gebhart/patrepeval huggingface dataset:
Regulation of Exit from Quiescence by p27 and Cyclin D1-CDK4 (1998)

The synthesis of cyclin D1 and its assembly with cyclin-dependent kinase 4 (CDK4) to form an active complex is a rate-limiting step in progression through the G1 phase of the cell cycle. Using an activated allele of mitogen-activated protein kinase kinase 1 (MEK1), we show that this kinase plays a significant role in positively regulating the expression of cyclin D1. This was found both in quiescent serum-starved cells and in cells expressing dominant-negative Ras. Despite the observation that cyclin D1 is a target of MEK1, in cycling cells, activated MEK1, but not cyclin D1, is capable of overcoming a G1 arrest induced by Ras inactivation. Either wild-type or catalytically inactive CDK4 cooperates with cyclin D1 in reversing the G1 arrest induced by inhibition of Ras activity. In quiescent NIH 3T3 cells expressing either ectopic cyclin D1 or activated MEK1, cyclin D1 is able to efficiently associate with CDK4; however, the complex is inactive. A significant percentage of the cyclin D1-CDK4 complexes are associated with p27 in serum-starved activated MEK1 or cyclin D1 cell lines. Reduction of p27 levels by expression of antisense p27 allows for S-phase entry from quiescence in NIH 3T3 cells expressing ectopic cyclin D1, but not in parental cells.
Partial Reduction of Esters to Aldehydes Using a Novel Modified Red-Al Reducing Agent (2014)

E-mail: dkan@kangwon.ac.kr Received February 11, 2014, Accepted March 12, 2014Key Words : Red-Al, cis-2,6-Dimethyl morpholine, Partial reduction, Ester, AldehydeAldehydes are valuable building blocks and reactive inter-mediates in organic synthesis. The general and classicalsyntheses of aldehydes from esters involve reduction-oxida-tion and partial reduction using efficient partial reducingagents. Obviously, one-step partial reduction methods aremore useful than two-step reduction-oxidation methodsowing to their simplicity, and generality in organic synthesis.Therefore, the partial reduction of esters to aldehydeswithout over-reduction to alcohols is useful for the synthesisof aldehydes, and a large number of reducing agents forthis purpose have been reported.
Aberration-corrected quantum temporal imaging system (2013)

We describe the design of a temporal imaging system that simultaneously reshapes the temporal profile and converts the frequency of a photonic wave packet, while preserving its quantum state. A field lens, which imparts a temporal quadratic phase modulation, is used to correct for the residual phase caused by field curvature in the image, thus enabling temporal imaging for phase-sensitive quantum applications. We show how this system can be used for temporal imaging of time-bin entangled photonic wave packets and compare the field lens correction technique to systems based on a temporal telescope and far-field imaging. The field-lens approach removes the residual phase using four dispersive elements. The group delay dispersion $D$ is constrained by the available bandwidth $\ensuremath{\Delta}\ensuremath{\nu}$ by $D>t/\ensuremath{\Delta}\ensuremath{\nu}$, where $t$ is the temporal width of the wave form associated with the dispersion $D$. This is compared to the much larger dispersion $D\ensuremath{\gg}\ensuremath{\pi}{t}^{2}/8$ required to satisfy the Fraunhofer condition in the far-field approach.
Characterization of the Arterial Anatomy of the Murine Hindlimb: Functional Role in the Design and Understanding of Ischemia Models (2013)

The detailed arterial anatomy of murine hindlimb and collateral routes deduced from the anatomy are described. Limitations on designs of ischemia models in view of anatomical variations are proposed. These observations will contribute to the development of animal studies of therapeutic angiogenesis using murine hindlimb ischemia models.
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics (2014)

EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis.
TH-4000, a hypoxia-activated EGFR/Her2 inhibitor to treat EGFR-TKI resistant T790M-negative NSCLC. (2015)

e13548 Background: TH-4000 is a clinical-stage hypoxia-activated prodrug that releases an irreversible tyrosine kinase inhibitor (TKI) of wild type (WT) EGFR, mutant (Δ19) EGFR and Her2. Hypoxia tumor targeting may allow for greater intratumoral dose intensity without dose limiting systemic toxicity. Tumor hypoxia upregulates WT EGFR signaling through several HIF-dependent mechanisms. Clinical studies indicate that mutant EGFR NSCLC with WT EGFR present (heterozygous) is associated with limited response to EGFR-TKIs. NSCLC is known to be a hypoxic tumor; thus, hypoxia-induced activation of WT EGFR signaling may be a mechanism of current EGFR-TKI resistance. Phase 1 clinical trial established the MTD of TH-4000 at 150 mg/m2/wk. Here we report translational studies supporting initiation of a Phase 2 trial. Methods: The activity of TH-4000 and erlotinib were assessed in a heterozygous (WT/ Δ19) EGFR PC9 tumor xenograft model (n = 6-9/grp). Erlotinib was dosed daily at a human-matched plasma PK equivalent (10 mg/kg, po). TH-4000 was dosed weekly (15 mg/kg, ip) as a single-agent or added to erlotinib at Day 14. Multi-time point detection of plasma and tumor TH-4000 and TKI were measured by LC/MS/MS. Tumor biomarkers were assessed by western blot. Results: PC9 was 8% hypoxic. All PC9 tumors progressed on erlotinib while all tumors regressed on TH-4000 alone or when added 14 days into erlotinib therapy, suggesting an ability to prevent or overcome resistance to TKI treatment. In the same model, single-dose administration of 15 mg/kg (ip) TH-4000 achieved a plasma AUC equivalent to 32 mg/m2 (IV) in humans, well below the MTD defined in Phase 1 trial. Preclinical PK/PD studies of single-dose TH-4000 (15 mg/kg) showed prolonged prodrug residency in tumor tissue (T½39 h) releasing TKI steadily over 7 days with EGFR shut down maintained for a week. Conclusions: TH-4000 was more effective than erlotinib in a heterozygous (WT/Δ19) EGFR PC9 model either upfront as a single-agent or when added to erlotinib after progression. Based on these data, once weekly administration of TH-4000 (150 mg/m2) is proposed in a Phase 2 trial planned in EGFR activating-mutation confirmed NSCLC patients who have progressed on TKI therapy and are T790M-negative.
Alpha 1-antichymotrypsin regulates Alzheimer beta-amyloid peptide fibril formation. (1995)

The major component of the cerebral plaques in Alzheimer disease is the beta-amyloid peptide, but serine proteinase inhibitors like alpha 1-antichymotrypsin (ACT) are also present. Their role in the pathogenesis of amyloid formation is unsettled. In addition to their function as proteinase inhibitors, serine proteinase inhibitors can interact with various hydrophobic compounds, a reaction accompanied by a transition from the stressed to the relaxed conformation. We report here on the ability of ACT to regulate the formation of beta-amyloid fibrils in vitro. In a molar ratio of 1:10 (ACT to beta-amyloid) ACT inhibits beta-amyloid fibril formation. Furthermore, ACT promotes rapid disaggregation of beta-amyloid fibrils when added in the same molar ratio to preformed beta-amyloid fibrils. These processes are accompanied by increased thermostability of ACT and loss of its biological activity, consistent with a conformational transition of ACT from the stressed to the relaxed state. The influence of ACT on beta-amyloid fibril formation may be an example of a hydrophobic interaction between the beta-amyloid peptide and the hydrophobic domain C terminal to the reactive center of ACT.
Generation of reactive oxygen species from porous silicon microparticles in cell culture medium (2009)

Nanostructured (porous) silicon is a promising biodegradable biomaterial, which is being intensively researched as a tissue engineering scaffold and drug-delivery vehicle. Here, we tested the biocompatibility of non-treated and thermally-oxidized porous silicon particles using an indirect cell viability assay. Initial direct cell culture on porous silicon determined that human lens epithelial cells only poorly adhered to non-treated porous silicon. Using an indirect cell culture assay, we found that non-treated microparticles caused complete cell death, indicating that these particles generated a toxic product in cell culture medium. In contrast, thermally-oxidized microparticles did not reduce cell viability significantly. We found evidence for the generation of reactive oxygen species (ROS) by means of the fluorescent probe 2',7'-dichlorofluorescin. Our results suggest that non-treated porous silicon microparticles produced ROS, which interacted with the components of the cell culture medium, leading to the formation of cytotoxic species. Oxidation of porous silicon microparticles not only mitigated, but also abolished the toxic effects.
Wideband frequency conversion with LiNbO3 optical single-sideband modulator (2001)

We demonstrated a wideband frequency conversion with a LiNbO3 optical single-sideband modulator. The operation wavelength more than 80 nm was attained at the 10 GHz frequency conversions. No degradation in the 10 Gb/s signals was found.
Utilizing Noise Addition for Data Privacy, an Overview (2013)

The internet is increasingly becoming a standard for both the production and consumption of data while at the same time cyber-crime involving the theft of private data is growing. Therefore in efforts to securely transact in data, privacy and security concerns must be taken into account to ensure that the confidentiality of individuals and entities involved is not compromised, and that the data published is compliant to privacy laws. In this paper, we take a look at noise addition as one of the data privacy providing techniques. Our endeavor in this overview is to give a foundational perspective on noise addition data privacy techniques, provide statistical consideration for noise addition techniques and look at the current state of the art in the field, while outlining future areas of research.
The SCID mouse: relevance as an animal model system for studying human disease. (1993)

The simultaneous description some 5 years ago of two methods for the partial reconstitution of a human immune system in severe combined immune-deficient (SCID) mice (collectively, human:SCID mice) was met with great enthusiasm. At the time, it was hoped that human:SCID mice would provide experimental animal model systems for studying human disease and the human immune system. Many of these hopes have been borne out. Importantly, the experimental results obtained from these chimeric human/animal studies appear to be relevant to human disease and immune function. In spite of these glowing achievements, the SCID mouse may not represent the optimal experimental system with which to address these questions. The incomplete penetrance ("leakiness") of the scid mutation and the recent discovery that the mutation is not lymphoid specific, but rather affects a general DNA repair pathway, will only serve to complicate the interpretation of already complex biological interactions. Recently other immune-deficient mice have been described that appear to overcome one or both of these problems and thus these mice could represent improved hosts for the adaptive transfer of a human immune system. The current status of the SCID mouse in light of these new findings is discussed.
Die Hüter des Hades. Zur Bedeutung und Interpretation der homerischen Kimmerier (2017)

This paper deals with the Homeric Cimmerians, who were located at the end of the world, on the doorsteps to Hades. At the beginning of the work, it was necessary to build up a concept of research 1st to find the relevant sources and 2nd to distinguish the mythical Cimmerians from the historical. Tools from the project eAQUA and eXChange illustrate the selection of sources.
A Novel Approach to the Segmentation of sEMG Data Based on the Activation and Deactivation of Muscle Synergies During Movement (2018)

The muscle-synergy hypothesis is a widely used method for describing simple motion patterns and how the central nervous system deals with the complexity of controlling a large set of muscles in parallel. However, the physiological interpretation of synergies and the mathematical techniques behind their computation are still far from being properly standardized. This letter proposes a novel approach to obtaining detailed and accurate information about how muscular synergies are triggered during different stages of a given motion. In that regard, a way to find the number of muscle synergies working in parallel is introduced based on the appearance of unexpected high-frequencies in the time series of electromyographic (EMG) signals during synergy extraction. This phenomenon allows the definition of a robust threshold for the number of synergies. The proposed methods are tested on muscle synergies computed from superficial EMG signals recorded during wheel steering. The results show the advantage of the proposed approach in relation to the currently used methods that require segmenting the signal according to the stages of the movement, and suggest future increases in the understanding of motor control from a neurological point of view.
Visible-Spectrum Gaze Tracking for Sports (2013)

In sports, wearable gaze tracking devices can enrich the viewer experience and be a powerful training tool. Because devices can be used for long periods of time, often outside, it is desirable that they do not use active illumination (infra-red light sources) for safety reasons and to minimize the interference of the sun. Unlike traditional wearable devices, in sports, the gaze tracking method must be robust to (often dramatic) movements of the user in relation to the device (i.e., the common assumption that because the device is wearable, the eye does not move with regards to the camera no longer holds.) This paper extends a visible-spectrum gaze tracker in the literature to handle the requirements of a motor-sports application. Specifically, the method presented removes the assumption (in the original method) that the eye position is fixed, and proposes the use of template matching to allow for changes in the eye location from frame to frame. Experimental results demonstrate that the proposed method can handle severe changes in the eye location and is very fast to compute (up to 60 frames per second in modern hardware.).
Delay-aware Conflict-free Scheduling for LTE-V, Sidelink 5G V2X Vehicular Communication, in Highways (2018)

V2X, “Vehicle-to-Everything” sidelink in 5G, facilitates communication between vehicles, pedestrians and cyclists while relying on a central scheduler in the main mode. In many applications, sidelinks in highways are formed based on the location of vehicles on the road. This defines an inherent ordered-tree structure to be used for delay-aware scheduling in LTE frame. Having these in mind, we propose the first two-dimensional expansion of a popular leading delay-aware scheduler in the literature. Our designed scheduler matches the V2X LTE multichannel environment and benefits from resource reuse while being capable of handling delay in sensitive vehicular safety applications. Compared to the existing competitors, delay control is the main feature of our scheduler. Having less or similar complexity order, this feature comes at the cost of less efficient resource reuse.
An integrated paper-based sample-to-answer biosensor for nucleic acid testing at the point of care (2015)

An integrated paper-based sample-to-answer biosensor is proposed, which enables simple paper-based nucleic acid extraction, amplification and detection for point-of-care testing.
Learning state space trajectories in recurrent neural networks (1989)

A number of procedures are described for finding delta E/ delta W/sub ij/ where E is an error functional of the temporal trajectory of the states of a continuous recurrent network and w/sub ij/ are the weights of that network. Computing these quantities allows one to perform gradient descent in the weights to minimize E, so these procedures form the kernels of connectionist learning algorithms. Simulations in which networks are taught to move through limit cycles are shown, along with some empirical perturbation sensitivity tests. The author describes a number of elaborations of the basic idea, including mutable time delays and teacher forcing. He includes a complexity analysis of the various learning procedures discussed and analyzed. Temporally continuous recurrent networks seems particularly suited for temporally continuous domains, such as signal processing, control, and speech.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pathology of small hepatocellular carcinoma. A proposal for a new gross classification (1987)

Review of 61 surgically resected small hepatocellular carcinomas (HCC) less than or equal to 3 cm in diameter yielded a simple gross classification system of five types based on tumor shape, which is highly correlated with microscopic and clinical features, including prognosis. Type 1 (single nodular type) tumors (n = 13) are expansile, roughly spheric, and often encapsulated. In Type 2 tumors (single nodular type with extranodular growth) (n = 21), replacing growth is often seen in the area of extranodular growth. Type 3 tumors (contiguous multinodular type) (n = 19) consist of small nodules growing in contiguity, often with replacing growth at the periphery. Type 4 (poorly demarcated nodular type) is a rare tumor showing infiltrating growth at its border. The authors define early HCC (n = 5) as the presence of tumor without destruction of the underlying liver structure. The lesions experienced are tiny (less than or equal to 1.2 cm) and well differentiated. Poorly differentiated histologic characteristics and elevated alpha fetoprotein are more common in Types 2 and 3 than in Type 1. Type 1 has the highest rates of positive serum hepatitis B surface antigen and liver cirrhosis; portal vein tumor thrombus (PT) and/or intrahepatic metastasis (IM) is rare (7.7%), and the effect of transcatheter arterial embolization (TAE) is remarkable. This contrasts with Type 2, which has a high rate of PT and/or IM (71.4%) and multiple local recurrences (40%), and with Type 3, which shows a poor response to TAE.
Image segmentation approach for realizing zoomable streaming HEVC video (2015)

The next generation compression technology High Efficiency Video Coding (HEVC) can provide a substantially higher compression capability than the existing H.264/AVC standard. It has received increased attention and is lauded as the enabler for a host of new services and capabilities [4]. A better user experience for browsing videos on the limited and heterogeneous screen sizes requires streaming of an arbitrary region of interest (ROI) from a high resolution video. It is essential to support cropping and zooming within a video stream which allows the users to view a cropped ROI at a high resolution, in effect, magnifying the ROI. This paper thesis explores two methods for ROI-based streaming, referring to them as tiled encoding which partitions video frames into grid of tiles and encodes each tile as an independently decodable stream and partial decoding where only the ROI and dependence area are decoded. Apart from these, slice structure dependency on tiled encoding was performed for further bandwidth efficiency. These two methods were evaluated in terms of bandwidth efficiency, storage requirements, and computational costs under different video encoding parameters. HM15.0 version reference software for HEVC was used [8]. Partial decoding results show that the decoding calculation cost was reduced by 40-55% for 32 buffered luma pixels around ROI. Tiled encoding results show optimal decoding calculation cost and bandwidth efficiency for a tile size of 16-16 pixels. Simulation results show that larger tiles significantly improve compression efficiency in tiled encoding, but it would lead to higher bandwidth while a larger slice size increases the bandwidth efficiency (reduces transmission overhead) but would result in lower compression. The results show that 1460 bytes slice structure improved bandwidth efficiency than 64 bytes slice structure.
Selfies (2018)

"No selfie zones" areas should be declared across tourist areas especially places such as water bodies, mountain peaks, and over tall buildings to decrease the incidence of selfie-related deaths.
Heat shock and thermotolerance in plant and animal embryogenesis. (1991)

Although the strategies of early embryogenesis differ greatly among multicellular eukaryotes, there are certain parallels in structure, form, and function that cross even kingdom lines: the extreme heat sensitivity of zygotes and very early embryos, followed by the acquisition of thermotolerance during subsequent development, is one such parallel. The heat sensitivity may be so extreme that even moderate increases in temperature result in lethality (generally associated with the earliest phases of embryogenesis), or the effects may be less severe, resulting in defects in development but not in lethality. Mechanistically, and molecularly, these two forms of thermosensitivity appear to have different origins. On the one hand, outright lethality appears to result from an inability to induce heat shock genes and proteins; on the other hand, heat-induced developmental defects appear to result from an alteration in expression of non-heat shock genes and from a delay in the overall developmental program that generally accompanies the cell's response to heat shock. This review is focused on the developmental regulation of the heat shock response during early embryogenesis and on the impact of this regulation on the development of both animal and plant embryos. The two basic issues that we address here are (i) the expression of heat shock genes in the absence of heat shock during embryogenesis and (ii) the expression (or lack of expression) of heat shock genes after deliberate exposure of the embryos to heat shock and the consequences of this expression on its subsequent survival and development.
Destabilizing Domains Mediate Reversible Transgene Expression in the Brain (2012)

Regulating transgene expression in vivo by delivering oral drugs has been a long-time goal for the gene therapy field. A novel gene regulating system based on targeted proteasomal degradation has been recently developed. The system is based on a destabilizing domain (DD) of the Escherichia coli dihydrofolate reductase (DHFR) that directs fused proteins to proteasomal destruction. Creating YFP proteins fused to destabilizing domains enabled TMP based induction of YFP expression in the brain, whereas omission of TMP resulted in loss of YFP expression. Moreover, induction of YFP expression was dose dependent and at higher TMP dosages, induced YFP reached levels comparable to expression of unregulated transgene., Transgene expression could be reversibly regulated using the DD system. Importantly, no adverse effects of TMP treatment or expression of DD-fusion proteins in the brain were observed. To show proof of concept that destabilizing domains derived from DHFR could be used with a biologically active molecule, DD were fused to GDNF, which is a potent neurotrophic factor of dopamine neurons. N-terminal placement of the DD resulted in TMP-regulated release of biologically active GDNF. Our findings suggest that TMP-regulated destabilizing domains can afford transgene regulation in the brain. The fact that GDNF could be regulated is very promising for developing future gene therapies (e.g. for Parkinson's disease) and should be further investigated.
Automatic Negation and Speculation Detection in Veterinary Clinical Text (2017)

The automatic detection of negation and speculation in clinical notes is vital when searching for genuine instances of a given phenomenon. This paper describes a new corpus of negation and speculation data, in the veterinary clinical note domain, and describes a series of experiments whereby we port a CRF-based method across from the BioScope corpus to this novel domain.