gebhart/patrepeval huggingface dataset:
HAMLeT: Hardware accelerated memory layout transform within 3D-stacked DRAM (2014)

Memory layout transformations via data reorganization are very common operations, which occur as a part of the computation or as a performance optimization in data-intensive applications. These operations require inefficient memory access patterns and roundtrip data movement through the memory hierarchy, failing to utilize the performance and energy-efficiency potentials of the memory subsystem. This paper proposes a high-bandwidth and energy-efficient hardware accelerated memory layout transform (HAMLeT) system integrated within a 3D-stacked DRAM. HAMLeT uses a low-overhead hardware that exploits the existing infrastructure in the logic layer of 3D-stacked DRAMs, and does not require any changes to the DRAM layers, yet it can fully exploit the locality and parallelism within the stack by implementing efficient layout transform algorithms. We analyze matrix layout transform operations (such as matrix transpose, matrix blocking and 3D matrix rotation) and demonstrate that HAMLeT can achieve close to peak system utilization, offering up to an order of magnitude performance improvement compared to the CPU and GPU memory subsystems which does not employ HAMLeT.
Self-powered autonomous wireless sensor node using vibration energy harvesting (2008)

This paper reports the development and implementation of an energy aware autonomous wireless condition monitoring sensor system (ACMS) powered by ambient vibrations. An electromagnetic (EM) generator has been designed to harvest sufficient energy to power a radio-frequency (RF) linked accelerometer-based sensor system. The ACMS is energy aware and will adjust the measurement/transmit duty cycle according to the available energy; this is typically every 3 s at 0.6 m s?2 rms acceleration and can be as low as 0.2 m s?2 rms with a duty cycle around 12 min. The EM generator has a volume of only 150 mm3 producing an average power of 58 ?W at 0.6m s?2 rms acceleration at a frequency of 52 Hz. In addition, a voltage multiplier circuit is shown to increase the electrical damping compared to a purely resistive load; this allows for an average power of 120 ?W to be generated at 1.7 m s?2 rms acceleration. The ACMS has been successfully demonstrated on an industrial air compressor and an office air conditioning unit, continuously monitoring vibration levels and thereby simulating a typical condition monitoring application
All Seven comG Open Reading Frames Are Required for DNA Binding during Transformation of Competent Bacillus subtilis (1998)

The seven proteins encoded by the comG operon of Bacillus subtilis exhibit similarity to gene products required for the assembly of type 4 pili and for the secretion of certain proteins in gram-negative bacteria. Although polar transposon insertions in comG result in the loss of transformability and in the failure of cells grown through the competence regimen to bind DNA, it was not known whether the ComG proteins are all required for competence. We have constructed strains missing each of these proteins individually and found that they are all nontransformable and fail to bind transforming DNA to the cell surface. The implications of these findings are discussed.
Gallium Maltolate Treatment EradicatesPseudomonas aeruginosaInfection in Thermally Injured Mice (2009)

Gallium (Ga) is a semimetallic element that has demonstrated therapeutic and diagnostic-imaging potential in a number of disease settings, including cancer and infectious diseases. Gallium's biological actions stem from its ionic radius being almost the same as that of ferric iron (Fe(3+)), whereby it can replace iron (Fe) in Fe(3+)-dependent biological systems, such as bacterial and mammalian Fe transporters and Fe(3+)-containing enzymes. Unlike Fe(3+), ionic gallium (Ga(3+)) cannot be reduced, and when incorporated, it inactivates Fe(3+)-dependent reduction and oxidation processes that are necessary for bacterial and mammalian cell proliferation. Most pathogenic bacteria require Fe for growth and function, and the availability of Fe in the host or environment can greatly enhance virulence. We examined whether gallium maltolate (GaM), a novel formulation of Ga, had antibacterial activity in a thermally injured acute infection mouse model. Dose-response studies indicated that a GaM dose as low as 25 mg/kg of body weight delivered subcutaneously was sufficient to provide 100% survival in a lethal P. aeruginosa-infected thermally injured mouse model. Mice treated with 100 mg/kg GaM had undetectable levels of Pseudomonas aeruginosa in their wounds, livers, and spleens, while the wounds of untreated mice were colonized with over 10(8) P. aeruginosa CFU/g of tissue and their livers and spleens were colonized with over 10(5) P. aeruginosa CFU/g of tissue. GaM also significantly reduced the colonization of Staphylococcus aureus and Acinetobacter baumannii in the wounds of thermally injured mice. Furthermore, GaM was also therapeutically effective in preventing preestablished P. aeruginosa infections at the site of the injury from spreading systemically. Taken together, our data suggest that GaM is potentially a novel antibacterial agent for the prevention and treatment of wound infections following thermal injury.
Macular Grid Photocoagulation After Intravitreal Triamcinolone Acetonide for Diffuse Diabetic Macular Edema (2006)

Macular laser coagulation effectively maintains improved visual acuity after IVTA for diffuse DME and is believed to reduce recurrent DME after IVTA.
Selection of Oligonucleotide Aptamers with Enhanced Uptake and Activation of Human Leukemia B Cells (2003)

The clinical use of oligonucleotide (ODN) therapeutics has been hampered by their limited ability to penetrate intact cells. To identify ODN properties that would facilitate cellular uptake, we developed a repetitive selection procedure using an ODN library containing at least 10(14) different molecules and human B lymphoma cells as a target. Natural phosphodiester single-stranded DNA ODNs (R-aptamers) were obtained after 10 rounds of selection. A common feature in the R-aptamers was guanine-rich 3' terminal sequences, and many also contained potential immunostimulatory (ISS) CpG sequence motifs. Two R-aptamers (R10-60 and D-R15-8) with the predominant shared characteristics were selected for further study on primary human chronic lymphocytic leukemia (CLL) B cells, which are well known to be difficult to transfect and activate. Flow cytometry analysis of the CLL cells demonstrated that the fluorochrome-labeled R-aptamers were internalized much more efficiently than nonselected random sequence ODN. Studies on sequence modifications indicated that efficient uptake required ODN multimerization, that was promoted by guanine-rich sequences at the 3' terminus. In addition, CLL cells that were exposed to the aggregating R-aptamers containing CpG motifs were strongly activated, as indicated by upregulation of CD40 levels as compared to cells treated with nonaggregating CpG R-aptamers. Together, these findings suggest that the sequence compositions in R-aptamers that promote multimerization and contain optimal ISS CpG motifs facilitate the delivery of ISS-ODN to CLL cells and enhance the activation of these cells.
Interaction of dimeric intercalating dyes with single-stranded DNA (1995)

The unsymmetrical cyanine dye thiazole orange homodimer (TOTO) binds to single-stranded DNA (ssDNA, M13mp18 ssDNA) to form a fluorescent complex that is stable under the standard conditions of electrophoresis. The stability of this complex is indistinguishable from that of the corresponding complex of TOTO with double-stranded DNA (dsDNA). To examine if TOTO exhibits any binding preference for dsDNA or ssDNA, transfer of TOTO from pre-labeled complexes to excess unlabeled DNA was assayed by gel electrophoresis. Transfer of TOTO from M13 ssDNA to unlabeled dsDNA proceeds to the same extent as that from M13 dsDNA to unlabeled dsDNA. A substantial amount of the dye is retained by both the M13 ssDNA and M13 dsDNA even when the competing dsDNA is present at a 600-fold weight excess; for both dsDNA and ssDNA, the pre-labeled complex retains approximately one TOTO per 30 bp (dsDNA) or bases (ssDNA). Rapid transfer of dye from both dsDNA and ssDNA complexes is seen at Na+ concentrations > 50 mM. Interestingly, at higher Na+ or Mg2+ concentrations, the M13 ssDNA-TOTO complex appears to be more stable to intrinsic dissociation (dissociation in the absence of competing DNA) than the complex between TOTO and M13 dsDNA. Similar results were obtained with the structurally unrelated dye ethidium homodimer. The dsDNA- and ssDNA-TOTO complexes were further examined by absorption, fluorescence and circular dichroism spectroscopy. The surprising conclusion is that polycationic dyes, such as TOTO and EthD, capable of bis-intercalation, interact with dsDNA and ssDNA with very similar high affinity.
Influence of transition rates and scan rate on kinetic simulations of differential scanning calorimetry profiles of reversible and irreversible protein denaturation (1992)

The thermodynamic parameters characterizing protein folding can be obtained directly using differential scanning calorimetry (DSC). They are meaningful only for reversible unfolding at equilibrium, which holds for small globular proteins; however, the unfolding or denaturation of most large, multidomain or multisubunit proteins is either partially or totally irreversible. The simplest kinetic model describing partially irreversible denaturation requires three states: Formula [see text] We obtain numerical solutions for N, U, and D as a function of temperature for this model and derive profiles of excess specific heat (Cp) in terms of the reduced variables v/ki and k1/k3, where v is the scan rate. The three-state model reduces to the two-state reversible or irreversible models for very large or very small values of k1/k3, respectively. The apparent transition temperature (Tapp) is always reduced by the irreversible step (U-->D). For all values of k3, Tapp is independent of v/k1 at sufficiently slow scan rates, even when denaturation is highly irreversible, but increases identically for all models at fast scan rates in which case the excess specific heat profile is determined by the rate of unfolding. Accurate values of delta H and delta S can be obtained for the reversible step only when k1 is more than 2000-50,000 times greater than k3. In principle, approximate values for the ratio k1/k3 can be obtained from plots of fraction unfolded vs fraction irreversibly denatured as a function of temperature; however, the fraction irreversibly denatured is difficult to measure accurately by DSC alone.(ABSTRACT TRUNCATED AT 250 WORDS)
Mesoporous and nanowire Co3O4as negative electrodes for rechargeable lithium batteries (2007)

The conversion reactions associated with mesoporous and nanowire Co(3)O(4) when used as negative electrodes in rechargeable lithium batteries have been investigated. Initially, Li is intercalated into Co(3)O(4) up to x approximately 1.5 Li in Li(x)Co(3)O(4). Thereafter, both materials form a nanocomposite of Co particles imbedded in Li(2)O, which on subsequent charge forms CoO. The capacities on cycling increase on initial cycles to values exceeding the theoretical value for Co(3)O(4) + 8 Li(+) + 8e(-) --> 4 Li(2)O + 3 Co, 890 mAhg(-1), and this is interpreted as due to charge storage in a polymer layer that forms on the high surface area of nanowire and mesoporous Co(3)O(4). After 15 cycles, the capacity decreases drastically for the nanowires due to formation of grains that are separated one from another by a thick polymer layer, leading to electrical isolation. In contrast, the mesoporous Co(3)O(4) losses its mesoporosity and forms a morphology similar to bulk Co(3)O(4) (Co particles imbedded in Li(2)O matrix) with which it exhibits a similar capacity on cycling. In contrast to mesoporous lithium intercalation compounds, which show superior capacity at high rates compared to bulk materials, mesoporosity does not seem to improve the capacity of conversion reactions on extended cycling. If, however, mesoporosity could be retained during the conversion reaction, then higher capacities could be obtained in such systems.
Oxygen-induced constriction of rabbit ductus arteriosus occurs via inhibition of a 4-aminopyridine-, voltage-sensitive potassium channel. (1996)

The ductus arteriosus is a vital fetal structure allowing blood ejected from the right ventricle to bypass the pulmonary circulation in utero. Closure of the ductus arteriosus at birth, essential for postnatal adaptation, is initiated by an increase in oxygen (O2) tension. We recently demonstrated the presence of O2-sensitive potassium channels in the fetal and adult pulmonary circulation which regulate vascular tone in response to changes in O2 tension. In this study, we assessed the cellular mechanisms underlying O2-induced constriction of the ductus arteriosus in late-gestation fetal rabbits. We report that O2 reversibly inhibits a 58-pS voltage- and 4-aminopyridine-sensitive potassium channel, causing membrane depolarization, an increase in intracellular calcium through L-type voltage-gated calcium channels, and constriction of the ductus arteriosus. We conclude that the effector mechanism for O2 sensing in the ductus arteriosus involves the coordinated action of delayed rectifier potassium channels and voltage-gated calcium channels.
Continuous fermentation with product recovery by in‐situ extraction (1994)

Abstract The productivity of fermentations is often limited by end product inhibition. This can be avoided by continuous removal of the inhibiting product from the broth. Such in‐situ separation can be conveniently accomplished by liquid‐liquid extraction. As an example, the continuous fermentation of ethanol by the thermophilic, anaerobic bacterium Clostridium thermohydrosulfuricum is investigated in a 20‐1 fermenter with simultaneous in‐situ extraction by oleyl alcohol as organic solvent. Continuous fermentations with and without in‐situextraction were carried out with systematic variation of the independent operating conditions, viz. feed glucose concentration, broth flow rate and solvent flow rate. The experimental results of 18 steady states are reported. They show that in‐situ extractions doubles the yield, selectivity and space‐time yield of ethanol in comparison to fermentations without in‐situ extraction. A biomodel elucidates the influence of feed glucose concentration, broth flow rate and solvent flow rate on the productivity of the fermentation process. Finally, a cost model was developed for the investigated fermentation which allows economic evaluation of the results of experiments and simulation. A sensitivity study elucidates the economic limits and advantages of fermentation with in‐situ extraction compared to a common fermentation without product separation.
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family (2009)

The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial for survival. After one- and two-component systems, extracytoplasmic function (ECF) sigma factors - the largest group of alternative sigma factors - represent the third fundamental mechanism of bacterial signal transduction, with about six such regulators on average per bacterial genome. Together with their cognate anti-sigma factors, they represent a highly modular design that primarily facilitates transmembrane signal transduction. A comprehensive analysis of the ECF sigma factor protein family identified more than 40 distinct major groups of ECF sigma factors. The functional relevance of this classification is supported by the sequence similarity and domain architecture of cognate anti-sigma factors, genomic context conservation, and potential target promoter motifs. Moreover, this phylogenetic analysis revealed unique features indicating novel mechanisms of ECF-mediated signal transduction. This classification, together with the web tool ECFfinder and the information stored in the Microbial Signal Transduction (MiST) database, provides a comprehensive resource for the analysis of ECF sigma factor-dependent gene regulation.
Substrate specificity of the 3-methylaspartate ammonia-lyase reaction: observation of differential relative reaction rates for substrate-product pairs (1988)

A range of substituted fumaric and aspartic acid substrates for the enzyme 3-methylaspartate ammonia-lyase (EC 4.3.1.2) have been synthesized and used to study the kinetics of the catalyzed reaction in both the forward (deamination) and reverse (conjugative amination) reaction directions. The rates of amination for all of the alpha, beta-unsaturated substrates studied (bearing substituents the size of an ethyl group or smaller) were similar under [s] much greater than KM conditions although KM values for the substrates varied by a factor of 25. The rates of deamination for the corresponding 3-substituted amino acid substrates varied widely with structure under [s] much greater than KM conditions, and thus for substrate-product pairs the ratio for V(forward)/V(reverse) also varied. These differential reaction rates indicate that there is a step in the deamination direction that is especially sensitive to the size of the 3-substituent of the substrate and that a relatively large group (methyl to ethyl in size) is required for binding in order to reduce the activation energy for this step. Given that it is proposed that the enzyme operates via an E1cb-type mechanism where C-N bond cleavage is rate limiting, it is likely that binding of the C-3 substituent of aspartic acid substrates affects the alignment of the nascent carbanion with the C-N bond for elimination.
COBALT: constraint-based alignment tool for multiple protein sequences (2007)

COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt
Segmental Spinal Instrumentation of the Lumbar Spine (1986)

Obtaining an arthrodesis of the lumbar spine has always been a problem, especially in the presence of severe disease. The understanding of the segmental character of the lesions and the application of sound orthopedic principles toward low-back spine pathology has led the way to improving arthrodesis with rigid internal fixation. For about eight years, segmental spinal instrumentation has been used in 352 cases to "stabilize" the spine. Many modifications have taken place and knowledge of the biomechanics of abnormal spine has increased through designs of new methods for different disorders. Fixation of low back, when indicated, should be rigid. The rectangular or rhomboid-shaped rod, bent to conform to the lamina cephalad and caudad, and fixed segmentally, proves to be the most rigid. It is contoured to maintain lordosis, sometimes in distraction, sometimes in compression. Fixation is not a substitute for correction of bony deformity or a good surgical arthrodesis. The objective is to maintain correction and promote prompt bony fusion.
Histopathological assessment of inflammation and expression of inflammatory markers in patients with ketamine-induced cystitis (2014)

The aim of the current study was to evaluate the histopathological features of inflammation and the expression levels of inflammatory markers in tissue samples from patients with ketamine‑induced cystitis. Bladder biopsy samples for histological analysis were obtained from 23 patients (18 men and 5 women) with a self‑reported history of ketamine use and who were treated for cystitis at the Tri‑Service General Hospital of Taipei, Taiwan. Immunohistochemical staining for cyclooxygenase‑2 (COX‑2), inducible nitric oxide synthase (iNOS), matrix metallopeptidase‑9 (MMP‑9), mammalian target of rapamycin (mTOR), and phosphorylated 40S ribosomal protein S6 (Phos‑S6) was performed. The results revealed urothelial atypia in all patients, and intravascular eosinophil accumulation in 22 patients. Histopathological features included denuded urothelial mucosa, ulceration, collagen deposition, smooth muscle degeneration and vessel proliferation. Tissue samples were immunopositive for all of the inflammation markers, including the urothelium, vessel walls, and smooth muscle. COX‑2 staining revealed a significant difference between the inflammatory levels in the urothelium and smooth muscle, and iNOS staining differed significantly between inflammatory levels in smooth muscle (p=0.029). A positive correlation was observed between the percentage of Phos‑S6‑positive cells and the levels of inflammation in the urothelium. These results add to the descriptive literature on the histopathological aspects of ketamine‑induced cystitis, emphasizing the inflammatory nature and a possible role for proteins such as COX‑2, iNOS and Phos‑S6 in the degree of inflammation.
OX 40 ligand newly expressed on bronchiolar progenitors mediates influenza infection and further exacerbates pneumonia (2016)

Influenza virus epidemics potentially cause pneumonia, which is responsible for much of the mortality due to the excessive immune responses. The role of costimulatory OX40-OX40 ligand (OX40L) interactions has been explored in the non-infectious pathology of influenza pneumonia. Here, we describe a critical contribution of OX40L to infectious pathology, with OX40L deficiency, but not OX40 deficiency, resulting in decreased susceptibility to influenza viral infection. Upon infection, bronchiolar progenitors increase in number for repairing the influenza-damaged epithelia. The OX40L expression is induced on the progenitors for the antiviral immunity during the infectious process. However, these defense-like host responses lead to more extensive infection owing to the induced OX40L with α-2,6 sialic acid modification, which augments the interaction with the viral hemagglutinin. In fact, the specific antibody against the sialylated site of OX40L exhibited therapeutic potency in mitigating the OX40L-mediated susceptibility to influenza. Our data illustrate that the influenza-induced expression of OX40L on bronchiolar progenitors has pathogenic value to develop a novel therapeutic approach against influenza.
Expression of Estrogen-Induced Genes and Estrogen Receptor β in Pancreatic Neuroendocrine Tumors (2014)

Our study showed that PanNETs with favorable prognostic features have higher ERβ expression, which is associated with up-regulated PR and EIG121 messenger RNA expression. Estrogen regulation in PanNETs could potentially help in risk stratification and provide a rational target for novel treatment strategies.
Transport of gigabit/sec data packets over SONET/ATM networks (2002)

A scheme is proposed to convert the data formats between the HIPPI (high performance parallel interface) and ATM (asynchronous transfer mode) protocols. A possible method of implementing the HIPPI broadband terminal adaptor (HIPPI-BTA), which interfaces multiple HIPPI channels to the SONET (synchronous optical network)/ATM network, is also presented. A preliminary study indicated that the HIPPI interface of the high performance computer hosts and the SONET/ATM standards of the future broadband communication networks have a high potential to work well with each other.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>