellular interactions potentially contribute to adverse events...”
Patterning of a Surface Immobilized ATRP Initiator with an Inkjet Printer (2010)

A new technique for patterning polymer brushes on the micrometer scale has been developed in which an inkjet printer was used to deposit droplets of acid on a surface-immobilized initiator for atom transfer radical polymerization (ATRP). The acid cleaved an ester bond in the ATRP initiator in a saponification reaction. As a result, the ATRP initiator was rendered inactive. To control the degree of defunctionalization, a new initiator containing a weak ester bond was derived from a tertiary alcohol. Comparison to an established ATRP initiator, derived from a primary alcohol, showed that the novel initiator was defunctionalized with a higher efficiency. Control of the reaction time allowed to partially defunctionalize the initiator molecules, leading to control of grafting densities within the written patterns.
Nonlinear Distortion Mitigation by Machine Learning of SVM Classification for PAM-4 and PAM-8 Modulated Optical Interconnection (2017)

We demonstrated a support vector machine (SVM) based machine learning method to mitigate modulation nonlinearity distortion for PAM-4 and PAM-8 vertical cavity surface emitter laser multi-mode fiber (VCSEL-MMF) optical link. Simulations at 100 Gb/s data rate and experimental work at 60 Gb/s data rate were carried out. We achieved a significant improvement in bit error rate (BER) when complete binary tree SVMs (CBT-SVMs) are applied for both PAM-4 and PAM-8 signals. Quantitative analysis of the sensitivity gain versus modulation nonlinearity distortion is presented with experimentally verification. The results indicate that CBT-SVMs have better performance for PAM-8 compared to PAM-4. The sensitivity gain increases almost linearly with the increase of eye-linearity (increase of modulation nonlinearity distortion). Up to 2.5-dB sensitivity improvement is achieved by the proposed CBT-SVMs at eye-linearity of 1.72 for PAM-4.
Dendritic cell-mimicking scaffolds for ex vivo T cell expansion (2022)

We propose an ex vivo T cell expansion system that mimics natural antigen-presenting cells (APCs) for adoptive cell therapy (ACT). Microfiber scaffolds coated with dendritic cell (DC) membrane replicate physicochemical properties of dendritic cells specific for T cell activation such as rapid recognition by T cells, long duration of T cell tethering, and DC-specific co-stimulatory cues. The DC membrane-coated scaffold is first surface-immobilized with T cell stimulatory ligands, anti-CD3 (αCD3) and anti-CD28 (αCD28) antibodies, followed by adsorption of releasable interleukin-2 (IL-2). The scaffolds present both surface and soluble cues to T cells ex vivo in the same way that these cues are presented by natural APCs in vivo. We demonstrate that the DC-mimicking scaffold promotes greater polyclonal expansion of primary human T cells as compared to αCD3/αCD28-functionalized Dynabead. More importantly, major histocompatibility complex molecules derived from the DC membrane of the scaffold allow antigen-specific T cell expansion with target cell-specific killing ability. In addition, most of the expanded T cells (∼97%) can be harvested from the scaffold by density gradient centrifugation. Overall, the DC-mimicking scaffold offers a scalable, modular, and customizable platform for rapid expansion of highly functional T cells for ACT.
<title>Motion-adaptive model-assisted compatible coding with spatiotemporal scalability</title> (1997)

We introduce the concept of motion adaptive spatio-temporal model-assisted compatible (MA-STMAC) coding, a technique to selectively encode areas of different importance to the human eye in terms of space and time in moving images with the consideration of object motion. PRevious STMAC was proposed base don the fact that human 'eye contact' and 'lip synchronization' are very important in person-to-person communication. Several areas including the eyes and lips need different types of quality, since different areas have different perceptual significance to human observers. The approach provides a better rate-distortion tradeoff than conventional image coding techniques base don MPEG-1, MPEG- 2, H.261, as well as H.263. STMAC coding is applied on top of an encoder, taking full advantage of its core design. Model motion tracking in our previous STMAC approach was not automatic. The proposed MA-STMAC coding considers the motion of the human face within the STMAC concept using automatic area detection. Experimental results are given using ITU-T H.263, addressing very low bit-rate compression.
PDM-16QAM WDM Transmission with 2nd-Order Forward-Pumped Distributed Raman Amplification Utilizing Incoherent Pumping (2019)

We experimentally shows second-order forward Raman pumping scheme combined with incoherent- and coherent-light sources can achieve 1.6-dB Q-improvement of PDM-16QAM signal in WDM configuration while keeping low RIN transfer after 1,760-km standard SMF transmission.
Total Knee Arthroplasty After Open Reduction and Internal Fixation of Fractures of the Tibial Plateau (2001)

On the basis of our results, we concluded that total knee arthroplasty after open reduction and internal fixation of a fracture of the tibial plateau decreases pain and improves knee function, but the procedure is technically demanding and is associated with a high failure rate (five of fifteen).
Supplementary Figure 7 from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers (2023)

&lt;p&gt;PDF file - 287K&lt;/p&gt;
In vivo transfer of hepatocyte growth factor gene accelerates proliferation of hepatic oval cells in a 2‐acetylaminofluorene/partial hepatectomy model in rats (2000)

To clarify the effect of hepatocyte growth factor (HGF) on proliferation of hepatic oval cells, we transferred HGF gene into liver of the Solt-Farber rat model. Male Fisher 344 rats were infected with a recombinant adenovirus carrying the cDNA for HGF (pAxCAHGF) from tail vein. HGF mRNA showed its peak at 4 days, and diminished thereafter. The total and proliferating cell nuclear antigen-positive hepatic oval cells were significantly elevated in HGF-transferred rats, in which stem cell factor and c-kit mRNA increased at each time point. Our results suggest that in vivo transfer of the HGF gene into liver accelerates proliferation of hepatic oval cells in the Solt-Farber model in rats.
Study of Cell-Lipid Film Interaction by Measuring Heat Shock Proteins mRNA Expression (2000)

The adhesion and function of HeLa S3 cells on lipid films were investigated. The function of the cells adhering to lipid films was estimated by HSP 70B and HSP 47 mRNA expression using a reverse transcription-polymerase chain reaction (RT-PCR) analysis. It is apparent that HeLa S3 cells adhere to lipid films as well as tissue culture poly(styrene)(TCPS). HSPs mRNA expression on the lipid film depended on each lipid film. HeLa S3 cells adhered to the lipid films of DPPC, DPPE and DPPS expressed the same level HSPs mRNA as TCPS. High HSPs mRNA expressions were observed in the HeLa S3 cells adhering to films of synthetic lipids. The serum proteins affected the HSPs expression in the case of the synthetic lipids. These results imply that cell-material interactions are not simple and that mRNA expression is a powerful tool in the investigation of cell function, especially the reaction by weak stimulus such as cell-material contact.