gebhart/patrepeval huggingface dataset:
Divide and Conquer: PC-Based Packet Trace Replay at OC-48 Speeds (2005)

Today's Internet backbone networking devices need to be tested under realistic traffic conditions at transmission rates of OC-48 and above. While commercially available synthetic traffic generators are capable of keeping up with high transmission rates, they fail to produce realistic mixes of flow, packet and address arrival patterns. We explore the alternative of replaying real packet traces from high-speed links using multiple commodity PCs equipped with lower-speed network interfaces. Such an approach is inherently cost-effective because of the use of commodity hardware and can scale up to any desired transmission rate. We first examine how to split a trace among multiple PCs for the purpose of replaying and validate our technique using simulations. We use a wavelet 'spectrum' or energy plot for this purpose which enables traffic processes to be viewed simultaneously on many time-scales. Then we present an implementation using Linux PCs with gigabit Ethernet interfaces to replay OC-48 packet traces from the Sprint backbone. Our results show that the replayed trace is very similar to the original trace at most time scales. We are also able to pinpoint the specific system components that contributed to the replay inaccuracy, as well as identify several important challenges that remain to be explored in-depth.
The inhibition of antigen-presenting activity of dendritic cells resulting from UV irradiation of murine skin is restored by<i>in vitro</i>photorepair of cyclobutane pyrimidine dimers (1997)

Exposing skin to UVB (280-320 nm) radiation suppresses contact hypersensitivity by a mechanism that involves an alteration in the activity of cutaneous antigen-presenting cells (APC). UV-induced DNA damage appears to be an important molecular trigger for this effect. The specific target cells in the skin that sustain DNA damage relevant to the immunosuppressive effect have yet to be identified. We tested the hypothesis that UV-induced DNA damage in the cutaneous APC was responsible for their impaired ability to present antigen after in vivo UV irradiation. Cutaneous APC were collected from the draining lymph nodes of UVB-irradiated, hapten-sensitized mice and incubated in vitro with liposomes containing a photolyase (Photosomes; Applied Genetics, Freeport, NY), which, upon absorption of photoreactivating light, splits UV-induced cyclobutane pyrimidine dimers. Photosome treatment followed by photoreactivating light reduced the number of dimer-containing APC, restored the in vivo antigen-presenting activity of the draining lymph node cells, and blocked the induction of suppressor T cells. Neither Photosomes nor photoreactivating light alone, nor photoreactivating light given before Photosomes, restored APC activity, and Photosome treatment did not reverse the impairment of APC function when isopsoralen plus UVA (320-400 nm) radiation was used instead of UVB. These controls indicate that the restoration of APC function matched the requirements of Photosome-mediated DNA repair for dimers and post-treatment photoreactivating light. These results provide compelling evidence that it is UV-induced DNA damage in cutaneous APC that leads to reduced immune function.
Mechanisms of resistance to imatinib mesylate in Bcr-Abl–positive leukemias (2002)

The constitutive activity of the Bcr-Abl tyrosine kinase plays a critical role in the molecular pathogenesis of not only the chronic but also the accelerated and blastic phases of chronic myelogenous leukemia. Therefore, Bcr-Abl tyrosine kinase is a rational therapeutic target in all phases of chronic myelogenous leukemia. Although imatinib mesylate (STI571, Gleevec, Novartis, Basal, Switzerland) produces high rates of complete clinical and cytogenetic responses in the chronic phase, resistance is universal and clinical relapse develops rapidly in the advanced phases of chronic myelogenous leukemia. This resistance has been shown to be caused by specific ATP binding site mutations or amplification of Bcr-Abl gene, resulting in a Bcr-Abl tyrosine kinase that is resistant to further inhibition by imatinib. Alternative (Bcr-Abl-independent) mechanisms driving the growth and survival of the malignant clone may also be responsible for imatinib resistance. Novel tyrosine kinase inhibitors that also target Bcr-Abl tyrosine kinase, or agents that downregulate Bcr-Abl levels regardless of its wild-type or mutant status, may need to be developed clinically for the future therapy of imatinib-resistant chronic myelogenous leukemia.
Characterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize. Novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton internal peptide segment. (1991)

Ribosome-inactivating proteins (RIPs) are a widely distributed family of plant enzymes that are remarkably potent catalytic inactivators of eukaryotic protein synthesis. All RIPs described to date, including the A-chain of the plant cytotoxin ricin, are polypeptides of 25-32 kDa and share significant amino acid sequence homologies. We have characterized and cloned an RIP from maize (Zea mays). In contrast to previously described RIPs, we have found that maize RIP is synthesized and stored in the kernel as a 34-kDa inactive precursor (isoelectric point = 6.5). During germination, this neutral precursor is converted into a basic, active form (isoelectric point greater than 9) by limited proteolysis, which removes 25 amino acids (2.8 kDa) of net charge -6 from the center of the polypeptide chain. Additional processing also occurs at the amino and carboxyl termini of the polypeptide. The sequence of the internal processed region is unique and it is equivalent to an insertion centered around Thr-156 in the amino acid sequence of ricin toxin A-chain, i.e. in the center of the enzymatically active domain. The generation of an active enzyme by removal of a large amino acid segment from the middle of a precursor polypeptide chain represents a novel mechanism of proenzyme activation that is distinct from more conventional activation mechanisms involving NH2-terminal proteolytic processing. A two-chain active RIP (comprised of 16.5- and 8.5-kDa fragments that remain tightly associated) is produced from this processing event.
Frontal lobe bioenergetic metabolism in depressed adolescents with bipolar disorder: a phosphorus‐31 magnetic resonance spectroscopy study (2012)

Our results support the view that frontal lobe mitochondrial function is altered in adolescent BD and may have implications for the use of Pi as a biomarker. These findings join volumetric studies of the amygdala, and proton MRS studies of n-acetyl aspartate in pointing to potential differences in neurobiology between pediatric and adult BD.
A hybrid method for 2-D/3-D registration between 3-D volumes and 2-D angiography for trans-catheter aortic valve implantation (TAVI) (2011)

Minimally invasive trans-catheter aortic valve implantation (TAVI) procedure can be greatly facilitated using smart visualization and guidance technology involving the 3-D model of the aorta. In this paper, a hybrid method is proposed for contrast-based registration between the 3-D model and angiography of the aorta during TAVI procedures. By integrating the information of aorta segmentation and aortic landmark detection into intensity-based registration, the proposed method combines the merits of intensity-based registration and feature/landmark-based registration. In addition, the challenging task of explicit feature/landmark extraction on 2-D images is avoided. Experiments on 9 real clinical data achieved an average registration error of 2.14±0.49 pixels, demonstrating the efficacy of the proposed method.
New fluorinated erythromycins obtained by mutasynthesis. (1983)

Following the previously described semisynthetic preparation of new aglycones (8S)-8-fluoroerythronolide A (I), (8S)-8-fluoroerythronolide B (II) and the monoglycoside 3-O-mycarosyl-(8S)-8-fluoroerythronolide B (III), their conversion into new fluoroerythromycins was attempted by mutational biosynthesis. The strain Streptomyces erythraeus ATCC 31772, a mutant blocked in the biosynthesis of erythromycin, was employed in the present investigation. Four new antibiotics, (8S)-8-fluoroerythromycin A (IV), (8S)-8-fluoroerythromycin B (V), (8S)-8-fluoroerythromycin C (VI) and (8S)-8-fluoroerythromycin D (VII) were successfully derived by such an approach. The result is also discussed in terms of the substrate specificity of the enzymes involved in the biosynthesis of erythromycins. The new antibiotics exhibited promising biological properties.
Peripherally Selective Cannabinoid 1 Receptor (CB1R) Agonists for the Treatment of Neuropathic Pain (2016)

Alleviation of neuropathic pain by cannabinoids is limited by their central nervous system (CNS) side effects. Indole and indene compounds were engineered for high hCB1R affinity, peripheral selectivity, metabolic stability, and in vivo efficacy. An epithelial cell line assay identified candidates with <1% blood-brain barrier penetration for testing in a rat neuropathy induced by unilateral sciatic nerve entrapment (SNE). The SNE-induced mechanical allodynia was reversibly suppressed, partially or completely, after intraperitoneal or oral administration of several indenes. At doses that relieve neuropathy symptoms, the indenes completely lacked, while the brain-permeant CB1R agonist HU-210 (1) exhibited strong CNS side effects, in catalepsy, hypothermia, and motor incoordination assays. Pharmacokinetic findings of ∼0.001 cerebrospinal fluid:plasma ratio further supported limited CNS penetration. Pretreatment with selective CB1R or CB2R blockers suggested mainly CB1R contribution to an indene's antiallodynic effects. Therefore, this class of CB1R agonists holds promise as a viable treatment for neuropathic pain.
<scp>AssistOn-Mobile</scp>: a series elastic holonomic mobile platform for upper extremity rehabilitation (2014)

SUMMARY We present the design, control, and human–machine interface of a series elastic holonomic mobile platform, AssistOn-Mobile , aimed to administer therapeutic table-top exercises to patients who have suffered injuries that affect the function of their upper extremities. The proposed mobile platform is a low-cost, portable, easy-to-use rehabilitation device targeted for home use. In particular, AssistOn-Mobile consists of a holonomic mobile platform with four actuated Mecanum wheels and a compliant, low-cost, multi-degrees-of-freedom series elastic element acting as its force sensing unit. Thanks to its series elastic actuation, AssistOn-Mobile is highly backdriveable and can provide assistance/resistance to patients, while performing omni-directional movements on plane. AssistOn-Mobile also features Passive Velocity Field Control (PVFC) to deliver human-in-the-loop contour tracking rehabilitation exercises. PVFC allows patients to complete the contour-tracking tasks at their preferred pace, while providing the proper amount of assistance as determined by the therapists. PVFC not only minimizes the contour error but also does so by rendering the closed-loop system passive with respect to externally applied forces; hence, ensures the coupled stability of the human-robot system. We evaluate the feasibility and effectiveness of AssistOn-Mobile with PVFC for rehabilitation and present experimental data collected during human subject experiments under three case studies. In particular, we utilize AssistOn-Mobile with PVFC (a) to administer contour following tasks where the pace of the tasks is left to the control of the patients, so that the patients can assume a natural and comfortable speed for the tasks, (b) to limit compensatory movements of the patients by integrating a RGB-D sensor to the system to continually monitor the movements of the patients and to modulate the task speeds to provide online feedback to the patients, and (c) to integrate a Brain–Computer Interface such that the brain activity of the patients is mapped to the robot speed along the contour following tasks, rendering an assist-as-needed protocol for the patients with severe disabilities. The feasibility studies indicate that AssistOn-Mobile holds promise in improving the accuracy and effectiveness of repetitive movement therapies, while also providing quantitative measures of patient progress.
On the design of efficient constrained parity-check codes for optical recording (2005)

This paper proposes a general and systematic way to efficiently combine constrained codes with parity-check (PC) codes for optical recording. The proposed constrained PC code includes two component codes: the normal constrained (NC) code and the parity-related constrained (PRC) code. They are designed based on the same finite state machine (FSM). The code rates are only a few tenths below the theoretical maximum. The parity-check constraint is defined by the generator matrix (or generator polynomial) of a linear binary PC code, which can detect any type of dominant error events as well as error event combinations of the system. Two approaches are proposed to design the code in the non-return-to-zero-inverse (NRZI) format and the non-return-to-zero (NRZ) format, respectively. Designing the codes in NRZ format may reduce the number of parity bits required for error detection and simplify post-processing for error correction. Finally, examples of several newly designed codes and their performances are illustrated
Accelerated focused ultrasound imaging (2009)

One of the most basic trade-offs in ultrasound imaging involves frame rate, depth, and number of lines. Achieving good spatial resolution and coverage requires a large number of lines, leading to decreases in frame rate. An even more serious imaging challenge occurs with imaging modes involving spatial compounding and 3-D/4-D imaging, which are severely limited by the slow speed of sound in tissue. The present work can overcome these traditional limitations, making ultrasound imaging many-fold faster. By emitting several beams at once, and by separating the resulting overlapped signals through spatial and temporal processing, spatial resolution and/or coverage can be increased by many-fold while leaving frame rates unaffected. The proposed approach can also be extended to imaging strategies that do not involve transmit beamforming, such as synthetic aperture imaging. Simulated and experimental results are presented where imaging speed is improved by up to 32-fold, with little impact on image quality. Object complexity has little impact on the method's performance, and data from biological systems can readily be handled. The present work may open the door to novel multiplexed and/or multidimensional protocols considered impractical today.
Novel chemical recycling of polycarbonate (PC) waste into bis-hydroxyalkyl ethers of bisphenol A for use as PU raw materials (2006)

An efficient process for the chemical recycling of polycarbonate (PC) waste into diols of bis-phenol A (BPA) for use as raw materials in PU production has been developed. Digestion of PC waste in alkylene glycols, i.e., ethylene glycol (EG) and propylene glycol (PG), with a catalytic amount of sodium carbonate at 180 °C under normal atmospheric pressure afforded partial alkoxylation products of BPA. This initial product mixture was found to consist of BPA (28%) and monohydroxyethyl ether (MHE-BPA, 40%) and bishydroxyethyl ether of bisphenol A (BHE-BPA, 25%) when digested in EG solution. Whereas, in PG digestion solution, the corresponding digestion products consist of monohydroxypropyl ether of BPA (MHP-BPA, 53%) and bishydroxypropyl ether of BPA (BHP-BPA, 21%), with the rest being un-propoxylated BPA. When these digested solutions were further treated with molar excess of urea with a catalytic amount of zinc oxide at 180 °C, BHE from EG or BHP-BPA from PG was produced in high yields. In both digestion processes, cyclic alkylene carbonates, i.e.ethylene carbonate (EC) or propylene carbonate (PPC), were observed as the transient intermediates which eventually disappear during the prolonged alkoxylation conditions. ZnO was added to the second step as the catalyst to accelerate urea's trans-esterification process. Both BHE and BHP products have been sucessfully utilized in making PU polymers with good mechanical properties. This chemical approach thus provides a viable alternative for PC recycling.
The Monotonic Lagrangian Grid for Rapid Air-Traffic Evaluation (2010)

The Air Traffic Monotonic Lagrangian Grid (ATMLG) is presented as a tool to evaluate new air traffic system concepts. The model, based on an algorithm called the Monotonic Lagrangian Grid (MLG), can quickly sort, track, and update positions of many aircraft, both on the ground (at airports) and in the air. The underlying data structure is based on the MLG, which is used for sorting and ordering positions and other data needed to describe N moving bodies and their interactions. Aircraft that are close to each other in physical space are always near neighbors in the MLG data arrays, resulting in a fast nearest-neighbor interaction algorithm that scales as N. Recent upgrades to ATMLG include adding blank place-holders within the MLG data structure, which makes it possible to dynamically change the MLG size and also improves the quality of the MLG grid. Additional upgrades include adding FAA flight plan data, such as way-points and arrival and departure times from the Enhanced Traffic Management System (ETMS), and combining the MLG with the state-of-the-art strategic and tactical conflict detection and resolution algorithms from the NASA-developed Stratway software. In this paper, we present results from our early efforts to couple ATMLG with the Stratway software, and we demonstrate that it can be used to quickly simulate air traffic flow for a very large ETMS dataset.
An Experimental Study on Prototype Lithium–Sulfur Cells for Aging Analysis and State-of-Health Estimation (2021)

Lithium-sulfur (Li-S) batteries offer potential for higher gravimetric energy density in comparison to lithium-ion batteries. Since they behave quite different from lithium-ion batteries, distinctive approaches to state estimation and battery management are required to be developed specifically for them. This article describes an experimental work to model and perform real-time estimation of the progression of use-induced aging in prototype Li-S cells. To do that, state-of-the-art 19-Ah Li-S pouch cells were subject to cycling tests in order to determine progressive changes in parameters of a nonlinear equivalent-circuit-network (ECN) model due to aging. A state-of-health (SoH) estimation algorithm was then designed to work based on identifying ECN parameters using forgetting-factor recursive least squares (FFRLS). Two techniques, nonlinear curve fitting and support vector machine (SVM) classification, were used to generate SoH values according to the identified parameters. The results demonstrate that Li-S cell's SoH can be estimated with an acceptable level of accuracy of 96.7% using the proposed method under realistic driving conditions. Another important outcome was that the “power fade” in Li-S cells happens at a much slower rate than the “capacity fade” which is a useful feature for applications where consistency of power delivery is important.
A New CAD System for Early Diagnosis of Detected Lung Nodules (2007)

A pulmonary nodule is the most common manifestation of lung cancer. Lung nodules are approximately-spherical regions of relatively high density that are visible in X-ray images of the lung. Large (generally defined as greater than 1 cm in diameter) malignant nodules can be easily detected with traditional imaging equipment and can be diagnosed by needle biopsy or bronchoscopy techniques. However, the diagnostic options for small malignant nodules are limited due to problems associated with accessing small tumors, especially if they are located deep in the tissue or away from the large airways; therefore, additional diagnostic and imaging techniques are needed. One of the most promising techniques for detecting small cancerous nodules relies on characterizing the nodule based on its growth rate. The growth rate is estimated by measuring the volumetric change of the detected lung nodules over time, so it is important to accurately measure the volume of the nodules to quantify their growth rate over time. In this paper, we introduce a novel Computer Assisted Diagnosis (CAD) system for early diagnosis of lung cancer. The proposed CAD system consists of five main steps. These steps are: (i) segmentation of lung tissues from low dose computed tomography (LDCT) images, (ii) detection of lung nodules from segmented lung tissues, (iii) a non-rigid registration approach to align two successive LDCT scans and to correct the motion artifacts caused by breathing and patient motion, (iv) segmentation of the detected lung nodules, and (v) quantification of the volumetric changes. Our preliminary classification results based on the analysis of the growth rate of both benign and malignant nodules for 10 patients (6 patients diagnosed as malignant and 4 diagnosed as benign) were 100% for 95% confidence interval. The preliminary results of the proposed image analysis have yielded promising results that would supplement the use of current technologies for diagnosing lung cancer.
Gene Cloning and Overexpression of a Geranylgeranyl Diphosphate Synthase of an Extremely Thermophilic Bacterium,<i>Thermus thermophilus</i> (1999)

A geranylgeranyl diphosphate (GGPP) synthase gene of an extremely thermophilic bacterium, Thermus thermophilus, was cloned and sequenced. T. thermophilus GGPP synthase, overexpressed in Escherichia coli cells as a glutathione S-transferase fusion protein, was purified and characterized. The fusion protein, retaining thermostability, formed a homodimer, and showed higher specific activity than did a partially purified thermostable enzyme previously reported. Optimal reaction conditions and kinetic parameters were also examined. The deduced amino acid sequence indicated that T. thermophilus GGPP synthase was excluded from the group of bacterial type GGPP synthases and lacked the insertion amino acid residues in the first aspartate-rich motif as do archaeal and eukaryotic short-chain prenyltransferases.
Performance of various quantum-key-distribution systems using<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mn>1.55</mml:mn><mml:mtext>‐</mml:mtext><mml:mi>μ</mml:mi><mml:mi mathvariant="normal">m</mml:mi></mml:mrow></mml:math>up-conversion single-photon detectors (2005)

We compare the performance of various quantum-key-distribution (QKD) systems using a single-photon detector, which combines frequency up-conversion in a periodically poled lithium niobate waveguide and a silicon avalanche photodiode (APD). The comparison is based on the secure communication rate as a function of distance for three QKD protocols: the Bennett-Brassard 1984, the Bennett-Brassard-Mermin 1992, and the coherent differential-phase-shift keying protocols. We show that the up-conversion detector allows for higher communication rates and longer communication distances than the commonly used $\mathrm{In}\mathrm{Ga}\mathrm{As}∕\mathrm{InP}$ APD for all three QKD protocols.
Phase-referenced doppler optical coherence tomography (2003)

A phase-referenced Doppler optical coherence tomography (OCT) system includes a low-coherence optical radiation source and a reference source co-propagated to a sample arm and a reference arm. The low-coherence and reference optical radiation reflected from the reference and arms is detected by a pair of detectors, yielding OCT and reference interferometric data output signals. The reference interferometric data output signal can be used to correct the OCT interferometric to yield velocity-indicating images that are free from defects due to sample motion and/or interferometer jitter.