gebhart/patrepeval huggingface dataset:
The Effect of Solvent on the Analysis of Secondary Organic Aerosol Using Electrospray Ionization Mass Spectrometry (2008)

This study examined the effect of solvent on the analysis of organic aerosol extracts using electrospray ionization mass spectrometry (ESI-MS). Secondary organic aerosol (SOA) produced by ozonation of d-limonene, as well as several organic molecules with functional groups typical for OA constituents, were extracted in methanol, d3-methanol, acetonitrile, and d3-acetonitrile to investigate the extent and relative rates of reactions between analyte and solvent. High resolution ESI-MS showed that reactions of carbonyls with methanol produce significant amounts of hemiacetals and acetals on time scales ranging from several minutes to several days, with the reaction rates increasing in acidified solutions. Carboxylic acid groups were observed to react with methanol resulting in the formation of esters. In contrast acetonitrile extracts showed no evidence of reactions with analyte molecules, suggesting that acetonitrile is the preferred solvent for SOA extraction. The use of solvent-analyte reactivity as a tool for the improved characterization of functional groups in complex organic mixtures was demonstrated. Direct comparison between mass spectra of the same SOA samples extracted in methanol versus acetonitrile was used to estimate the lower limits for the relative fractions of carbonyls (> or = 42%) and carboxylic acids (> or = 55%) in d-limonene SOA.
Vitamin B <sub>12</sub> modulates the transcriptome of the skin microbiota in acne pathogenesis (2015)

Various diseases have been linked to the human microbiota, but the underlying molecular mechanisms of the microbiota in disease pathogenesis are often poorly understood. Using acne as a disease model, we aimed to understand the molecular response of the skin microbiota to host metabolite signaling in disease pathogenesis. Metatranscriptomic analysis revealed that the transcriptional profiles of the skin microbiota separated acne patients from healthy individuals. The vitamin B12 biosynthesis pathway in the skin bacterium Propionibacterium acnes was significantly down-regulated in acne patients. We hypothesized that host vitamin B12 modulates the activities of the skin microbiota and contributes to acne pathogenesis. To test this hypothesis, we analyzed the skin microbiota in healthy subjects supplemented with vitamin B12. We found that the supplementation repressed the expression of vitamin B12 biosynthesis genes in P. acnes and altered the transcriptome of the skin microbiota. One of the 10 subjects studied developed acne 1 week after vitamin B12 supplementation. To further understand the molecular mechanism, we revealed that vitamin B12 supplementation in P. acnes cultures promoted the production of porphyrins, which have been shown to induce inflammation in acne. Our findings suggest a new bacterial pathogenesis pathway in acne and provide one molecular explanation for the long-standing clinical observation that vitamin B12 supplementation leads to acne development in a subset of individuals. Our study discovered that vitamin B12, an essential nutrient in humans, modulates the transcriptional activities of skin bacteria, and provided evidence that metabolite-mediated interactions between the host and the skin microbiota play essential roles in disease development.
Fibrinogen Baltimore I: polymerization defect associated with a gamma 292Gly----Val (GGC----GTC) mutation (1990)

Fibrinogen Baltimore I is one of the very first congenital abnormal fibrinogens reported over several decades ago; however, the molecular defect of this dysfibrinogen has eluded identification. In fact, several reports misidentified the functional defect of Baltimore I, which has impaired fibrin monomer polymerization. Reversed-phase high- performance liquid chromatography analysis of lysyl endopeptidase digest of the purified Baltimore I gamma-chain showed an abnormal peptide not found in the co-existing normal gamma-chain of this heterozygote. Amino acid sequencing of this peptide indicated that gamma-chain Gly292 is replaced by valine. This observation was confirmed, and the genetic defect was determined by direct nucleotide sequencing of a polymerase chain reaction product containing codon gamma 292, which is mutated: GGC----GTC. The molecular defect of Fibrinogen Baltimore I lies in a region of the gamma-chain required for fibrin polymerization, suggesting that the integrity of gamma Gly292 is critical for fibrin assembly.
Miscibility and Hydrogen Bonding in Blends of Poly(vinylphenol-<i>co</i>-methyl methacrylate) with Poly(ethylene oxide) (2001)

ABSTRACT: Blends of poly(vinylphenol-co-methyl methacrylate) (PVPh-co-PMMA) with poly(ethylene oxide) (PEO) were prepared by solution casting from tetrahydrofuran (THF) solution. The miscibility behavior and hydrogen bonding of blends were investigated by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and solid-state nuclear magnetic resonance (NMR). Experimental results indicate that PEO was miscible with PVPh-co-PMMA as shown by the existence of single composition-dependent glass transition temperatures over the entire composition range by DSC. In addition, a negative polymer-polymer interaction energy density “B ” was calculated based on the melting depression of PEO using the Nishi-Wang equation. Solid-state NMR reveals single-exponential decay of proton spin-lattice relaxation times in the rotating frame (T1FH) in the amorphous PVPh-co-PMMA phase. Furthermore, FTIR and solid-state NMR results reveal that at least three competing equilibria are present in the blend; self-association of PVPh-co-PMMA copolymer (hydroxyl-hydroxyl and hydroxyl-carbonyl) and hydroxyl-ether interassociation between PVPh and PEO. Quantitative results show that although the hydroxyl-ether interassociation is favored at room temperature, the hydroxyl-carbonyl self-association dominates at higher temperatures (&gt;70 °C). The Painter-Coleman association model (PCAM) can predict three interacting functional groups based on our experimental results at various temperatures.
Analyzing and Correlating Security Events Using State Machine (2010)

It is unfeasible to analyze the security events by the manual way for the security manager, because the number of the events is huge and the information contained in the events is meaningless. After analyzing the existing algorithms of security events correlation, we propose an attack scenario reconstruction technology based on state machine. The processes of attackers intruding into the cyberspace can be restored and the more comprehensive attack scenario description information will be generated using this technology. This working lets the security manager more comfy. The state machine based attack scenario reconstruction technology processes security events using clustering analysis and causal analysis concurrently, it builds a correlation state machine in memory for every attack scenario tree which is predefined by the security manager, when security events are coming, the certain state machines will process them, if the condition is satisfied, an attack scenario description information will be generated and then sent to the security manager. The correlating technology based on state machine is more timely and accurately, and at last, we use the DARPA2000 Intrusion Scenario Specific Data Sets to validate the technology, the experiment results show that it is feasible to analyze security events using the technology we proposed.
The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation. (1994)

Halocyanin, a small blue copper protein, was isolated from the haloalkaliphilic archaeon Natronobacterium pharaonis. The NH2 terminus was not accessible to Edman degradation. About 70% of the amino acid sequence was determined by protein sequence analysis. The sequence information of two peptides was used for cloning and sequencing the halocyanin gene (hcy). The open reading frame codes for 489 base pairs, which account for a protein with 163 amino acids and a molecular mass of 17,223 Da. The discrepancy between this value and the molecular mass of 15,456 +/- 1.5 Da for the copper-free protein determined by electrospray mass spectrometry can be explained by a post-translational processing of the gene product. The NH2-terminal sequence of the open reading frame contains a motif that is characteristic for prokaryotic lipoproteins. Assuming a similar processing for halocyanin, Cys at position 25 of the primary transcript would be modified by a diphytanyl (glycerol)diether. Subsequently, the precursor is cleaved by a signal peptidase II-like protease and then acetylated at its NH2-terminal alpha-amino group. These modifications would yield a protein with a calculated molecular mass of 15,456 Da. A comparison of the primary structure of halocyanin with a number of other blue copper proteins places it into the plastocyanin-related group.
Single agent and combination studies of pralatrexate and molecular correlates of sensitivity (2010)

Pralatrexate was more potent than methotrexate in a panel of solid tumour lines. Our findings support the further clinical development of pralatrexate in combination with certain cytotoxics and targeted therapies, and suggest that RFC-1, FPGS and DHFR may be potential biomarkers of outcome.
The RASE (Rapid, Accurate Simulation Environment) for chip multiprocessors (2005)

We present RASE, a full system high performance simulation methodology for simulating complex server applications and server class chip multiprocessors enabled with fine-grain multithreading (CMTs). RASE combines application knowledge, operating system information, and data access patterns with an instruction stream from a highly-tuned, scalable steady-state benchmark [5] [22] to generate multiple representative instruction streams that can be mapped to a variety of CMT configurations. We use execution-driven simulation to generate instruction streams for M processors and store them as instruction trace files (several billion instructions per processor) that can be post-processed and augmented for larger than M processor system simulation. We use SPEC JBB2000, TPC-C, and an XML server benchmark to compare the performance estimates of RASE to a reference prototype CMT system. By varying M, we find that our trace-driven simulation methodology predicts within 5% of the instructions per cycle (IPC) of the reference hardware for the applications. Without post-processing the traces, in the best cases, the performance prediction accuracy degrades to 20-40% of the real IPC for instruction traces that require a high replication factor.
Cu<sub>4</sub>I<sub>4</sub> Clusters Supported by P<sup>∧</sup>N-type Ligands: New Structures with Tunable Emission Colors (2011)

A series of Cu(4)I(4) clusters (1-5) supported by two P^N-type ligands 2-[(diRphosphino)methyl]pyridine (1, R = phenyl; 2, R = cyclohexyl; 3, R = tert-butyl; 4, R = iso-propyl; 5, R = ethyl) have been synthesized. Single crystal X-ray analyses show that all five clusters adopt a rare "octahedral" geometry. The central core of the cluster consists of the copper atoms arranged in a parallelogram with μ(4)-iodides above and below the copper plane. The copper atoms on the two short edges of the parallelogram (Cu-Cu = 2.525(2)-2.630(1) Å) are bridged with μ(2)-iodides, whereas the long edges (Cu-Cu = 2.839(3)-3.035(2) Å) are bridged in an antiparallel fashion by the P^N ligands. This Cu(4)I(4) geometry differs significantly from the "cubane" and "stairstep" geometries reported for other Cu(4)I(4)L(4) clusters. Luminescence spectra of clusters 3 and 4 display a single emission around 460 nm at room temperature that is assigned to emission from a triplet halide-to-ligand charge-transfer ((3)XLCT) excited state, whereas clusters 1, 2, and 5 also have a second band around 570 nm that is assigned to a Cu(4)I(4) cluster-centered ((3)CC) excited state. The structural and photophysical properties of a dinuclear Cu(2)I(2)(P^N)(2) complex obtained during the sublimation of cluster 3 is also provided.
The Fas protein is expressed at high levels on CD4+CD8+ thymocytes and activated mature lymphocytes in normal mice but not in the lupus-prone strain, MRL lpr/lpr. (1993)

The lymphoproliferation (lpr) mutation in the MRL strain of mice is caused by the insertion of the early transposable element ETn in the Fas gene. The insertion causes a striking decrease in Fas mRNA expression and is associated clinically with marked acceleration of the lupus-like disease. To further explore the role of the Fas protein in T-cell selection in the thymus and tolerance in the peripheral immune system, we produced a monospecific polyclonal anti-murine Fas antibody that binds to a polymorphic region of the protein. Fas protein expression was detected on approximately 90% of BALB/c and MRL +/+ thymocytes, and the expression was highest on CD4+CD8+ thymocytes, the stage at which most thymocytes die by apoptosis. In contrast to the high level of expression of Fas on thymocytes, Fas was detected on < 10% of normal splenic T cells. After activation of splenic T cells with Con A or anti-CD3 and interleukin 2, Fas expression increased approximately 10-fold. Fas expression on splenic B cells was also markedly up-regulated after activation with lipopolysaccharide or anti-mu antibodies. The Fas protein was not detected on resting or activated lymphocytes obtained from MRL lpr/lpr mice. Together, these findings suggest that Fas plays a role in both thymic selection and T-cell survival in the periphery and that the accelerated autoimmunity in MRL lpr/lpr mice results from a defect in both of these pathways.
Hydrogel-Forming Microneedles Prepared from “Super Swelling” Polymers Combined with Lyophilised Wafers for Transdermal Drug Delivery (2014)

We describe, for the first time, hydrogel-forming microneedle arrays prepared from "super swelling" polymeric compositions. We produced a microneedle formulation with enhanced swelling capabilities from aqueous blends containing 20% w/w Gantrez S-97, 7.5% w/w PEG 10,000 and 3% w/w Na2CO3 and utilised a drug reservoir of a lyophilised wafer-like design. These microneedle-lyophilised wafer compositions were robust and effectively penetrated skin, swelling extensively, but being removed intact. In in vitro delivery experiments across excised neonatal porcine skin, approximately 44 mg of the model high dose small molecule drug ibuprofen sodium was delivered in 24 h, equating to 37% of the loading in the lyophilised reservoir. The super swelling microneedles delivered approximately 1.24 mg of the model protein ovalbumin over 24 h, equivalent to a delivery efficiency of approximately 49%. The integrated microneedle-lyophilised wafer delivery system produced a progressive increase in plasma concentrations of ibuprofen sodium in rats over 6 h, with a maximal concentration of approximately 179 µg/ml achieved in this time. The plasma concentration had fallen to 71±6.7 µg/ml by 24 h. Ovalbumin levels peaked in rat plasma after only 1 hour at 42.36±17.01 ng/ml. Ovalbumin plasma levels then remained almost constant up to 6 h, dropping somewhat at 24 h, when 23.61±4.84 ng/ml was detected. This work represents a significant advancement on conventional microneedle systems, which are presently only suitable for bolus delivery of very potent drugs and vaccines. Once fully developed, such technology may greatly expand the range of drugs that can be delivered transdermally, to the benefit of patients and industry. Accordingly, we are currently progressing towards clinical evaluations with a range of candidate molecules.
Dissemination of New Methicillin-Resistant <i>Staphylococcus aureus</i> Clones in the Community (2002)

Multiple methicillin-resistant Staphylococcus aureus (MRSA) clones carrying type IV staphylococcal cassette chromosome mec were identified in the community-acquired MRSA strains of both the United States and Australia. They multiplied much faster than health-care-associated MRSA and were resistant to fewer non-beta-lactam antibiotics. They seem to have been derived from more diverse S. aureus populations than health-care-associated MRSA strains.
Automatic Verification of In-Order Execution In Microprocessors with Fragmented Pipelines and Multicycle Functional Units (2002)

As embedded systems continue to face increasingly higher performance requirements, deeply pipelined processor architectures are being employed to meet desired system performance. System architects critically need modeling techniques that allow exploration, evaluation, customization and validation of different processor pipeline configurations, tuned for a specific application domain. We propose a novel finite state machine (FSM) based modeling of pipelined processors and define a set of properties that can be used to verify the correctness of in-order execution in the presence of fragmented pipelines and multicycle functional units. Our approach leverages the system architect's knowledge about the behavior of the pipelined processor through architecture description language (ADL) constructs, and thus allows a powerful top-down approach to pipeline verification. We applied this methodology to the DLX processor to demonstrate the usefulness of our approach.
Giant magnetoresistance effect in grain-type alloy thin films (1993)

FeCo-Ag thin films with a grain structure, in which the FeCo alloy and the Ag metal are mutually insoluble, were prepared by a vacuum deposition method. The maximum magnetoresistance (MR) ratio observed in these films was 13.0% at room temperature in the magnetic field region between -1 and 1 T. Here the features of the MR curve corresponded well with those of the magnetization curve. This indicates the appearance of a giant MR effect in such grain-type alloy thin films. Though the magnetic anisotropy field (Hk) associated with the MR characteristics that were obtained is extremely large (>1 T), proper annealing was found to be effective for decreasing the Hk value without causing a drop in the MR ratio.
Sensorless quasi-standstill and very low-speed position detection in non-salient PMSMs based on current injection and back-EMF observer (2012)

Accuracy and robustness of sensorless speed control of non-salient PMSMs in the low-speed region and at start-up is a critical issue, due to the low amplitude of the back-EMF which prevents estimation and then closed-loop control in the zero speed range. This problem is usually overcome by adopting an open-loop control (e.g. constant amplitude rotating current space vector), which is normally able to start the motor up to an enough high speed, where sensorless closed-loop control is possible. Open-loop startup is however not robust against load torque and inertia variations and random initial rotor position conditions. Also the extension of the closed-loop operating range towards zero is strongly desired. Standard techniques relying on magnetic saliency are not applicable (i.e. no relevant anisotropy is present in the considered machine), and some methods based on the detection of torque production by signal injection can be adopted. The methods proposed and studied in this paper belongs to this last class. Two different application cases will be considered: an initial high-accuracy position detection at quasi-standstill and a position and speed tracking for closed-loop sensorless speed control. A complete theoretical analysis is reported to demonstrate the features of the proposal and highlight the dependence on certain design parameters. Then extensive simulation and experimental investigations based on an industrial drive system are included to prove the feasibility of the method and validity of the theoretical analysis.
POSTOPERATIVE NAUSEA AND VOMITING IV (1960)

Presented at the Annual Meeting of the American Society of Anesthesiologists, Inc., Miami Beach. Florida, October 9, 1959. and accepted for publication December 2, 1959. Drs. Bellville and Howland are in the Department of Anesthesiology, Memorial Center for Cancer and Allied Diseases, and the Section of Experimental Anesthesia, Division of Experimental Surgery. Sloan-Kettering Institute, New York. New York. Dr. Bross is Chief. Department of Statisties. Roswell Park Memorial Institute. Buffalo, New York.
Translational control by influenza virus. Selective translation is mediated by sequences within the viral mRNA 5'-untranslated region. (1993)

In cells infected by influenza virus type A, host cell protein synthesis declines rapidly and dramatically, while influenza viral protein synthesis occurs efficiently throughout infection. Previously, we had shown that the selective translation of influenza viral mRNAs in infected cells occurred in a cap-dependent manner and was due at least in part to structures inherent in the mRNAs. Using chimeras containing the noncoding and coding regions of cellular and viral mRNAs, we can now report that the selective translation is mediated by sequences within the 5'-untranslated regions (UTR) of the viral mRNAs. Polysome analysis confirmed that a 45-nucleotide sequence contained in the 5'-UTR of the influenza viral nucleocapsid protein was necessary and sufficient to allow the host cell translational machinery to discriminate between viral and cellular mRNAs. In reciprocal experiments in which the 5'-UTR of the cellular mRNA-secreted embryonic alkaline phosphatase replaced the nucleocapsid protein 5'-UTR, viral protein synthesis was inhibited in virus-infected cells, resembling host protein synthesis. Finally, we demonstrated that the 5'-UTR of another influenza viral mRNA, that encoding the nonstructural protein, also conferred resistance to the shutoff of protein synthesis in influenza virus-infected cells.
Anomalous dynamics of cell migration (2008)

Cell movement--for example, during embryogenesis or tumor metastasis--is a complex dynamical process resulting from an intricate interplay of multiple components of the cellular migration machinery. At first sight, the paths of migrating cells resemble those of thermally driven Brownian particles. However, cell migration is an active biological process putting a characterization in terms of normal Brownian motion into question. By analyzing the trajectories of wild-type and mutated epithelial (transformed Madin-Darby canine kidney) cells, we show experimentally that anomalous dynamics characterizes cell migration. A superdiffusive increase of the mean squared displacement, non-Gaussian spatial probability distributions, and power-law decays of the velocity autocorrelations is the basis for this interpretation. Almost all results can be explained with a fractional Klein-Kramers equation allowing the quantitative classification of cell migration by a few parameters. Thereby, it discloses the influence and relative importance of individual components of the cellular migration apparatus to the behavior of the cell as a whole.