gebhart/patrepeval huggingface dataset:
Competing isomeric product channels in the 193 nm photodissociation of 2-chloropropene and in the unimolecular dissociation of the 2-propenyl radical (2001)

This paper presents product translational energy spectroscopy measurements of the primary photofragmentation channels of 2-chloropropene excited at 193 nm and of the unimolecular dissociation of the 2-propenyl radical. Tunable vacuum ultraviolet (VUV) photoionization of the products allows us to distinguish between the various product isomers formed in these processes. The data show evidence for three significant primary reaction channels in the dissociation of 2-chloropropene: An excited-state C–Cl fission channel producing fast Cl atoms, a C–Cl fission channel producing slow Cl atoms, and HCl elimination. A minor C–CH3 fission channel contributes as well. The measured branching of the major primary product channels is: [fast C–Cl]:[slow C–Cl]:[HCl elimination]=62%:23%:15%. The experiments also allow us to resolve selectively the product branching between the unimolecular dissociation channels of the 2-propenyl radical, a high energy C3H5 isomer; we measure how the branching ratio between the two competing C–H fission channels changes as a function of the radical’s internal energy. The data resolve the competition between the unimolecular H+allene and H+propyne product channels from the radical with internal energies from 0 to 18 kcal/mol above the H+propyne barrier. We find that the barrier to H+allene formation from this high-energy C3H5 radical is higher than the barrier to H+propyne formation, in agreement with recent theoretical calculations but in sharp contrast to that predicted for the most stable C3H5 isomer, the allyl radical. The experiments demonstrate a general technique for selectively forming a particular CnHm isomer dispersed by internal energy due to the primary photolysis, thus allowing us to determine the branching between unimolecular dissociation channels as a function of the selected radical isomer’s internal energy.
3D Printing PDMS Elastomer in a Hydrophilic Support Bath via Freeform Reversible Embedding (2016)

Polydimethylsiloxane (PDMS) elastomer is used in a wide range of biomaterial applications including microfluidics, cell culture substrates, flexible electronics, and medical devices. However, it has proved challenging to 3D print PDMS in complex structures due to its low elastic modulus and need for support during the printing process. Here we demonstrate the 3D printing of hydrophobic PDMS prepolymer resins within a hydrophilic Carbopol gel support via freeform reversible embedding (FRE). In the FRE printing process, the Carbopol support acts as a Bingham plastic that yields and fluidizes when the syringe tip of the 3D printer moves through it, but acts as a solid for the PDMS extruded within it. This, in combination with the immiscibility of hydrophobic PDMS in the hydrophilic Carbopol, confines the PDMS prepolymer within the support for curing times up to 72 h while maintaining dimensional stability. After printing and curing, the Carbopol support gel releases the embedded PDMS prints by using phosphate buffered saline solution to reduce the Carbopol yield stress. As proof-of-concept, we used Sylgard 184 PDMS to 3D print linear and helical filaments via continuous extrusion and cylindrical and helical tubes via layer-by-layer fabrication. Importantly, we show that the 3D printed tubes were manifold and perfusable. The results demonstrate that hydrophobic polymers with low viscosity and long cure times can be 3D printed using a hydrophilic support, expanding the range of biomaterials that can be used in additive manufacturing. Further, by implementing the technology using low cost open-source hardware and software tools, the FRE printing technique can be rapidly implemented for research applications.
Kinetics of the enzymatic hydrolysis of cellulose (1984)

Enzymatic hydrolysis of cellulose for sugar production offers advantages of higher conversion, minimal by-product formation, low energy requirements, and mild operating conditions over other chemical conversions. The development of a kinetic model, based on observable, macroscopic properties of the overall system, is helpful in design and economic evaluation of processes for sugar conversion and ethanol production. A kinetic model is presented, incorporating enzyme adsorption, product inhibition, and considers a multiple enzyme and substrate system. This model was capable of simulating saccharification of a lignocellulosic material, rice straw, at high substrate (up to 333 g/L) and enzyme concentrations (up to 9.2 FPU/mL) that are common to proposed process designs.
Structural organization and differential expression of rice α-amylase genes (1990)

Rice alpha-amylases are encoded by a multigene family that has previously been classified into 5 hybridization groups. DNA sequence and Southern blot analysis identified three genes (RAmy1A, RAmy1B and RAmy1C) in Group 1 with DNA sequence identity of at least 90%. Hybridization Group 2 is represented by only one gene, RAmy3D, which is identical to a previously characterized cDNA, pOS137. RAmy3D is physically linked to the sole representative of Group 5, RAmy3E. The identity between these two genes is 81.4% in the coding region but less than 50% in the 5' and 3' flanking regions. Northern blot analysis and RNA-PCR were used to detect the expression of alpha-amylase genes in various tissues. Alpha-amylase mRNA was abundant in germinating seeds and callus. Some genes were also expressed at much lower levels in roots, young leaves and immature seeds. RAmy1A and RAmy3E were expressed in all tissues while RAmy3D was expressed in all tissues except the immature seeds. RAmy1B was weakly expressed only in callus. RAmy1A transcript was most abundant in the germinating seeds, while RAmy3D and RAmy3E transcripts were most abundant in callus and immature seeds, respectively.
Three-phase fast decoupled power flow for distribution networks (1996)

Power system single-phase models assume that generation, transmission and distribution systems are perfectly balanced. The great appeal of this type of model is its simplicity, for all the calculations become quite simple, when compared with the three-phase model, and the results obtained are well suited for most applications. There are cases, however, in which its results may not be accurate enough, as may happen with distribution system analysis (unbalanced loads), non-transposed transmission lines, large mutual impedances between lines, etc. These problems require a more accurate three-phase model. The paper extends decoupling theory in order to obtain a fast decoupled three-phase load flow which is suited for distribution power system analysis.
A Modification of the Jaccard–Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings (2002)

Determination of molecular similarity plays an important role in analyzing large compound databases in chemical and pharmaceutical research. When molecules are described by binary vectors with bits corresponding to the presence or absence of structural features, the Tanimoto association coefficient is the most commonly used measure of similarity or chemical distance between two compounds. However, when used to select compounds for an optimal spread design, the Tanimoto coefficient produces an intrinsic bias toward smaller compounds. We have developed a new association coefficient that overcomes this bias. This article gives details of the new coefficient and contrasts the two coefficients for selecting diverse sets of compounds from a large collection. When the Tanimoto coefficient is modified as suggested to select a diverse set in the National Cancer Institute and Registry of Toxic Effects of Chemical Substances databases, the average number of features among the selected compounds increases by more than 50%.
The brain: integrated three-dimensional display of MR and PET images. (1989)

Three patients with intractable epilepsy, two with brain tumors, and one with encephalitis were imaged with magnetic resonance (MR) and positron emission tomography (PET). MR data were used to construct a three-dimensional (3D) computer model of the brain surface depicting the precentral (movement), postcentral (sensation), left inferior frontal (speech), and left superior temporal (hearing) gyri. PET-derived measurements of average surface metabolism were encoded as colors and mapped onto the 3D model by means of a retrospective technique for registering the two scans. The integrated 3D model depicted the location of PET-detected metabolic abnormalities with respect to the gyral anatomy visualized with MR. In each case, the predicted relationships were confirmed intraoperatively by means of inspection of the brain and electroencephalography. Multimodality 3D displays are likely to be particularly valuable for interpreting PET studies of epileptic patients and others with normal MR anatomy.
Review paper: Crystal fibre technology (2000)

Crystal fibres offer an attractive supplement to conventional fibres for both telecommunication, sensor and medical applications. Crystal fibres are in the cross section characterized by a micro-scale structure and are generally divided into two types, namely those that are operating by total internal reflection and those operating by photonic bandgap effects. In this paper, we discuss fundamental and advanced properties of both types of crystal fibres and illustrate their uniqueness compared to conventional fibres. Furthermore, we address the various types of future applications that can be expected using crystal fibre technology.
Inhibition of mannosidase in hybridomas yields monoclonal antibodies with greater capacity for carbohydrate labeling. (1988)

Labeling an antibody site specifically through its carbohydrate residues preserves more of its antigen-binding activity than does labeling through protein moieties. To boost the amount of immunoglobulin G carbohydrate capable of being labeled, we treated hybridoma cells with a mannosidase inhibitor, deoxymannojirimycin (dMM). Polyacrylamide gel electrophoresis showed formation of a glycoprotein with high mannose content, in that endo-beta-N-acetylglucosaminidase H (EC 3.2.1.96) could digest the antibody from the dMM-treated cells, but not from control cultures. Carbohydrate analysis confirmed this conclusion, indicating that the antibody from the dMM-treated cells had twice as much mannose as did the control antibody. The glucosamine content of the treated-cells' antibodies was half that of the control, and no additional carbohydrate residues were detectable in the antibodies secreted by the dMM-treated cells. We conjugated both the dMM and control antibodies through their carbohydrate to a chelator. In labeling, the dMM antibody conjugate incorporated approximately threefold as much 111In isotope as the control conjugate. The two labeled antibodies were injected into mice and showed similar organ distributions.
Physiologic mucosal changes within the nose and ethmoid sinus: Imaging of the nasal cycle by MRI (1988)

Magnetic resonance studies frequently demonstrate increased T2-weighted signal in the nasal area. To further evaluate this phenomenon, several MRI examinations of the nasal cavity were performed within an 8- to 12-hour period. The study demonstrated that changes alternated from side to side and were interrupted by the administration of topical vasoconstriction, confirming imaging of the normal nasal cycle. Changes were also observed within the ethmoid sinuses. Signal intensity on T2-weighted images during the congested phase was similar to inflammatory mucosa. Occasionally, these changes make interpretation of the extent of pathology difficult in patients with sinus disease, and raise the possibility of inflammatory pathology in asymptomatic patients. Awareness of MRI imaging of nasal cycle should reduce the likelihood of diagnostic errors and provides another method for study of this physiologic phenomenon.
The Sorption of Gases and Vapours by Solids. (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Sorption of Gases and Vapours by Solids.J. W. McBainJ. W. McBainMore by J. W. McBainCite this: J. Phys. Chem. 1933, 37, 1, 149–150Publication Date (Print):January 1, 1933Publication History Published online1 May 2002Published inissue 1 January 1933https://doi.org/10.1021/j150343a021RIGHTS & PERMISSIONSArticle Views259Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (182 KB) Get e-Alerts
TNF inhibitors: a review of the recent patent literature. (2002)

Overproduction of the inflammatory cytokine tumor necrosis factor (TNF)-alpha is implicated in a wide range of pathological conditions, including inflammatory bowel disease (IBD), rheumatoid arthritis (RA), multiple sclerosis and stroke. This review focuses on recent developments in the patent literature, which are aimed principally at the suppression of TNF release. The review will separately detail the development of biological agents, such as soluble TNF receptors and engineered antibodies, and small molecules, which primarily target TNF.
Rapid acquisition of ultra-wideband signals in the dense multipath channel (2003)

Efficient serial search strategies are presented and shown to reduce drastically the mean acquisition time for UWB signals in a dense multipath environment. Inherent in traditional serial search problems is the assumption that only a single bin or a small number of consecutive bins can properly terminate the search. This assumption leads to search strategies which tend to be linear in nature, e.g., a linear sweep of the uncertainty region. Because of the dense multipath channel present in most UWB systems, this assumption is invalid as seen by the channel's relatively large delay spread. A generalized analysis of various search algorithms is presented based on a Markov chain model of a simple single-dwell serial search. The results from this analysis reveal that the linear search has a considerably larger mean acquisition time than the more efficient search strategy termed the bit reversal search.
Correction of CD18-Deficient Lymphocytes by Retrovirus-Mediated Gene Transfer (1990)

Leukocyte adhesion deficiency (LAD) is an inherited disorder of leukocyte function caused by derangements in CD18 expression. The genetic and functional abnormalities in a lymphocyte cell line from a patient with LAD have been corrected by retrovirus-mediated transduction of a functional CD18 gene. Lymphocytes from patients with LAD were exposed to CD18-expressing retrovirus and enriched for cells that express CD11a and CD18 (LFA-1) on the cell surface. Molecular and functional analyses of these cells revealed (i) one copy of proviral sequence per cell, (ii) viral-directed CD18 RNA that exceeded normal endogenous levels, (iii) normal quantities of CD11a and CD18 protein on the cell surface, and (iv) reconstitution of LFA-1-dependent adhesive function.
Molecular cloning of a pancreatic islet-specific glucose-6-phosphatase catalytic subunit-related protein. (1999)

A pancreatic islet-specific glucose-6-phosphatase-related protein (IGRP) was cloned using a subtractive cDNA expression cloning procedure from mouse insulinoma tissue. Two alternatively spliced variants that differed by the presence or absence of a 118-bp exon (exon IV) were detected in normal balb/c mice, diabetic ob/ob mice, and insulinoma tissue. The longer, 1901-bp full-length cDNA encoded a 355-amino acid protein (molecular weight 40,684) structurally related (50% overall identity) to the liver glucose-6-phosphatase and exhibited similar predicted transmembrane topology, conservation of catalytically important residues, and the presence of an endoplasmic reticulum retention signal. The shorter transcript encoded two possible open reading frames (ORFs), neither of which possessed His174, a residue thought to be the phosphoryl acceptor (Pan CJ, Lei KJ, Annabi B, Hemrika W, Chou JY: Transmembrane topology of glucose-6-phosphatase. J Biol Chem 273:6144-6148, 1998). Northern blot and reverse transcription-polymerase chain reaction analysis showed that the mRNA was highly expressed in pancreatic islets and expressed more in beta-cell lines than in an alpha-cell line. It was notably absent in tissues and cell lines of non-islet neuroendocrine origin, and no other major tissue source of the mRNA was found. During development, it was expressed in parallel with insulin mRNA. The mRNA was efficiently translated and glycosylated in an in vitro translation/membrane translocation system and readily transcribed into COS 1, HIT, and CHO cells using cytomegalovirus or Rous sarcoma virus promoters. Whereas the liver glucose-6-phosphatase showed activity in these transfection systems, the IGRP failed to show glucose phosphotransferase or phosphatase activity with p-nitrophenol phosphate, inorganic pyrophosphate, or a range of sugar phosphates hydrolyzed by the liver enzyme. While the metabolic function of the enzyme is not resolved, its remarkable tissue-specific expression warrants further investigation, as does its transcriptional regulation in conditions where glucose responsiveness of the pancreatic islet is altered.
Bacterial glucuronidase as general marker for oncolytic virotherapy or other biological therapies (2011)

GusA therefore has the potential to be used as a general marker in the preclinical and clinical evaluation of (novel) biological therapies as well as being useful for the detection of rare cells such as circulating tumor cells.
Nanocapillarity in fullerene tubules (1992)

Fullerene tubules are shown to be highly polarizable ``molecular straws'' capable of ingesting dipolar molecules. Local-density-functional calculations on HF molecules within a finite-length tubule, of size 144 atoms, demonstrate this effect. The energy of incarceration is several times the thermal ambient at room temperature. These calculations, now feasible on desktop workstations, open the way to the study of nanoscale capillarity and to, perhaps, precise control over shielding of specific ``guest'' compounds from external electric and magnetic fields.
The human splicing code reveals new insights into the genetic determinants of disease (2014)

To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation-driven aberrant splicing. Intronic disease mutations that are more than 30 nucleotides from any splice site alter splicing nine times as often as common variants, and missense exonic disease mutations that have the least impact on protein function are five times as likely as others to alter splicing. We detected tens of thousands of disease-causing mutations, including those involved in cancers and spinal muscular atrophy. Examination of intronic and exonic variants found using whole-genome sequencing of individuals with autism revealed misspliced genes with neurodevelopmental phenotypes. Our approach provides evidence for causal variants and should enable new discoveries in precision medicine.
Comparative analysis of genes frequently regulated by drugs based on connectivity map transcriptome data (2017)

Gene expression is perturbated by drugs to different extent. Analyzing genes whose expression is frequently regulated by drugs would be useful for the screening of candidate therapeutic targets and genes implicated in side effect. Here, we obtained the differential expression number (DEN) for genes profiled in Affymetrix microarrays from the Connectivity Map project, and conducted systemic comparative computational analysis between high DEN genes and other genes. Results indicated that genes with higher down-/up-regulation number (down_h/up_h) tended to be clustered in genome, and have lower homologous gene number, higher SNP density and more disease-related SNP. Down_h and up_h were significantly enriched in cancer related pathways, while genes with lower down-/up-regulation number (down_l/up_l) were mainly involved in the development of nervous system diseases. Besides, up_h had lower interaction network degree, later developmental stage to express, higher tissue expression specificity than up_l, while down_h showed reversed tendency in comparison with down_l. Together, our analysis suggests that genes frequently regulated by drugs are more likely to be associated with disease-related functions, but the extensive activation of conserved and widely expressed genes by drugs is disfavored.
Role of the PAS1 gene of Pichia pastoris in peroxisome biogenesis. (1994)

Several groups have reported the cloning and sequencing of genes involved in the biogenesis of yeast peroxisomes. Yeast strains bearing mutations in these genes are unable to grow on carbon sources whose metabolism requires peroxisomes, and these strains lack morphologically normal peroxisomes. We report the cloning of Pichia pastoris PAS1, the homologue (based on a high level of protein sequence similarity) of the Saccharomyces cerevisiae PAS1. We also describe the creation and characterization of P. pastoris pas1 strains. Electron microscopy on the P. pastoris pas1 cells revealed that they lack morphologically normal peroxisomes, and instead contain membrane-bound structures that appear to be small, mutant peroxisomes, or "peroxisome ghosts." These "ghosts" proliferated in response to induction on peroxisome-requiring carbon sources (oleic acid and methanol), and they were distributed to daughter cells. Biochemical analysis of cell lysates revealed that peroxisomal proteins are induced normally in pas1 cells. Peroxisome ghosts from pas1 cells were purified on sucrose gradients, and biochemical analysis showed that these ghosts, while lacking several peroxisomal proteins, did import varying amounts of several other peroxisomal proteins. The existence of detectable peroxisome ghosts in P. pastoris pas1 cells, and their ability to import some proteins, stands in contrast with the results reported by Erdmann et al. (1991) for the S. cerevisiae pas1 mutant, in which they were unable to detect peroxisome-like structures. We discuss the role of PAS1 in peroxisome biogenesis in light of the new information regarding peroxisome ghosts in pas1 cells.