gebhart/patrepeval huggingface dataset:
Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway (1998)

Aromatic compounds are important growth substrates for microorganisms. They form a large group of diverse compounds including lignin monomers, amino acids, quinones, and flavonoids. Aerobic aromatic metabolism is characterized by the extensive use of molecular oxygen which is essential for the hydroxylation and cleavage of aromatic ring structures. The anaerobic metabolism of low molecular mass soluble aromatic compounds requires, of necessity, a quite different strategy. In most known cases, aromaticity is broken by reduction and the ring is subsequently opened hydrolytically. A small number of different central aromatic intermediates can be reduced, the most common of which is benzoyl-CoA, a compound that is formed as a central intermediate in the degradation of a large number of aromatic growth substrates. This review concentrates on the anaerobic aromatic metabolism via the benzoyl-CoA pathway. The peripheral pathways that transform growth substrates to benzoyl-CoA include various types of novel reactions, for example carboxylation of phenolic compounds, reductive elimination of ring substituents like hydroxyl or amino groups, oxidation of methyl substituents, O-demethylation reactions and shortening of aliphatic side chains. The central benzoyl-CoA pathway differs in several aspects in the denitrifying, phototrophic and fermenting bacteria studied. In denitrifying and phototrophic bacteria it starts with the two-electron reduction of benzoyl-CoA to a cyclic dienoyl-CoA driven by the hydrolysis of two molecules of ATP to ADP+Pi. This ring reduction is catalyzed by benzoyl-CoA reductase and requires a low-potential ferredoxin as an electron donor. In Rhodopseudomonas palustris the cyclic diene is further reduced to cyclohex-1-ene-1-carboxyl-CoA. In the denitrifying species Thauera aromatica, the cyclic diene is hydrated to give 6-hydroxycyclohex-1-ene-1-carboxyl-CoA. Subsequent β-oxidation results in the formation of a cyclic β-oxo compound, followed by hydrolytic carbon ring opening yielding 3-hydroxypimelyl-CoA in the case of T. aromatica and pimelyl-CoA in the case of R. palustris. These intermediates are further β-oxidized via glutaryl-CoA; final products are 3 acetyl-CoA and 1 CO2. In fermenting bacteria benzoyl-CoA may possibly be reduced to the level of cyclohex-1-ene-1-carboxyl-CoA in an ATP-independent reaction. The genes coding for the enzymes of the central benzoyl-CoA pathway have been cloned and sequenced from R. palustris, T. aromatica, and Azoarcus evansii. Sequence analyses of the genes support the concept that phototrophic and denitrifying bacteria use two slightly different pathways to metabolize benzoyl-CoA. The gene sequences have in some cases been very helpful for the identification of possible catalytic mechanisms that were not obvious from initial characterizations of purified enzymes.
Durability of Anti-Infective Effect of Long-Term Silicone Sheath Catheters Impregnated with Antimicrobial Agents (2001)

This study was performed to test the long-term antimicrobial efficacy of impregnated silicone catheters comprising an antimicrobial layer sandwiched between an external surface sheath and a luminal surface silicone sheath. The design of the catheter permits the introduction of various antimicrobials in addition to anticoagulants or antifibrins in the antimicrobial layer and allows their gradual release over a period of months after insertion. The in vitro data presented show that the catheter can provide antimicrobial activity for 90 days, after being replated for 15 7-day cycles of replating. When the catheters were immersed in human serum and incubated at 37 degrees C, they demonstrated significant antimicrobial activity after more than 325 days of incubation. The significant long-term in vitro antimicrobial activity observed may imply effective in vivo activity for almost 1 year after insertion and could serve as a cost-effective alternative to surgically implantable silicone catheters.
Antitubular Basement-Membrane Antibodies in Methicillin-Associated Interstitial Nephritis (1974)

Abstract Antitubular basement-membrane antibodies were detected by indirect immunofluorescence in the serum of a patient in whom severe renal failure developed while he was receiving methicillin. A renal biopsy showed a severe mononuclear interstitial infiltrate with focal areas of tubular degeneration. IgG, C3 and a methicillin antigen assumed to be dimethoxyphenylpenicilloyl were present in a linear pattern along the tubular basement membrane but not along the glomerular basement membrane. The dimethoxyphenylpenicilloyl-tubular-basement-membrane hapten protein conjugate apparently led to an immune response with antitubular basement-membrane antibodies being involved in the immunopathogenesis of the patient's interstitial nephritis. (N Engl J Med 291:381–384, 1974)
Immunotargeting of streptavidin to the pulmonary endothelium. (1994)

Conjugation of Mab 9B9 with streptavidin enhances selective pulmonary uptake of the preparation, providing a background for intrapulmonary immunotargeting of various biotinylated agents.
A Multilinear Singular Value Decomposition (2000)

We discuss a multilinear generalization of the singular value decomposition. There is a strong analogy between several properties of the matrix and the higher-order tensor decomposition; uniqueness, link with the matrix eigenvalue decomposition, first-order perturbation effects, etc., are analyzed. We investigate how tensor symmetries a ect the decomposition and propose a multilinear generalization of the symmetric eigenvalue decomposition for pair-wise symmetric tensors.
Isolation and partial characterization of a protease involved in Fas‐induced apoptosis (1995)

Protease involvement has been implicated in the signalling process of activation-induced apoptosis. Here we report the isolation of a protease from Jurkat T cells undergoing Fas-induced apoptosis. Although the protease probably is a serine protease, it seems to be distantly related to members of the ICE/ced-3/Ich-1(nedd-2) family. In a cell-free system using isolated thymocyte nuclei, the protease rapidly induces DNA fragmentation and morphological changes typically seen in apoptosis. Our results clearly show protease activation downstream to Fas-ligation and implicate an important role for the isolated protease in signalling of Fas-induced apoptosis.
Cross-sectional Anatomy of Acupoints (1995)

Cross-Sectional Anatomy of the Upper Extremities. Cross-Sectional Anatomy of the Lower Extremities. Cross-Sectional Anatomy of the Head. Cross-Sectional Anatomy of the Neck. Cross-Sectional Anatomy of the Trunk. Cross-Sectional Anatomy of High Risk Acupoints. Point Index. Meridian Index. Subject Index
Induction of Indoleamine 2,3-Dioxygenase by Interferon-γ in Human Islets (2006)

Indoleamine 2,3-dioxygenase (IDO) catalyzes the initial, rate-limiting step of tryptophan (Trp) catabolism along the kynurenine (KYN) pathway, and its induction in cells of the immune system in response to cytokines has been implicated in the regulation of antigen presentation and responses to cell-mediated immune attack. Microarray and quantitative PCR analyses of isolated human islets incubated with interferon (IFN)-gamma for 24 h revealed increased expression of IDO mRNA (>139-fold) and Trp-tRNA synthase (WARS) (>17-fold) along with 975 other transcripts more than threefold, notably the downstream effectors janus kinase (JAK)2, signal transducer and activator of transcription (STAT)1, IFN-gamma regulatory factor-1, and several chemokines (CXCL9/MIG, CXCL10/IP10, CXCL11/1-TAC, CCL2, and CCL5/RANTES) and their receptors. IDO protein expression was upregulated in IFN-gamma-treated islets and accompanied by increased intracellular IDO enzyme activity and the release of KYN into the media. The response to IFN-gamma was countered by interleukin-4 and 1alpha-methyl Trp. Immunohistochemical localization showed IDO to be induced in cells of both endocrine, including pancreatic duodenal homeobox 1-positive beta-cells, and nonendocrine origin. We postulate that in the short term, IDO activation may protect islets from cytotoxic damage, although chronic exposure to various Trp metabolites could equally lead to beta-cell attrition.
Analysis of Synergistic and Antagonistic Effects of Herbicides Using Nonlinear Mixed-Model Methodology (2004)

When herbicides are applied in mixture, and infestation by weeds is less than expected compared with when herbicides are applied alone, a synergistic effect is said to exist. The inverse response is described as being antagonistic. However, if the expected response is defined as a multiplicative, nonlinear function of the means for the herbicides when applied alone, then standard linear model methodology for tests of hypotheses does not apply directly. Consequently, nonlinear mixed-model methodology was explored using the nonlinear mixed-model procedure (PROC NLMIXED) of SAS System ® . Generality of the methodology is illustrated using data from a randomized block design with repeated measures in time. Nonlinear mixed-model estimates and tests of synergistic and antagonistic effects were more sensitive in detecting significance, and PROC NLMIXED was a versatile tool for implementation.
The Role of Absorption, Distribution, Metabolism, Excretion and Toxicity in Drug Discovery (2003)

Major reasons preventing many early candidates reaching market are the inappropriate ADME (absorption, distribution, metabolism and excretion) properties and drug-induced toxicity. From a commercial perspective, it is desirable that poorly behaved compounds are removed early in the discovery phase rather than during the more costly drug development phases. As a consequence, over the past decade, ADME and toxicity (ADMET) screening studies have been incorporated earlier in the drug discovery phase. The intent of this review is to introduce the desirable attributes of a new chemical entity (NCE) to the medicinal chemist from an ADMET perspective. Fundamental concepts, key tools, reagents and experimental approaches used by the drug metabolism scientist to aid a modern project team in predicting human pharmacokinetics and assessing the "drug-like" molecule are discussed.
A new optimal wavelength for treatment of port wine stains? (1995)

In this study we investigate light penetration into skin in order to define the optimal wavelength for the treatment of port wine stains. A two-layer model (epidermis and dermis) is applied with a cylindric tube representing the ectatic blood vessel. Light propagation is calculated by the Monte Carlo method. Values for the optical properties of the skin were not only taken from the literature, but also derived from measurements of the spatially resolved reflectance on the human forearm applying a multilayer model. Using the new values, the maximal depth of selective vascular injury better fits experimental and clinical observations, compared to the values in literature. In addition, the optimal wavelength for treatment of port wine stains is shifted to longer wavelengths.
Pulse Release of Sugars and Polyols from Canopy Bryophytes in Tropical Montane Rain Forest (Guadeloupe, French West Indies) (1992)

D. S. Coxson, D. D. McIntyre, H. J. Vogel, Pulse Release of Sugars and Polyols from Canopy Bryophytes in Tropical Montane Rain Forest (Guadeloupe, French West Indies), Biotropica, Vol. 24, No. 2, Part A (Jun., 1992), pp. 121-133
In vivomolecular and genomic imaging: new challenges for imaging physics (2004)

The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.
Activation of JNK in the Inner Ear following Impulse Noise Exposure (2008)

Noise exposure is known to induce cell death signaling in the cochlea. Since c-Jun N-terminal kinase (JNK) signaling is known to induce both cell survival and apoptosis, the present study focused on early changes (within 24 h) after impulse noise exposure, inquiring whether cell death is always related to phosphorylation of JNK in the inner ear. Anesthetized adult albino rats were exposed to a single impulse noise exposure (194 kPa) and sacrificed 3 or 24 h later. Paraffin-embedded sections were examined for positive staining of phosphorylated JNK and the presence of cells with fragmented DNA (TUNEL staining). Positive TUNEL staining was observed at the spiral limbus and in the stria vascularis at 24 h following impulse noise exposure, but no correlation with JNK activation was found at these locations. In the hearing organ (organ of Corti) and in the lateral wall, TUNEL-reactive cells were observed at 24 h following trauma. This was preceded by p-JNK staining at 3 h, indicating JNK-activated cell death in these regions. Finally, p-JNK reactivity was observed in the spiral ganglion with no correlation to TUNEL staining within the time frame of this study. These results suggest that JNK activation following impulse noise exposure may not always be related to cell death, and conversely, some cells may die through JNK-independent signaling.
Wideband vibro-impacting vibration energy harvesting using magnetoelectric transduction (2012)

This article reports on proof-of-concept experimental work carried out to demonstrate a wideband vibro-impacting energy harvesting approach based on a magnet/bearing arrangement coupled with a magnetoelectric transducer. The harvesting arrangement uses a Terfenol-D/Pz27 laminate transducer (disc with radius 5 mm) positioned between an oscillating spherical chrome-steel bearing and a rare earth magnet. The oscillating bearing steers magnetic field through the magnetoelectric transducer, generating an oscillating charge that can be harvested. A vibro-impacting arrangement between the oscillating bearing (radius 12.7 mm) and a pair of aluminium mechanical stops is designed to produce a wideband frequency response. For a 434 mG host acceleration, the vibro-impact mechanism produced a bandwidth of ∼7.2 Hz (between 6 and ∼13.2 Hz). The issue of damage to the mechanical stops caused by the vibro-impacting process is also explored and was demonstrated experimentally and theoretically to be inconsequential. This non-optimized wideband harvesting approach has demonstrated a generated power of 3.3 µW from a root mean square host acceleration of 180 m-g at 8.0 Hz.
White matter integrity and cognition in chronic traumatic brain injury: a diffusion tensor imaging study (2007)

Traumatic brain injury (TBI) is a serious public health problem. Even injuries classified as mild, the most common, can result in persistent neurobehavioural impairment. Diffuse axonal injury is a common finding after TBI, and is presumed to contribute to outcomes, but may not always be apparent using standard neuroimaging. Diffusion tensor imaging (DTI) is a more recent method of assessing axonal integrity in vivo. The primary objective of the current investigation was to characterize white matter integrity utilizing DTI across the spectrum of chronic TBI of all severities. A secondary objective was to examine the relationship between white matter integrity and cognition. Twenty mild, 17 moderate to severe TBI and 18 controls underwent DTI and neuropsychological testing. Fractional anisotropy, axial diffusivity and radial diffusivity were calculated from the DTI data. Fractional anisotropy was the primary measure of white matter integrity. Region of interest analysis included anterior and posterior corona radiata, cortico-spinal tracts, cingulum fibre bundles, external capsule, forceps minor and major, genu, body and splenium of the corpus callosum, inferior fronto-occipital fasciculus, superior longitudinal fasciculus and sagittal stratum. Cognitive domain scores were calculated from executive, attention and memory testing. Decreased fractional anisotropy was found in all 13 regions of interest for the moderate to severe TBI group, but only in the cortico-spinal tract, sagittal stratum and superior longitudinal fasciculus for the mild TBI group. White Matter Load (a measure of the total number of regions with reduced FA) was negatively correlated with all cognitive domains. Analysis of radial and axial diffusivity values suggested that all severities of TBI can result in a degree of axonal damage, while irreversible myelin damage was only apparent for moderate to severe TBI. The present data emphasize that white matter changes exist on a spectrum, including mild TBI. An index of global white matter neuropathology (White Matter Load) was related to cognitive function, such that greater white matter pathology predicted greater cognitive deficits. Mechanistically, mild TBI white matter changes may be primarily due to axonal damage as opposed to myelin damage. The more severe injuries impact both. DTI provides an objective means for determining the relationship of cognitive deficits to TBI, even in cases where the injury was sustained years prior to the evaluation.
New CMOS Shallow Junction Well FET Structure (CMOS-S JET) for Low Power-Supply Voltage (1992)

A novel CMOS device structure called as CMOS shallow junction well FET (CMOS-SJET) has been proposed for high speed operation at low power-supply voltage. Since well regions underneath the channel regions of both n-channel and p-channel MOSFETs in the CMOSSJET are fully depleted, steeper subthreshold characteristics can be achieved. Furthermore, junction capacitances are reduced by half compared with those of the conventional CMOS structure. Therefore the gate delay of 52psec/stage at 1.5V operation and low power-delay product of 1fJ are verified with 0.35pm gate length design. The CMOS-SJET structure appears to offer high performance with low power-delay product at low voltage operation.
Successful treatment of metastatic renal cell carcinoma with a biologically active dose of recombinant interferon-gamma. (1989)

We tested the clinical efficacy of a biologically active dose (BAD) of interferon (IFN)-gamma for treatment of progressive renal cell carcinoma (RCC). Twenty-two RCC patients with disease progression subsequent to nephrectomy were entered on a phase II clinical trial. During an initial dose-finding phase, biochemical responses to repeated once-weekly subcutaneous injections of 10, 100, or 500 micrograms of recombinant IFN-gamma were tested in 16 patients. Results indicated that 100 micrograms IFN-gamma applied once weekly was biologically active with induction of serum beta 2-microglobulin and neopterin. Such a dose induced a nearly maximum response of both markers lasting more than 4 days. This dose was also associated with minimal side effects. A dose of 100 micrograms IFN-gamma given once weekly was, therefore, subsequently given weekly for long-term treatment. During a median time of therapy of 10 months (range, 2 to 32 months) two complete (CR; 20+, 20+ months) and four partial tumor responses (PR; 6+, 7+, 8+, 24+ months) were seen (30% CR plus PR; 95% confidence limits, 12% to 54%) among 20 patients evaluable for response. Patients with refractory disease had significantly lower IFN-gamma-induced increments of serum beta 2-microglobulin than those who achieved clinical remission or stable disease.
Current measurements within the electrospray emitter (2007)

A movable disc-like wire probe electrode placed inside the electrospray (ES) capillary was used to measure currents flowing within the ES device for the first time. Currents were measured between the wire probe and the ES capillary. Current maps revealing measured current versus wire probe position were generated for a variety of solution conditions in the positive and negative ion modes and are compared to potential maps. The electrospray device was found to subsist on highly stable total currents; this current regulator aspect of the ES device showed remarkable resiliency regardless of the proportion of current produced at the wire probe electrode versus the ES capillary. However, kinks observed in the current and potential maps are attributed to adsorbed air participating in electrochemical reactions, and turbulence in solution flow in the region of the Taylor cone. From differential electrospray emitter potential (DEEP) maps, current maps, and cyclic voltammetry experiments performed at different wire probe locations, evidence is provided for separate regimes of current flow in the bulk solution and in the thin "skin" of highly conductive electrolyte constituting the outer surface (air interface) of the Taylor cone. Current maps reveal that current is drawn more evenly along the length of the ES capillary when solutions are highly conductive, in agreement with previous results for DEEP maps. In less conductive solutions, the area close to the capillary exit contributes more heavily to current production. Evidence that contaminant participation in electrochemical processes occurring within the electrospray device can be largely responsible for production of the excess charge in ES droplets is also provided. These investigations complement previous DEEP mapping studies to further elucidate the details of the electrochemical processes occurring within the electrospray device.
Packet Speech Systems Technology (1982)

Abstract : The long-range objectives of the Packet Speech Systems Technology Program are to develop and demonstrate techniques for efficient digital speech communication on networks suitable for both voice and data, and to investigate and develop techniques for integrated voice and data communication in packetized networks, including wideband common-user satellite links. Specific areas of concern are: the concentration of statistically fluctuating volumes of voice traffic, the adaptation of communication strategies to varying conditions of network links and traffic volume, and the interconnection of wideband satellite networks to terrestrial systems. The current program has two major thrusts: i.e. , the development and refinement of practical low-cost, robust, narrowband, and variable-rate speech algorithms and voice terminal structures; and the establishment of an experimental wideband satellite network to serve as a unique facility for the realistic investigation of voice/data networking strategies. This report covers work in the following areas: digital channel vocoder development; embedded CVSD-based speech waveform encoder design and implementation; development and experimental tests of modular packet voice terminals (PVTs) and local access area (LEXNET) facilities; development of a miniconcentrator facility to mediate the flow of traffic from the LEXNET onto the wideband satellite network, and execution of packet speech experiments using this facility; and definition and planning of, and participation in, experiments on the wideband integrated voice/data network.