gebhart/patrepeval huggingface dataset:
Inference of flow statistics via packet sampling in the internet (2008)

We show in this note that by deterministic packet sampling, the tail of the distribution of the original flow size can be obtained by rescaling that of the sampled flow size. To recover information on the flow size distribution lost through packet sampling, we propose a parametric method based on measurements from different backbone IP networks. This method allows us to recover the complete flow size distribution and has successfully been tested by using a real ADSL traffic trace.
Sub-1 GHz Frequency Band Wireless Coexistence for the Internet of Things (2021)

Motivated by the explosion of the Internet of Things (IoT), we examined Sub-1 GHz (frequencies below 1 GHz) band wireless technologies that are essential to enable various IoT applications. IEEE 802.15.4g and IEEE 802.11ah are two wireless technologies developed for outdoor IoT applications such as smart utility, smart city and infrastructure monitoring, for which both technologies operate in Sub-1 GHz Bands. Our coexistence simulation of IEEE 802.15.4g and IEEE 802.11ah using standard defined coexistence mechanisms shows serious interference problems due to fundamental protocol differences and channel access parameter differences. Accordingly, we proposed IEEE 802.19.3 Task Group formation to lead the standard development of IEEE 802.15.4g and IEEE 802.11ah coexistence in the Sub-1 GHz band. In addition to our coexistence methods contributed to IEEE 802.19.3 standard, we propose a novel Active Carrier Sense based CSMA/CA mechanism for IEEE 802.15.4g to reduce CSMA/CA failure packet discard under interference from IEEE 802.11ah traffic, and to keep interoperability with conventional IEEE 802.15.4g CSMA/CA mechanism. Our proposed coexistence techniques can improve fair spectrum sharing between IEEE 802.15.4g and IEEE 802.11ah networks for IoT applications.
A role of Wnt/β-catenin signals in hepatic fate specification of human umbilical cord blood-derived mesenchymal stem cells (2007)

Human umbilical cord blood-derived mesenchymal stem cells (UCBMSCs) are expected to be an excellent source of cells for transplantation. In addition, the stem cell plasticity of human UCBMSCs, which can transdifferentiate into hepatocytes, has been reported. However, the mechanisms involved remain to be clarified. To identify the genes and/or signals that are important in specifying the hepatic fate of human UCBMSCs, we analyzed gene expression profiles during the hepatic differentiation of UCBMSCs with human telomerase reverse transcriptase, UCBMSCs immortalized by infection with a retrovirus carrying telomerase reverse transcriptase, but whose differentiation potential remains unchanged. Efficient differentiation was induced by 5-azacytidine (5-aza)/hepatocyte growth factor (HGF)/oncostatin M (OSM)/fibroblast growth factor 2 (FGF2) treatment in terms of function as well as protein expression: 2.5-fold increase in albumin, 4-fold increase in CCAAT enhancer-binding protein alpha, 1.5-fold increase in cytochrome p450 1A1/2, and 8-fold increase in periodic acid-Schiff staining. Consequently, we found that the expression of Wnt/beta-catenin-related genes downregulated, and the translocation of beta-catenin was observed along the cell membrane and in the cytoplasm, although some beta-catenin was still in the nucleus. Downregulation of Wnt/beta-catenin signals in the cells by Fz8-small interference RNA treatment, which was analyzed with a Tcf4 promoter-luciferase assay, resulted in similar hepatic differentiation to that observed with 5-azacytidine/HGF/OSM/FGF2. In addition, the subcellular distribution of beta-catenin was similar to that of cells treated with 5-azacytidine/HGF/OSM/FGF2. In conclusion, the suppression of Wnt/beta-catenin signaling induced the hepatic differentiation of UCBMSCs, suggesting that Wnt/beta-catenin signals play an important role in the hepatic fate specification of human UCBMSCs.
A novel input matching topology for improved digital pre-distortion of RF power amplifiers (2015)

Signal linearity is becoming an increasingly important requirement for the high power amplifiers used in current wireless communications systems. In this paper we demonstrate an input matching topology to improve the overall linearity performance of the base-station power amplifier. We then show simulation and measurement results using high-power laterally diffused metal oxide semiconductor (LDMOS) RF transistor and digital predistortion system for prototype design.
Supplementary figure and table legends from A Threshold of Systemic MAGE-A Gene Expression Predicting Survival in Resected Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Supplementary figures and table legend&lt;/p&gt;
Genetic and Functional Effects of Membrane Metalloendopeptidase on Diabetic Nephropathy Development (2011)

The present study provides the first evidence that MME has genetic and biological effects on the development of DN, and suggests that the inhibition of MME expression in the kidney with the agent of vasopeptidase may be a useful therapeutic approach for this disease.
NF-κB suppression synergizes with E7386, an inhibitor of CBP/β-catenin interaction, to block proliferation of patient-derived colon cancer spheroids (2021)

Dysregulated activation of the WNT/β-catenin signaling pathway is essential for the initiation and development of various cancers. E7386, a small-molecule compound, attenuates WNT signaling by blocking the interaction between β-catenin and CREB-binding protein (CBP); hence, it is regarded as a therapeutic candidate for cancers with activated WNT signaling. In the present study, we evaluated the biological characteristics associated with E7386 sensitivity by using a panel of patient-derived colon cancer spheroids. An integrative approach that combined E7386 sensitivity and gene expression profiles revealed that the resistance of the cancer spheroids to E7386 was associated with the activation of the NF-κB pathway. NF-κB pathway inhibitors acted synergistically with E7386 to block proliferation and induce cell cycle arrest in E7386-resistant spheroids. These findings suggest a possibility that a combination of E7386 and NF-κB inhibition may effectively block the proliferation of a subset of colon cancer cells.
Cry2 Is Critical for Circadian Regulation of Myogenic Differentiation by Bclaf1-Mediated mRNA Stabilization of Cyclin D1 and Tmem176b (2018)

Circadian rhythms regulate cell proliferation and differentiation; however, little is known about their roles in myogenic differentiation. Our synchronized differentiation studies demonstrate that myoblast proliferation and subsequent myotube formation by cell fusion occur in circadian manners. We found that one of the core regulators of circadian rhythms, Cry2, but not Cry1, is critical for the circadian patterns of these two critical steps in myogenic differentiation. This is achieved through the specific interaction between Cry2 and Bclaf1, which stabilizes mRNAs encoding cyclin D1, a G1/S phase transition regulator, and Tmem176b, a transmembrane regulator for myogenic cell fusion. Myoblasts lacking Cry2 display premature cell cycle exit and form short myotubes because of inefficient cell fusion. Consistently, muscle regeneration is impaired in Cry2<sup>-/-</sup> mice. Bclaf1 knockdown recapitulated the phenotypes of Cry2 knockdown: early cell cycle exit and inefficient cell fusion. This study uncovers a post-transcriptional regulation of myogenic differentiation by circadian rhythms.
NEW MODEL OF COLD ISCHEMIA/REPERFUSION INJURY: CCR1 KNOCKOUT MICE ARE PROTECTED AGAINST RENAL INJURY. (1999)

961 As the numbers of patients awaiting a renal transplant increases, attention to donor factors influencing graft survival has proven relevant to enlarging the donor pool and facilitating successful engraftment. Ischemia/reperfusion injury is a key determinant of acute tubular necrosis and delayed graft function after renal transplantation. We have developed the first mouse model of cold ischemia leading to reperfusion injury, which will allow dissection of ischemia/reperfusion using knockout (KO) mice. We have used this model to begin to dissect the contribution of various chemokine pathways to development of renal ischemia/reperfusion injury. Kidneys of inbred CCR1 KO mice or control B6/129 were perfused in situ until pale, using cold saline, and packed in ice for varying periods prior to revascularization. After preliminary studies, we undertook 60′ of cold ischemia and follow-up for 48-72 hours, with analysis of renal function, histology, immunopathology (with quantitative image analysis) and mRNA analysis. (Table)TableIschemia/reperfusion led to widespread tubular necrosis and was accompanied by accumulation of CCR1+ neutrophils within peritubular capillaries and in direct contact within tubular cells, whereas CCR1 KO showed only minor tubular injury and lacked neutrophil infiltration. The results of chemokine and caspase mRNA analysis are pending. These studies document a new mouse model of cold ischemia/reperfusion injury suitable for testing of gene KO on tissue injury. The current studies suggest that ischemia/reperfusion causes induction of chemokines and recruitment of CCR1+ neutrophils, and demonstrate an important potential application for CCR1 antagonists in mediating renoprotection post-transplant or after other surgical procedures.
Gastric Stromal Tumors in Carney Triad Are Different Clinically, Pathologically, and Behaviorally From Sporadic Gastric Gastrointestinal Stromal Tumors: Findings in 104 Cases (2009)

Carney triad, as originally described in 1977, was the association of 3 tumors: gastric epithelioid leiomyosarcoma [later renamed gastrointestinal stromal tumor (GIST)], extra-adrenal paraganglioma, and pulmonary chondroma. The disorder affected mostly young women and was not familial. We studied the clinical and pathologic features of the gastric neoplasm in 104 patients with the syndrome. Most (88%) were young women (mean age, 22 y), and the usual presentation was gastric bleeding. The tumors, commonly antral-based (61%), were multifocal, and ranged from 0.2 to 18.0 cm in dimension. Most (86%) featured round and polygonal (epithelioid) cells. Metastasis occurred in 49 patients (47%): to gastric lymph nodes (29%), liver (25%), and peritoneum (13%). Immunopositivity was detected in the tumors tested as follows: KIT, 100%; CD34, 75%; PKCtheta, 21%; PDGFRA, 90%; and smooth muscle actin, 6%. Fourteen patients (13%) died of metastatic GIST at a mean age of 45 years (range, 30 to 69 y). Estimated 10 and 40-year survivals were 100% and 73%, respectively. Median survival time was 26.5 years (range, 16 to 60 y). There was no correlation between the National Institutes of Health tumor risk classification and the tumor behavior. Compared with sporadic gastric GISTs, the gastric stromal tumor in Carney triad showed distinctive features: female predilection, young patient age, epithelioid cell predominance, multifocality, frequent lymph node metastasis, serial tumor occurrence, and unpredictable behavior. Thus, the Carney triad gastric stromal tumor is different clinically, pathologically, and behaviorally from sporadic gastric GIST.
Hybrid FDTD-Fresnel modeling of the scanning confocal microscopy (2009)

Scanning confocal microscopy is a widely recognized technique due to its applicability to the imaging of 3D geometries. Image formation in this technique is often analyzed using the Fresnel approximation. However, such an approximation is not sufficient when object dimensions are comparable to the operating wavelength and, most of all, when the target is composed of different semi-transparent materials. Yet, this is very typical for modern integrated circuits where we work with subwavelength features. In such a case target needs to be modeled using full-wave Maxwell theory. However, most of electromagnetic modeling methods (like well established FDTD method) become computationally impractical when the modeled scenario has dimensions measured in hundreds or even thousands of wavelengths like in the far-field microscopy. Therefore, in this paper we propose a hybrid approach that takes advantage of both FDTD and Fresnel approximation methods. The first method will be applied to the modeling of close vicinity of the target. The advantage of that is versatility in definition of arbitrarily shaped geometries as well as wideband approach of the FDTD method. Subsequently, results provided by the FDTD solver will be transferred to the procedure based on the scalar Fresnel approximation used to process the final image pixel by pixel. We will show that the presented method allows imaging of 3D shape of targets proving unique advantage of using FDTD method to the modeling of scanning confocal microscopy.
28nm FDSOI Platform with Embedded PCM for IoT, ULP, Digital, Analog, Automotive and others Applications (2019)

This paper proposes a general overview of Fully Depleted Silicon On Insulator (FDSOI) technology advantages leveraging body bias capability as a key enabler for digital, analog and memories performance enhancement. 2x total power contraction for digital designs has been demonstrating without any frequency degradation thanks to Forward Body Biasing (FBB), combined with 70% transistor variability reduction. Power of analog blocks has been strongly reduced with body bias technique while keeping trans-conductance efficiency increasing and output voltage gain. Finally, excellent memories performances has been achieved by applying FBB/RBB solution, dropping the leakage of unselected word-line in Phase Change Memory (PCM) array and improving Vmin operation for static RAM across a wide temperature range.
Purification of a 40-kilodalton methyltransferase active in the aflatoxin biosynthetic pathway (1993)

The penultimate step in the aflatoxin biosynthetic pathway of the filamentous fungi Aspergillus flavus and A. parasiticus involves conversion of sterigmatocystin to O-methylsterigmatocystin. An S-adenosylmethionine-dependent methyltransferase that catalyzes this reaction was purified to homogeneity (> 90%) from 78-h-old mycelia of A. parasiticus SRRC 163. Purification of this soluble enzyme was carried out by five soft-gel chromatographic steps: cell debris remover treatment, QMA ACELL chromatography, hydroxylapatite-Ultrogel chromatography, DEAE-Spherodex chromatography, and Octyl Avidgel chromatography, followed by MA7Q high-performance liquid chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the protein peak from this step on silver staining identified a single band of approximately 40 kDa. This purified protein was distinct from the dimeric 168-kDa methyltransferase purified from the same fungal strain under identical growth conditions (D. Bhatnagar, A. H. J. Ullah, and T. E. Cleveland, Prep. Biochem. 18:321-349, 1988). The chromatographic behavior and N-terminal sequence of the 40-kDa enzyme were also distinct from those of the 168-kDa methyltransferase. The molar extinction coefficient of the 40-kDa enzyme at 278 nm was estimated to be 4.7 x 10(4) M-1 cm-1 in 50 mM potassium phosphate buffer (pH 7.5).
Juvenile Traumatic Brain Injury Induces Long-Term Perivascular Matrix Changes Alongside Amyloid-Beta Accumulation (2014)

In our juvenile traumatic brain injury (jTBI) model, emergence of cognitive dysfunctions was observed up to 6 months after trauma. Here we hypothesize that early brain injury induces changes in the neurovascular unit (NVU) that would be associated with amyloid-beta (Aβ) accumulation. We investigated NVU changes for up to 6 months in a rat jTBI model, with a focus on the efflux protein P-glycoprotein (P-gp) and on the basement membrane proteins perlecan and fibronectin, all known to be involved in Aβ clearance. Rodent-Aβ staining is present and increased after jTBI around cerebral blood microvessels, and the diameter of those is decreased by 25% and 34% at 2 and 6 months, respectively, without significant angiogenesis. P-glycoprotein staining in endothelium is decreased by 22% and parallels an increase of perlecan and fibronectin staining around cerebral blood vessels. Altogether, these results strongly suggest that the emergence of long-term behavioral dysfunctions observed in rodent jTBI may be related to endothelial remodeling at the blood-brain barrier alongside vascular dysfunction and altered Aβ trafficking. This study shows that it is important to consider jTBI as a vascular disorder with long-term consequences on cognitive functions.
Characterization of neuronal discharge in the thoracic spinal cord during cardiac stress in a porcine model (2018)

Sudden cardiac death is the leading cause of death in the United States and is often caused by ventricular tachyarrhythmias (VT; Mozaffarian et al., 2015). Myocardial ischemia triggers imbalances in sympathetic and parasympathetic modulation, via the autonomic nervous system, and leads to the pathophysiology of cardiac arrhythmias. However, the spinal mechanism of this sympathetic neural control remains poorly understood. We hypothesize that cardiac stressors elicit distinct neural signatures in the dorsal horn (DH; the spinal relay point for cardiac afferents) and the intermediolateral (IML) nucleus of the thoracic spinal cord (the primary nexus for modulation of sympathetic efferent outflow). Adult, anesthetized Yorkshire pigs (n=9; 42 ± 1.6 kg) were implanted with high‐density microarrays (64–256 electrodes; Neuronexus) in the thoracic spinal cord to record extracellular potentials. Antidromic stimulation of the T 2 paravertebral chain allowed identification of sympathetic preganglionic neurons located in the IML (53 of total 1,757 neurons recorded). To characterize neuronal discharge, after a baseline recording, pigs repeatedly received: 1) chest scratch (SCR), 2) heart touch (THR), 3) ligation of the left anterior descending coronary artery (LAD), 4) occlusion of the inferior vena cava (IVC), or 5) occlusion of the descending aorta (AOC). Preliminary investigation of percent change in firing rate from baseline suggests complex neural signatures in DH and IML neurons during perturbations. A subset of DH neurons increased firing rate during SCR (8.29% of DH neurons), THR (10.70%), LAD (14.40%), IVC (21.57%), and AOC (6.13%). Firing rate increased in a subset of IML neurons as well (3.84% during SCR, 26.92% during THR, 18.87% during LAD, 20.75% during IVC, and 12.12% during AOC). In contrast, firing rate decreased in 4.89% of DH neurons during SCR, 20.88% during THR, 21.63% during LAD, 16.44% during IVC, and 9.85% during AOC. Additionally, rates decreased in a small population of IML neurons (3.84% during SCR, 7.69% during THR, 28.30% during LAD, 5.66% during IVC, and 18.18% during AOC). Subsequent analysis revealed positive correlations between DH and IML neurons, indicating excitatory neuronal connectivity. Further investigation is warranted to understand the temporally related discharge patterns as well as the inhibitory or excitatory nature of these connections. These preliminary data pave a potential pathway to develop targeted neuraxial interventions in cases of intractable ventricular arrhythmia. Support or Funding Information HL084261, T32‐HD043730 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction (2022)

Abstract AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ±80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).
Transparent Embedded Compression in Systems-on-Chip (2006)

Bandwidth to off-chip memory is a scarce resource in complex systems-on-chip for embedded media processing. We apply embedded compression for bandwidth-hungry image processing functions in order to alleviate this bandwidth bottleneck. In our solution embedded compression is implemented as part of the system-on-chip infrastructure, fully transparent for the hardware and software image processing components. Hence it can be applied without requiring changes to these components. We present the compression algorithm and demonstrate that we achieve significant bandwidth reductions (20%-40%) for image data at acceptable cost (approximately 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 90 nm CMOS) while preserving high image quality
Highly sensitive low-frequency Raman spectroscopy enabled by Sagnac-enhanced impulsive stimulated Raman scattering (Conference Presentation) (2020)

By virtue of its chemical specificity and label-free nature, Raman spectroscopy is a ubiquitous tool in analytical chemistry which has recently found increasing interest in biology and medicine, as technical improvements steadily enable applications. In particular, the low-frequency region of the Raman spectrum, which contains rich information about intermolecular interactions and higher-order structure, has promise for biological applications. However, detection of low-frequency modes remains a challenge with conventional techniques for Raman spectroscopy. Here, we propose and experimentally demonstrate Sagnac-enhanced impulsive stimulated Raman scattering (SE-ISRS), a method for time-domain Raman spectroscopy that provides highly sensitive low-frequency Raman spectra at all probe frequencies.
Drop circulation and liquid<U+2010>liquid extraction in Hele<U+2010>Shaw flow. (2016)

Abstract not provided.
Sequence Specific Alkylation of DNA by Polyamide-Chlorambucil Conjugates (2012)

Small molecules that bind selectively to a DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of "pairing rules" with affinities and specificities similar to many naturally occurring DNA binding proteins. Two alternate routes of synthesis of polyamides are presented that allowed improved synthesis of commonly used motifs as well as access to polyamides with truncated tails which increase the number of DNA sequences targetable by polyamides with high affinity. Py-Im polyamides may offer a general approach to chemical regulation of gene expression provided inhibition of DNA binding for a variety of transcription factor families can be achieved. Two successful strategies are shown for the inhibition of DNA binding by two such proteins, GCN4 and NF-κB. An alternate method of gene regulation would be inhibition of transcription during the elongation phase by site-specific alkylation in the coding region of genes. A new class of compounds is created by the attachment of a bis (dichloroethylamino)-benzene nonspecific DNA alkylator to polyamides, which alkylate DNA with high yield and specificity. The biological activity and cell permeability of one of these compounds in several systems is studied.