gebhart/patrepeval huggingface dataset:
Modeling digital substrate noise injection in mixed-signal IC's (1999)

Techniques are presented to compactly represent substrate noise currents injected by digital networks. Using device-level simulation, every gate in a given library is modeled by means of the signal waveform it injects into the substrate, depending on its input transition scheme. For a given sequence of input vectors, the switching activity of every node in the Boolean network is computed. Assuming that technology mapping has been performed, each node corresponds to a gate in the library, hence, to a specific injection waveform. The noise contribution of each node is computed by convolving its switching activity with the associated injection waveforms. The total injected noise for the digital block is then obtained by summing all the noise contributions in the circuit. The resulting injected noise can be viewed as a random process, whose power spectrum is computed using standard signal processing techniques. A study was performed on a number of standard benchmark circuits to verify the validity of the assumptions and to measure the accuracy of the obtained power spectra.
Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages (2006)

Studies of human mitochondrial (mt) DNA genomes demonstrate that the root of the human phylogenetic tree occurs in Africa. Although 2 mtDNA lineages with an African origin (haplogroups M and N) were the progenitors of all non-African haplogroups, macrohaplogroup L (including haplogroups L0-L6) is limited to sub-Saharan Africa. Several L haplogroup lineages occur most frequently in eastern Africa (e.g., L0a, L0f, L5, and L3g), but some are specific to certain ethnic groups, such as haplogroup lineages L0d and L0k that previously have been found nearly exclusively among southern African "click" speakers. Few studies have included multiple mtDNA genome samples belonging to haplogroups that occur in eastern and southern Africa but are rare or absent elsewhere. This lack of sampling in eastern Africa makes it difficult to infer relationships among mtDNA haplogroups or to examine events that occurred early in human history. We sequenced 62 complete mtDNA genomes of ethnically diverse Tanzanians, southern African Khoisan speakers, and Bakola Pygmies and compared them with a global pool of 226 mtDNA genomes. From these, we infer phylogenetic relationships amongst mtDNA haplogroups and estimate the time to most recent common ancestor (TMRCA) for haplogroup lineages. These data suggest that Tanzanians have high genetic diversity and possess ancient mtDNA haplogroups, some of which are either rare (L0d and L5) or absent (L0f) in other regions of Africa. We propose that a large and diverse human population has persisted in eastern Africa and that eastern Africa may have been an ancient source of dispersion of modern humans both within and outside of Africa.
Spun linear birefringence fibres and their sensing mechanism in current sensors with temperature compensation (1994)

A single-mode spun linear birefringence fibre is investigated as a periodic structure. By using coupled-mode theory, the modal fields and the propagation coefficients of the two eigenmodes in this fibre are given theoretically for the first time. A spun highly linear birefringence (SHB) fibre is capable of acting as a sensing coil of relatively high sensitivity and temperature stability in current sensors. The mechanism of compensation and the sensitivities of current with SHB fibres and temperature compensation are studied extensively with the above eigenmode theory. The relations of sensitivity and temperature stability to parameters of SHB fibres and light sources are derived. The averaging effect caused by the broadband spectrum of the light source, which effectively eliminate the temperature instability, is investigated quantitatively with the partial-coherent-light theory.
Membrane Association and Protein Conformation of α-Synuclein in Intact Neurons (2000)

Two missense mutations (Ala-30 --> Pro and Ala-53 --> Thr) in the gene encoding alpha-synuclein are associated with rare autosomal dominant forms of familial Parkinson's disease. In addition, alpha-synuclein is an abundant component of Lewy bodies in sporadic Parkinson's disease and diffuse Lewy body disease. However, the normal conformation of alpha-synuclein, its cellular localization in neurons, and the effects of the mutations remain to be determined. In the present study, we examine these questions using sensitive fluorescence resonance energy transfer techniques. Transient transfection of alpha-synuclein expression constructs into primary cortical neurons and counterstaining with the lipophilic fluorescent marker, DiI, demonstrates a close association between alpha-synuclein and cellular membranes. Both the N- and C-terminal regions of alpha-synuclein are tightly associated with membranes. A weak interaction also occurs between the N and C termini themselves. The Parkinson's disease-associated mutations have no effect on membrane interaction; however, the Ala-30 --> Pro mutation alters the three-dimensional conformation of alpha-synuclein, as measured by significantly increased fluorescence resonance energy transfer between the N and C termini.
Synthesis of FPGA Implementations from Loop Algorithms (2001)

Soil pollution is an important ecological problem worldwide. Phytoremediation is an environmental-friendly option for reducing metal pollution. A greenhouse experiment was conducted to determine the growth and physiological response, metal uptake, and the phytostabilization potential of a nontoxic Jatropha curcas L. genotype when grown in multimetal-polluted conditions. Plants were established on a mine residue (MR) amended or not amended with corn biochar (B) and inoculated or not inoculated with the mycorrhizal fungus Acaulospora sp. (arbuscular mycorrhizal fungus, AMF). J. curcas was highly capable of growing in an MR and showed no phytotoxic symptoms. After J. curcas growth (105 days), B produced high desorption of Cd and Pb from the MR; however, no increases in metal shoot concentrations were observed. Therefore, Jatropha may be useful for phytostabilization of metals in mine tailings. The use of B is recommended because improved MR chemical properties conduced to plant growth (cation-exchange capacity, organic matter content, essential nutrients, electrical conductivity, water-holding capacity) and plant growth development (higher biomass, nutritional and physiological performance). Inoculation with an AMF did not improve any plant growth or physiological plant characteristic. Only higher Zn shoot concentration was observed, but it was not phytotoxic. Future studies of B use and its long-term effect on MR remediation should be conducted under field conditions.
Cationic polymers and their therapeutic potential (2012)

The last decade has witnessed enormous research focused on cationic polymers. Cationic polymers are the subject of intense research as non-viral gene delivery systems, due to their flexible properties, facile synthesis, robustness and proven gene delivery efficiency. Here, we review the most recent scientific advances in cationic polymers and their derivatives not only for gene delivery purposes but also for various alternative therapeutic applications. An overview of the synthesis and preparation of cationic polymers is provided along with their inherent bioactive and intrinsic therapeutic potential. In addition, cationic polymer based biomedical materials are covered. Major progress in the fields of drug and gene delivery as well as tissue engineering applications is summarized in the present review.
Leukemia inhibitory factor improves survival of retroviral vector-infected hematopoietic stem cells in vitro, allowing efficient long-term expression of vector-encoded human adenosine deaminase in vivo. (1991)

Low recovery and poor retroviral vector infection efficiency of hematopoietic stem cells has hindered application of gene therapy for disease affecting blood-forming tissues. Developmental restriction (or death) of stem cells during ex vivo infection has contributed to these difficulties. In these studies we report that the cytokine leukemia inhibitory factor (LIF) directly or indirectly supported the survival of hematopoietic stem cells during culture of bone marrow with vector-producing fibroblasts, resulting in efficient recovery of stem cells able to compete for engraftment in irradiated recipient animals. The infection efficiency of hematopoietic stem cells recovered from these cultures was approximately 80%; and all recipients (20/20) of the LIF-treated marrow were stably engrafted with the progeny of provirus-bearing stem cells. Expression of vector-encoded human adenosine deaminase (hADA) was detected in all recipients at levels averaging 15-50% of endogenous murine ADA in all their hematolymphoid tissues. Survival of stem cells in untreated cultures was approximately 10% of that observed from LIF-treated cultures, resulting in poor engraftment of recipient animals with transplanted cells. The infection efficiency of the few stem cells recovered from untreated cultures, however, was high (approximately 80%), suggesting that LIF did not have an effect on infection efficiency per se, but acted at the level of stem cell survival. Consistent with the poor engraftment observed in the control animals, expression of vector-encoded ADA was only approximately 4-20% of the endogenous levels. These results support the postulated role of LIF as a regulator of hematopoiesis and suggest that cytokine stimulation can positively affect inefficient retroviral vector transduction in hematopoietic stem cells.
Pulse Wave Analysis (2011)

Cardiovascular refers to the Cardio (heart) and vascular (blood vessels). The system has two major functional parts: central circulation system and systemic circulation system. Central circulation includes the pulmonary circulation and the heart from where the pulse wave is generated. Systemic circulation is the path that the blood goes from and to the heart. (Green 1984) Pulse wave is detected at arteries which include elastic arteries, medium muscular arteries, small arteries and arterioles. The typical muscular artery has three layers: tunica intima as inner layer, tunica media as middle layer, and tunica adventitia for the outer layer. (Kangasniemi & Opas 1997) The material properties of arteries are highly nonlinear. (langewouters et al. 1984) It depends on the contents of arterial wall: how collagen, elastin and protein are located in the arteries. Functional and structural changes in the arterial wall can be used as early marker for the hypertensive and cardiac diseases. Blood flow is the key to monitor the cardiovascular health condition since it is generated and restrict within such system. Currently the most widely used method for haemodynamic parameters detecting is invasive thermo-dilution method. Impedance-cardiography is the most commonly used non-invasive method nowadays; however, it is too complex for clinical routine check. Pulse wave analysis is an innovative method in the market to do fast and no burden testing (Zhang et al. 2008) Pulse is one of the most critical signals of human life. It comes directly from heart to the blood vessel system. As pulse transmitted, reflections will occur at different level of blood vessels. Other conditions such as resistance of blood flow, elastic of vessel wall, and blood viscosity have clear influence on pulse. Pathological changes affect pulse in different ways: the strength, reflection, and frequency. So pulse provides abundant and reliable information about cardiovascular system. Pulse can be recorded to a set of time series data and represented as a diagraph which is called pulse waveform or pulse wave for short. Gathering pulse at wrist by finger has been a major diagnosis method in China since 500 BC. Physicians used palpation of the pulse as a diagnostic tool during the examination. In 300AD, “Maijing” categoried pulse into 24 types and became the first systematic literature about the pulse. Grecian started to notice the rhythm, strength, and velocity at 400BC. Struthius described a method to watch the pulse wave by putting a leaf on the artery, which is considered as early stage of pulse wave monitoring. In 1860, Etienne Jules Mary invented a level based sphygmograph to measure the pulse rate. It is the first device can actually record the pulse wave. Frederick observed normal radial pressure wave and the carotid
Atomistic Insights into the Conversion Reaction in Iron Fluoride: A Dynamically Adaptive Force Field Approach (2012)

Nanoscale metal fluorides are promising candidates for high capacity lithium ion batteries, in which a conversion reaction upon exposure to Li ions enables access to the multiple valence states of the metal cation. However, little is known about the molecular mechanisms and the reaction pathways in conversion that relate to the need for nanoscale starting materials. To address this reaction and the controversial role of intercalation in a promising conversion material, FeF(2), a dynamically adaptive force field that allows for a change in ion charge during reactions is applied in molecular dynamics simulations. Results provide the atomistic view of this conversion reaction that forms nanocrystals of LiF and Fe(0) and addresses the important controversy regarding intercalation. Simulations of Li(+) exposure on the low energy FeF(2) (001) and (110) surfaces show that the reaction initiates at the surface and iron clusters as well as crystalline LiF are formed, sometimes via an amorphous Li-F. Li intercalation is also observed as a function of surface orientation and rate of exposure to the Li, with different behavior on (001) and (110) surfaces. Intercalation along [001] rapid transport channels is accompanied by a slight reduction of charge density on multiple nearby Fe ions per Li ion until enough Li saturates a region and causes the nearby Fe to lose sufficient charge to become destabilized and form the nanocluster Fe(0). The resultant nanostructures are fully consistent with postconversion TEM observations, and the simulations provide the solution to the controversy regarding intercalation versus conversion and the atomistic rationale for the need for nanoscale metal fluoride starting particles in conversion cathodes.
Control in building energy management systems: the role of simulation (2001)

Technological advances in real-time data collection, data transfer and ever-increasing computational power are bringing simulation assisted control and on-line fault detection and diagnosis closer to reality than was imagined when Building Energy Management Systems were introduced in the 1970s. This paper describes the development and testing of a prototype simulation assisted controller, in which adetailed simulation program is embedded in realtime control decision making. Results from an experiment in a full-scale environmental test facility demonstrate the feasibility of predictive control using a physically-based thermal simulation program.
Ultra-High Dose Rate (FLASH) Radiotherapy: Silver Bullet or Fool's Gold? (2020)

Radiotherapy is a cornerstone of both curative and palliative cancer care. However, radiotherapy is severely limited by radiation-induced toxicities. If these toxicities could be reduced, a greater dose of radiation could be given therefore facilitating a better tumor response. Initial pre-clinical studies have shown that irradiation at dose rates far exceeding those currently used in clinical contexts reduce radiation-induced toxicities whilst maintaining an equivalent tumor response. This is known as the FLASH effect. To date, a single patient has been subjected to FLASH radiotherapy for the treatment of subcutaneous T-cell lymphoma resulting in complete response and minimal toxicities. The mechanism responsible for reduced tissue toxicity following FLASH radiotherapy is yet to be elucidated, but the most prominent hypothesis so far proposed is that acute oxygen depletion occurs within the irradiated tissue. This review examines the tissue response to FLASH radiotherapy, critically evaluates the evidence supporting hypotheses surrounding the biological basis of the FLASH effect, and considers the potential for FLASH radiotherapy to be translated into clinical contexts.
Oligodeoxynucleotides containing 2'-fluoro-arabino-nucleotide and C-nucleotide. (1993)

Oligonucleotides containing 2'-fluoro-ara-pyrimidines and 1-methyl-2'-deoxy-psi-uridine were synthesized. The melting profiles show that the presence of FMAU has a large stabilizing effect on the duplex. Replacement of dT with FAU or psi-dT, or dC with FAC resulted in the formation of less stable duplexes. Temperature-dependent CD spectroscopy demonstrated that the structures of these oligomers are very similar to those of unmodified oligomers, however, these minor alterations in structure of dodecamers resulted in faster splitting by endonuclease EcoR1.
<title>Affine-transform-based image vector quantizer</title> (1993)

In this paper, we propose an affine transform based vector quantization (ATVQ) technique for image coding applications. Vector quantization (VQ) is intrinsically superior to predictive coding, transform coding, and other suboptimal and ad hoc procedures. The limitation of VQ is the very large codebook that must be generated and stored. The proposed affine transform based vector quantization technique addresses this problem. The image to be coded is partitioned into disjoint square blocks. Each block is regarded as a vector and is encoded by searching through a set of affine transforms and a codebook of templates. The transform- template pair that can reconstruct an approximate input vector with minimum distortion is selected. The parameters and the index of the affine transform and the index of the template constitute the codeword of the input vector. In decoding, the image vector is reconstructed by applying the inverse of the affine transform on the template. ATVQ can reconstruct more input vectors without any distortion than conventional VQ can reconstruct, using the same codebook. Simulation results show that the technique performs well using a universal codebook. This technique is also suitable for progressive image transmission as its performance is good at very low bit rates.
Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzer (2003)

Parallel collision-induced dissociation (CID) of peptides rather than serial, as is customary, results in loss of the obvious parent-fragment ion lineage available from CID on a single ion. We report proof-of-principle results suggesting the feasibility of parallel peptide CID, referred to here as shotgun CID, for protein identification when using the measured mass accuracies available from a time of flight mass analyzer and currently available search routines such as SEQUEST. Additionally, we report that parent-fragment ion lineage may be reconstructed from information encoded in the chromatographic single ion current traces of peptides.
Hyaluronidase induces a transcapillary pressure gradient and improves the distribution and uptake of liposomal doxorubicin (Caelyx™) in human osteosarcoma xenografts (2005)

Liposomal drug delivery enhances the tumour selective localisation and may improve the uptake compared to free drug. However, the drug distribution within the tumour tissue may still be heterogeneous. Degradation of the extracellular matrix is assumed to improve the uptake and penetration of drugs. The effect of the ECM-degrading enzyme hyaluronidase on interstitial fluid pressure and microvascular pressure were measured in human osteosarcoma xenografts by the wick-in-needle and micropipette technique, respectively. The tumour uptake and distribution of liposomal doxorubicin were studied on tumour sections by confocal laser scanning microscopy. The drugs were injected i.v. 1 h after the hyaluronidase pretreatment. Intratumoral injection of hyaluronidase reduced interstitial fluid pressure in a nonlinear dose-dependent manner. Maximum interstitial fluid pressure reduction of approximately 50% was found after injection of 1500 U hyaluronidase. Neither intratumoral nor i.v. injection of hyaluronidase induced any changes in the microvascular pressure. Thus, hyaluronidase induced a transcapillary pressure gradient, resulting in a four-fold increase in the tumour uptake and improving the distribution of the liposomal doxorubicin. Hyaluronidase reduces a major barrier for drug delivery by inducing a transcapillary pressure gradient, and administration of hyaluronidase adjuvant with liposomal doxorubicin may thus improve the therapeutic outcome.
Mouse Model for Hereditary Hemorrhagic Telangiectasia Has a Generalized Vascular Abnormality (2003)

These findings have relevance to our understanding of the molecular basis of vascular integrity in a wide range of diseases.
Mucopolysaccharidosis type II (Hunter syndrome): a clinical review and recommendations for treatment in the era of enzyme replacement therapy (2007)

Mucopolysaccharidosis type II (MPS II; Hunter syndrome) is a rare X-linked recessive disease caused by deficiency of the lysosomal enzyme iduronate-2-sulphatase, leading to progressive accumulation of glycosaminoglycans in nearly all cell types, tissues and organs. Clinical manifestations include severe airway obstruction, skeletal deformities, cardiomyopathy and, in most patients, neurological decline. Death usually occurs in the second decade of life, although some patients with less severe disease have survived into their fifth or sixth decade. Until recently, there has been no effective therapy for MPS II, and care has been palliative. Enzyme replacement therapy (ERT) with recombinant human iduronate-2-sulphatase (idursulfase), however, has now been introduced. Weekly intravenous infusions of idursulfase have been shown to improve many of the signs and symptoms and overall wellbeing in patients with MPS II. This paper provides an overview of the clinical manifestations, diagnosis and symptomatic management of patients with MPS II and provides recommendations for the use of ERT. The issue of treating very young patients and those with CNS involvement is also discussed. ERT with idursulfase has the potential to benefit many patients with MPS II, especially if started early in the course of the disease.
Regional myocardial blood flow and necrosis in primates following coronary occlusion (1984)

The effects of acute coronary artery occlusion on regional myocardial blood flow distribution in the remote nonischemic zone, the central ischemic zone, and the lateral border zone of the infarct were evaluated in conscious primates. Prior to coronary artery occlusion, blood flow was 1.51 +/- 0.11 in endocardial (Endo) and 1.36 +/- 0.11 ml X min-1g-1 in epicardial (Epi) layers with an Endo-to-Epi ratio of 1.17 +/- 0.05. Regional blood flow in the remote nonischemic zone increased by 28.0 +/- 4.7 and 31.7 +/- 3.6% for Endo and Epi layers, respectively, following coronary occlusion and remained elevated during the subsequent 24 h. At the center of infarct, Endo and Epi blood flows were depressed by 97.9 +/- 0.7 and by 97.9 +/- 0.8%, respectively, at 5 min after coronary occlusion and remained severely depressed throughout the 24-h observation period. Blood flow at the ischemic lateral border of the infarct was severely depressed and similar to the flow at the center of the infarct, whereas the nonischemic lateral border of the infarct had blood flow levels similar to the remote, nonischemic myocardium. Microsphere loss was not a feature of the primate infarct.