gebhart/patrepeval huggingface dataset:
Intact polar membrane lipids in prokaryotes and sediments deciphered by high‐performance liquid chromatography/electrospray ionization multistage mass spectrometry—new biomarkers for biogeochemistry and microbial ecology (2004)

Lipids from prokaryotic cell membranes can serve as sources of information on the biogeochemistry and microbial ecology of natural ecosystems. Traditionally, apolar derivatives of the intact polar membrane molecules, e.g., fatty acids, have been the major target of lipid-based biogeochemical studies. However, when still intact, i.e., as glycerol esters and ethers with attached polar headgroups, membrane lipids are diagnostic for living prokaryotes, which makes them excellent biomarkers for the study of in situ microbial processes in geological systems such as sediments or soils. Intact polar lipids (IPLs) are attractive analytical targets because they are taxonomically more specific than their apolar derivatives and avoid exclusion of signals from prokaryotes that primarily build their membranes with ether-bound lipids such as archaea and some bacteria. Here we report results from analyses of IPLs in pure cultures of biogeochemically relevant prokaryotes and marine sediments by high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry (HPLC/ESI-IT-MSn). This technique is suitable for screening of biomass and environmental samples for distinctive taxonomic structural features such as distribution of polar lipid headgroups, types of bonds between alkyl moiety and glycerol backbone, and the chain length and degree of unsaturation in the alkyl moieties. We present analytical protocols to decipher structural information from mass spectral data. The IPL contents in selected archaeal and bacterial species are diverse and qualify as molecular fingerprints. Applied to marine sediments, the approach provided detailed information on the dominant microbial groups. The IPLs from bacterial members of anaerobic methanotrophic communities in surface sediments at Hydrate Ridge resemble those found in Desulfosarcina variabilis. The presence of dietherglycerophospholipids, however, suggests the presence of other bacteria possibly affiliated with the deepest phylogenetic branches in the tree of life. Sediments from approximately 90 m below the seafloor on the Peruvian continental margin are dominated by intact archaeal tetraethers with glycosidically bound hexoses as headgroups, consistent with a significant fraction of the community being archaea. Additional calditol-based tetraethers imply that the sedimentary archaea are taxonomically linked to the crenarchaeal Sulfolobales.
Size-Dependent Chemistry: Properties of Nanocrystals (2002)

Properties of materials determined by their size are indeed fascinating and form the basis of the emerging area of nanoscience. In this article, we examine the size dependent electronic structure and properties of nanocrystals of semiconductors and metals to illustrate this aspect. We then discuss the chemical reactivity of metal nanocrystals which is strongly dependent on the size not only because of the large surface area but also a result of the significantly different electronic structure of the small nanocrystals. Nanoscale catalysis of gold exemplifies this feature. Size also plays a role in the assembly of nanocrystals into crystalline arrays. While we owe the beginnings of size-dependent chemistry to the early studies of colloids, recent findings have added a new dimension to the subject.
Effect of the 5-HTTLPR polymorphism in the serotonin transporter gene on major depressive disorder and related comorbid disorders (2008)

The effect of the 5-HTTLPR polymorphism on MDD is co-dependent on the presence of comorbid disorders and sex. In this study, the s-allele of the 5-HTTLPR polymorphism was associated with significantly lower rates of particular lifetime comorbid disorders. Therefore, the presence of comorbid psychiatric disorders should be taken into account to clarify the association of the 5-HTTLPR polymorphism with MDD phenotypes.
Utility of Cyanothioformamides in Synthesis of Some Bis(imidazole, oxazole, thiazole, oxadiazole, triazole, benzoxazinethione and quinazoline) Derivatives. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Wavelength tracking of a remote WDM router in a passive optical network (1996)

We propose, analyze, and demonstrate a simple, robust method which enables a laser to track uncontrolled changes in a remotely located WDM device. As opposed to locking to a wavelength standard, our method locks the wavelength comb of a tunable DBR to a waveguide grating router (200-GHz channel spacing). We have demonstrated tracking at a 1 C/min temperature slew rate without requiring sacrificial channels, a pilot tone, or analog dithering circuitry. We discuss tradeoffs between step size, slew rate, measurement accuracy, and power penalty.
Isolation of a Tarantula Toxin Specific for a Class of Proton-gated Na+ Channels (2000)

Acid sensing is associated with nociception, taste transduction, and perception of extracellular pH fluctuations in the brain. Acid sensing is carried out by the simplest class of ligand-gated channels, the family of H(+)-gated Na(+) channels. These channels have recently been cloned and belong to the acid-sensitive ion channel (ASIC) family. Toxins from animal venoms have been essential for studies of voltage-sensitive and ligand-gated ion channels. This paper describes a novel 40-amino acid toxin from tarantula venom, which potently blocks (IC(50) = 0.9 nm) a particular subclass of ASIC channels that are highly expressed in both central nervous system neurons and sensory neurons from dorsal root ganglia. This channel type has properties identical to those described for the homomultimeric assembly of ASIC1a. Homomultimeric assemblies of other members of the ASIC family and heteromultimeric assemblies of ASIC1a with other ASIC subunits are insensitive to the toxin. The new toxin is the first high affinity and highly selective pharmacological agent for this novel class of ionic channels. It will be important for future studies of their physiological and physio-pathological roles.
Chapter 5. Prevention of infection by trimethoprim-sulfamethoxazole plus amphotericin B in patients with acute nonlymphocytic leukaemia (1984)

Chapter 5. Prevention of infection by trimethoprim-sulfamethoxazole plus amphotericin B in patients with acute nonlymphocytic leukaemia was published in Acute Nonlymphocytic Leukaemia in Adults on page 41.
Serum high-mobility group box 1 is correlated with interferon-α and may predict disease activity in patients with systemic lupus erythematosus (2019)

Sensing self-nucleic acids through toll-like receptors in plasmacytoid dendritic cells (pDCs), and the dysregulated type I IFN production, represent pathogenic events in the development of the autoimmune responses in systemic lupus erythematosus (SLE). Production of high-mobility group box-1 protein (HMGB1) promotes type I IFN response in pDCs. To better understand the active pathogenic mechanism of SLE, we measured serum levels of HMGB1, thrombomodulin, and cytokines (IL-1β, IL-2, IL-4, IL-5, IL-6, IL-10, IL-13, IL-17A, IL-17F, IFNα, IFNγ, TNFα) in 35 patients with SLE. Serum HMGB1 and IFNα were significantly higher in patients with active SLE (SLE Disease Activity Index (SLEDAI) score ≥ 6) compared with healthy donors or patients with inactive SLE. Furthermore, the HMGB1 levels were significantly correlated with IFNα levels. By qualitative analysis, the detection of serum IFNα or HMGB1 suggests active SLE and the presence of SLE-related arthritis, fever, and urinary abnormality out of SLEDAI manifestations. Collectively, HMGB1 and IFNα levels are biomarkers reflecting disease activity, and qualitative analysis of IFNα or HMGB1 is a useful screening test to estimate SLE severity and manifestations. Our results suggest the clinical significance of type I IFNs and HMGB1 as key molecules promoting the autoimmune process in SLE.
A Simplified New Assay for Assessment of Fungal Cell Damage with the Tetrazolium Dye, (2,3)-bis-(2-Methoxy-4-Nitro-5-Sulphenyl)-(2H)-Tetrazolium-5-Carboxanilide (XTT) (1995)

Studies of antimycotic host defenses have been limited by the paucity of rapid, reproducible quantitative assays for fungal cell damage. Prior studies defined a colorimetric method that uses MTT, a tetrazolium dye, to quantify polymorphonuclear leukocyte (PMNL)-mediated damage to fungi. These relatively simple, rapid, and reproducible assays require cumbersome extraction of precipitated MTT-formazan and high cell densities to overcome relatively low sensitivity. In experiments that compared assays with MTT and another tetrazolium dye, 2,3-bis-(2-methoxy-4-nitro-5-sulphenyl)-(2H)-tetrazolium-5-+ ++carboxanilide (XTT), estimates of damage to Aspergillus fumigatus hyphae by human PMNL were similar with both dyes. However, XTT reduction was more rapid and sensitive, yielding accurate results with fewer organisms and PMNL. The water-soluble XTT-formazan product also simplified measurements by eliminating the need for solvent-extraction steps that are obligatory in MTT assays. Thus, XTT is advantageous for quantitative assessment of fungal cell damage, although MTT remains useful for assessing fungal cell viability by direct microscopic visualization of precipitated formazan.
Hepatic encephalopathy—Definition, nomenclature, diagnosis, and quantification: Final report of the Working Party at the 11th World Congresses of Gastroenterology, Vienna, 1998 (2002)

Research on hepatic encephalopathy is hampered by the imprecise definition of this disabling complication of liver disease. Under this light, the Organisation Mondiale de Gastroentérologie commissioned a Working Party to reach a consensus in this area and to present it at the 11th World Congress of Gastroenterology in Vienna (1998). The Working Party continued its work thereafter and now present their final report. In summary, the Working Party has suggested a modification of current nomenclature for clinical diagnosis of hepatic encephalopathy; proposed guidelines for the performance of future clinical trials in hepatic encephalopathy; and felt the need for a large study to redefine neuropsychiatric abnormalities in liver disease, which would allow the diagnosis of minimal (subclinical) encephalopathy to be made on firm statistical grounds. In the interim, it proposes the use of a psychometric hepatic encephalopathy score, based on the result of 5 neuropsychologic tests. Finally, the need for a careful evaluation of the newer neuroimaging modalities for the diagnosis of hepatic encephalopathy was stressed.
Drug cocktails for effective treatment of glioblastoma multiforme (2008)

Glioblastoma multiforme (GBM) is the most prevalent primary brain tumor and also one of the most difficult human malignancies to manage. In fact, only 7 months was added to the mean survival rate o...
Twin Networks: Matching the Future for Sequence Generation (2017)

We propose a simple technique for encouraging generative RNNs to plan ahead. We train a "backward" recurrent network to generate a given sequence in reverse order, and we encourage states of the forward model to predict cotemporal states of the backward model. The backward network is used only during training, and plays no role during sampling or inference. We hypothesize that our approach eases modeling of long-term dependencies by implicitly forcing the forward states to hold information about the longer-term future (as contained in the backward states). We show empirically that our approach achieves 9% relative improvement for a speech recognition task, and achieves significant improvement on a COCO caption generation task.
Preparation of Optically Active Tertiary Alcohols by Enzymatic Methods. Application to the Synthesis of Drugs and Natural Products (1997)

By the catalysis of AK or porcine pancreas lipases, 3-iodo-2-phenyl-1,2-propanediol, 1-(hydroxymethyl)-1-phenyloxirane, 2-(iodomethyl)-4-phenyl-3-butyne-1,2-diol, 2-(iodomethyl)-4-(trimethylsilyl)-3-butyne-1,2-diol, and 5,5-dimethyl-2-(iodomethyl)-3-hexyne-1,2-diol were resolved in very high enantioselectivities (E >/= 153). The obtained enantiomerically pure or optically enriched compounds, containing an iodo atom, an oxirane moiety, or an alkynyl group, are versatile building blocks for the synthesis of chiral azido diols, sulfanyl diols, cyano diols, the side chain of a vitamin D(3) metabolite, the omega-chain of a prostaglandin analog, and an aggregation pheromone (1S,5R)-(-)-frontalin. Models based on the consideration of the importance of size, distance, and electron effect are proposed to interpret the observed stereospecificity in the enzymatic reactions. Thus, the lipase-catalyzed reactions of 1,1-disubstituted 1,2-diols occurred efficiently at the primary hydroxyl groups while the enantioselectivity was controlled by the tertiary carbinyl centers.
Wrapper–Filter Feature Selection Algorithm Using a Memetic Framework (2007)

This correspondence presents a novel hybrid wrapper and filter feature selection algorithm for a classification problem using a memetic framework. It incorporates a filter ranking method in the traditional genetic algorithm to improve classification performance and accelerate the search in identifying the core feature subsets. Particularly, the method adds or deletes a feature from a candidate feature subset based on the univariate feature ranking information. This empirical study on commonly used data sets from the University of California, Irvine repository and microarray data sets shows that the proposed method outperforms existing methods in terms of classification accuracy, number of selected features, and computational efficiency. Furthermore, we investigate several major issues of memetic algorithm (MA) to identify a good balance between local search and genetic search so as to maximize search quality and efficiency in the hybrid filter and wrapper MA.
Fluid Residuals and Drug Exposure in Nasal Irrigation (2009)

Quantification of the residual volume has important implications for the treatment of inflammatory disease with saline, as well as for potentially novel topical therapies. The information helps to define the fluid dynamics during nasal irrigation. The data are important to address concerns regarding drug or salt exposure from a very common intervention.
Monte Carlo study of phase transitions in ferromagnetic bilayers (1991)

We have used Monte Carlo computer simulations to study the behavior of an Ising model consisting of two ferromagnetic layers with different interaction constants coupled weakly together. For the range of lattice sizes studied it appears as though the system undergoes a single transition at the transition temperature of an isolated layer with the stronger coupling, but substantial changes in the thermodynamic properties also occur near the transition temperature of an isolated layer with the weaker of the two couplings.
STRUCTURE AND FUNCTION OF VOLTAGE-GATED ION CHANNELS (1995)

Voltage-gated ion channels are responsible for generation of electrical signals in cell membranes. Their principal subunits are members of a gene family and can function as voltage-gated ion channels by themselves. They are expressed in association with one or more auxiliary subunits which increase functional expression and modify the functional properties of the principal subunits. Structural elements that are required for voltage-dependent activation, selective ion conductance, and inactivation have been identified, and their mechanisms of action are being explored through mutagenesis, expression in heterologous cells, and functional analysis. These experiments reveal that this family of channels is built upon a common structural theme with variations appropriate for functional specialization of each channel type.
Improving the biodegradative capacity of subsurface bacteria (1993)

The continual release of large volumes of synthetic materials into the environment by agricultural and industrial sources over the last few decades has resulted in pollution of the subsurface environment. Cleanup has been difficult because of the relative inaccessibility of the contaminants caused by their wide dispersal in the deep subsurface, often at low concentrations and in large volumes. As a possible solution for these problems, interest in the introduction of biodegradative bacteria for in situ remediation of these sites has increased greatly in recent years (Timmis et al. 1988). Selection of biodegradative microbes to apply in such cleanup is limited to those strains that can survive among the native bacterial and predator community members at the particular pH, temperature, and moisture status of the site (Alexander, 1984). The use of microorganisms isolated from subsurface environments would be advantageous because the organisms are already adapted to the subsurface conditions. The options are further narrowed to strains that are able to degrade the contaminant rapidly, even in the presence of highly recalcitrant anthropogenic waste mixtures, and in conditions that do not require addition of further toxic compounds for the expression of the biodegradative capacity (Sayler et al. 1990). These obstacles can be overcome by placing the genes of well-characterized biodegradative enzymes under the control of promoters that can be regulated by inexpensive and nontoxic external factors and then moving the new genetic constructs into diverse groups of subsurface microbes. ne objective of this research is to test this hypothesis by comparing expression of two different toluene biodegradative enzymatic pathways from two different regulatable promoters in a variety of subsurface isolates.
Loss of expression of receptor tyrosine kinase family genesPTK7 andSEK in metastatic melanoma (1997)

Protein tyrosine kinases (PTKs) have been implicated in the development of many common human tumours including melanoma. Previously we isolated PTK gene sequences expressed in normal melanocytes. Here we examined expression of 9 of these genes in cell lines derived from defined stages of melanoma progression, by Northern blotting and in some cases immunoblotting. We also tested cells from 2 animal models of particular stages in progression, as well as uncultured biopsies of metastatic melanoma. The expression of 2 receptor kinase family members found in melanocytes, PTK7/CCK-4 and SEK/TYRO1, was decreased or lost in advanced melanomas. PTK7 mRNA was found in only 54% of melanoma cell lines and 20% of melanoma biopsies. Similarly, expression was lost in 2 advanced cell lines selected from an early melanoma line that did express PTK7 mRNA. SEK/TYRO1 expression was observed in 75% and 17% of cell lines from primary and metastastic melanomas, respectively. Conversely, mRNA for the non-receptor kinase PTK6/BRK was not detected in normal melanocytes or primary melanoma lines, but was found in 9% of metastatic melanoma cell lines.
Studies on pyrimidine derivatives. XXXVIII. Cross-coupling reaction of N-heteroaryl iodides with ethoxycarbonylmethylzinc bromide in the presence of palladium catalyst. (1985)

In the presence of tetrakis (triphenylphosphine) palladium, 2-iodo-4, 6-dimethylpyrimidine and 4-iodo-2, 6-dimethylpyrimidine reacted with ethoxycarbonylmethylzinc bromide (Reformatsky reagent) to give ethyl 4, 6-dimethyl-2-pyrimidineacetate and ethyl 2, 6-dimethyl-4-pyrimidineacetate, respectively. In contrast, the reaction of 5-iodo-2, 4-dimethylpyrimidine with the same reagent resulted in recovery of the starting iodide. Similar results were observed in the reactions of various N-heteroaryl iodides.
War Wounds: Lessons Learned from Operation Iraqi Freedom (2008)

The authors' results reflect a higher limb salvage rate than that achieved during previous wars. They feel their success was attributable to the use of wound vacuum-assisted closure, an aggressive surgical approach, and appropriate antibiotic therapy. Wound vacuum-assisted closure is the single intervention that is new among the authors' choices of techniques for treating combat wounds.
Majorana Fermions and a Topological Phase Transition in Semiconductor-Superconductor Heterostructures (2010)

We propose and analyze theoretically an experimental setup for detecting the elusive Majorana particle in semiconductor-superconductor heterostructures. The experimental system consists of one-dimensional semiconductor wire with strong spin-orbit Rashba interaction embedded into a superconducting quantum interference device. We show that the energy spectra of the Andreev bound states at the junction are qualitatively different in topologically trivial (i.e., not containing any Majorana) and nontrivial phases having an even and odd number of crossings at zero energy, respectively. The measurement of the supercurrent through the junction allows one to discern topologically distinct phases and observe a topological phase transition by simply changing the in-plane magnetic field or the gate voltage. The observation of this phase transition will be a direct demonstration of the existence of Majorana particles.
Single Event Transients in Logic Circuits—Load and Propagation Induced Pulse Broadening (2008)

The generation and propagation of single event transients (SET) in logic gate chains is studied and modeled. Regarding SET generation, we investigate the dependence of the generated SET pulse width on the struck node capacitance. Rising node capacitance may lead to amplified pulse width, indicating that increasing load capacitance alone is not an option for radiation hardening. SET propagation in logic chains is also studied, and it is shown that significant broadening or attenuation of the propagated transient pulse width may be observed. It is shown that the chain design (propagation delay of high to low and low to high transitions) has a major impact on broadening or attenuation of the propagated transient pulse. For the first time a suitable model for SET broadening is provided.
1,2‐Dioxetanes: Novel chemiluminescent enzyme substrates. Applications to immunoassays (1989)

We have synthesized and studied two 1,2-dioxetane-based chemiluminescent enzyme substrates: 3-(2'-spiroadamantane)-4-methoxy-4-(3"-phosphoryloxy)phenyl- 1,2-dioxetane (AMPPD), and, 3-(2'-spiroadamantane)-4-methoxy-4-(3"-beta-D'-galactopyrano -yloxy)phenyl-1,2- dioxetane (AMPGD), which can be activated to chemiluminescence at 470 nm by alkaline phosphatase and beta-D-galactosidase, respectively. In addition, we observed that certain macromolecules enhance the luminescence of AMPPD. For example, the addition of 0.1% bovine serum albumin amplifies the luminescent signal and improves the detection limit for alkaline phosphatase by approximately one order of magnitude under certain conditions. This effect is due to the presence of a hydrophobic microenvironment provided by the enhancer which 'stabilizes' the dephosphorylated AMPPD emitter. Alkaline phosphatase catalysed chemiluminescence from AMPPD is constant for a prolonged period of time. Using AMPPD we were able to detect 0.01 attomole quantities of alkaline phosphatase immobilized on membrane supports and imaged on photographic film and, in solution, measured in a luminometer. AMPPD and AMPGD offer alternatives to colorimetric and fluorescent substrates for alkaline phosphatase and beta-D-galactosidase labels used in enzyme immunoassays. The simplicity and sensitivity of this chemiluminescent readout allowed the development of rapid clinical assays (e.g. beta-hCG, LH, TSH and others).