gebhart/patrepeval huggingface dataset:
Molybdate and regulation of mod (molybdate transport), fdhF, and hyc (formate hydrogenlyase) operons in Escherichia coli (1995)

Escherichia coli mutants with defined mutations in specific mod genes that affect molybdate transport were isolated and analyzed for the effects of particular mutations on the regulation of the mod operon as well as the fdhF and hyc operons which code for the components of the formate hydrogenlyase (FHL) complex. phi (hyc'-'lacZ+) mod double mutants produced beta-galactosidase activity only when they were cultured in medium supplemented with molybdate. This requirement was specific for molybdate and was independent of the moa, mob, and moe gene products needed for molybdopterin guanine dinucleotide (MGD) synthesis, as well as Mog protein. The concentration of molybdate required for FHL production by mod mutants was dependent on medium composition. In low-sulfur medium, the amount of molybdate needed by mod mutants for the production of half-maximal FHL activity was increased approximately 20 times by the addition of 40 mM of sulfate, mod mutants growing in low-sulfur medium transported molybdate through the sulfate transport system, as seen by the requirement of the cysA gene product for this transport. In wild-type E. coli, the mod operon is expressed at very low levels, and a mod+ merodiploid E. coli carrying a modA-lacZ fusion produced less than 20 units of beta-galactosidase activity. This level was increased by over 175 times by a mutation in the modA, modB, or modC gene. The addition of molybdate to the growth medium of a mod mutant lowered phi (modA'-'lacZ+) expression. Repression of the mod operon was sensitive to molybdate but was insensitive to mutations in the MGD synthetic pathway. These physiological and genetic experiments show that molybdate can be transported by one of the following three anion transport system in E. coli: the native system, the sulfate transport system (cysTWA gene products), and an undefined transporter. Upon entering the cytoplasm, molybdate branches out to mod regulation, fdhF and hyc activation, and metabolic conversion, leading to MGD synthesis and active molybdoenzyme synthesis.
OR Practice—Application of a Probabilistic Decision Model to Airline Seat Inventory Control (1989)

The application of booking limits on the number of seats available at different prices on the same flight allows airlines to increase revenues. Effective seat inventory control by an airline depends on forecasts of future bookings, the revenue values associated with each fare type, and an ability to make systematic tradeoffs between booking requests so as to maximize total flight revenues. This article describes the implementation of a computerized system for making these tradeoffs and setting booking limits on future flights at Western Airlines in early 1987. The Expected Marginal Seat Revenue (EMSR) decision model developed for this application takes account of the uncertainty associated with estimates of future demand as well as the nested structure of booking limits in airline reservations systems. The Automated Booking Limit System implemented at Western made use of the EMSR model to set and revise booking limits periodically prior to flight departure. Although the system did not take into account several important components of the seat inventory control problem, a revenue impact test on a sample of actual flights showed a significant revenue improvement over the judgmental methods used previously.
AN EXPLANATION OF INTERNATIONAL FRANCHISORS' PREFERENCE FOR MULTI-UNIT FRANCHISING (2006)

Most international franchisors seem to follow multi-unit franchising. But it is often treated as an anomaly from an agency theory perspective. We argue that multi-unit franchising can be explained by agency theory, if we consider the full range of agency problems. These include: shirking, adverse selection, information flow, inefficient risk bearing, free-riding, and quasi-rent appropriation. Although past agency theoretic examinations have mostly focused on single-unit franchising, our analysis shows that in the international context, multi-unit franchising may be more appropriate considering the significant geographic and cultural distance between franchisors and franchisees.
Backbone Dynamics of the 269‐residue Protease Savinase Determined from 15N‐NMR Relaxation Measurements (1996)

Backbone dynamics of Savinase, a subtilisin of 269 residues secreted by Bacillus lentus, have been studied using 15N relaxation measurements derived from proton-detected dimensional 1H-15N-NMR spectroscopy. 15N spin-lattice rate constants (R1), spin-spin relaxation-rate constants(R2), and 1H-15N nuclear Overhauser effects (NOE) were determined for 84% of the backbone amide 15N nuclei. The model-free formalism [Lipari, G. & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559] was used to derive values for a generalized order parameter, S2, interpretable as a measure of the amplitude of motion on the picosecond-nanosecond timescale, for each N-H bond vector. Additional terms used to fit the data include an effective correlation time for internal motions (taue) and an exchange term (Rex) to account for exchange contributions to R2. The overall rotational correlation time (taum) is 9.59 +/- 0.02 ns; the average order parameter (S2) is 0.90 +/- 0.07, indicative of a rigid structure consistent with Savinase's high degree of secondary structure and compact tertiary fold. Residues S125-S128, located in the substrate-binding region, represent the longest stretch of protein which exhibits disorder on the picosecond-nanosecond timescale. These residues also exhibit significant exchange terms, possibly indicative of motion on the microsecond-millisecond timescale, which could also be influenced by the proximity of the phenyl ring of the substituted aryl boronic acid inhibitor used in this study. S103 and G219 in the substrate-binding region, represent the longest stretch of protein which exhibits disorder on the picosecond-nanosecond timescale. These residues also exhibit significant exchange terms, possibly indicative of motion on the microsecond-millisecond timescale, which could also be influenced by the proximity of the phenyl ring of the substituted aryl boronic acid inhibitor used in this study. S103 and G219 in the substrate-binding region also show flexibility on the picosecond-nanosecond timescale. There is also significant motion in the turn, G258-T260, of a small solvent-exposed loop region which may make the protein vulnerable autolysis at that point. Some residues in both calcium-binding sites and nearby also show mobility.
Antidepressants and Hypothalamic-Pituitary-Adrenocortical Regulation (1996)

PAST studies of antidepressants have focused almost exclusively on their effects on the metabolism and receptors of monoamine neurotransmitters in various brain regions. These studies have been extended to the molecular effects of antidepressants and have led to a profoundly expanded understanding of their actions in the central nervous system. For example, long-term administration of antidepressants decreases the expression of tyrosine hydroxylase, down-regulates cAMP-dependent protein kinase, modulates the mRNA expression of central β-adrenoceptors and serotonin (5-HT) receptors, and alters the functional activity of specific G protein subunits and adenylyl cyclase (1). Taken together, these and many other recent observations clearly indicate that antidepressants interfere not only with the production and release of catecholamines and indolamines but also with the signal transduction of those neurotransmitters that have long been implicated in the pathogenesis and treatment of depression. More recently, additional target genes of antidepressant treatment have been identified, the most intriguing being those related to hypothalamic-pituitary-adrenocortical (HPA) activity. Altered regulation of this neuroendocrine system has been the subject of investigative efforts in depression research since Gibbons (2) reported more than 30 yr ago that plasma cortisol concentrations are elevated in depression and are normalized after clinical remission. Numerous clinical observations are consistent with the possibility that there is a causal link between HPA dysregulation and psychopathology (3). Recently, a large number of preclinical studies have provided evidence pointing in the same direction.
Characterization of Guanylate Kinase-Associated Protein, a Postsynaptic Density Protein at Excitatory Synapses That Interacts Directly with Postsynaptic Density-95/Synapse-Associated Protein 90 (1997)

The structure of central synapses is poorly understood at the molecular level. A recent advance came with the identification of the postsynaptic density-95 (PSD-95)/synapse-associated protein 90 family of proteins as important mediators of the synaptic clustering of certain classes of ion channels. By yeast two-hybrid screening, a novel protein termed guanylate kinase-associated protein (GKAP) has been isolated that binds to the GK-like domain of PSD-95 (). Here we present a detailed characterization of GKAP expression in the rat brain and report the cloning of a novel GKAP splice variant. By Northern blot, GKAP mRNAs (4, 6.5, and 8 kB) are expressed predominantly in the rat brain. By in situ hybridization, GKAP is expressed widely in neurons of cortex and hippocampus and in the Purkinje and granule cells of the cerebellum. On brain immunoblots, two prominent bands of 95 and 130 kDa are detected that correspond to products of short and long N-terminal splice variants of GKAP. Two independent GKAP antibodies label somatodendritic puncta in neocortical and hippocampal neurons in a pattern consistent with synaptic elements. Immunogold electron microscopy reveals GKAP to be predominantly postsynaptic and present at asymmetric synapses and in dendritic spines. The distribution of GKAP immunogold particles is uniform in the lateral plane of the PSD but peaks in the perpendicular axis approximately 20 nm from the postsynaptic membrane. In cultured hippocampal neurons GKAP immunoreactive puncta colocalize with the AMPA receptor subunit Glu receptor 1 but not with the GABAA receptor subunits beta2 and beta3. Thus GKAP is a widely expressed neuronal protein localized specifically in the PSD of glutamatergic synapses, consistent with its direct interaction with PSD-95 family proteins.
Biallelic Germline Transcription at the κ Immunoglobulin Locus (2003)

Rearrangement of antigen receptor genes generates a vast array of antigen receptors on lymphocytes. The establishment of allelic exclusion in immunoglobulin genes requires differential treatment of the two sequence identical alleles. In the case of the kappa immunoglobulin locus, changes in chromatin structure, methylation, and replication timing of the two alleles are all potentially involved in regulating rearrangement. Additionally, germline transcription of the kappa locus which precedes rearrangement has been proposed to reflect an opening of the chromatin structure rendering it available for rearrangement. As the initial restriction of rearrangement to one allele is critical to the establishment of allelic exclusion, a key question is whether or not germline transcription at the kappa locus is monoallelic or biallelic. We have used a sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay and an RNA-fluorescence in situ hybridization (FISH) to show that germline transcription of the kappa locus is biallelic in wild-type immature B cells and in recombination activating gene (RAG)-/-, mu+ B cells. Therefore, germline transcription is unlikely to dictate which allele will be rearranged first and rather reflects a general opening on both alleles that must be accompanied by a mechanism allowing one of the two alleles to be rearranged first.
Lipopolysaccharide Increases the Incidence of Collagen‐Induced Arthritis in Mice Through Induction of Protease HTRA‐1 Expression (2013)

Our findings indicate that TLR-4 activation increases HTRA-1 expression through the NF-κB pathway in fibroblasts and macrophages. HTRA-1 expression is involved in the enhancing effects of LPS on CIA. This study offers new insights into the regulation of HTRA-1 expression via LPS/TLR-4 and the role of HTRA-1 in RA pathogenesis.
Complement-dependent damage to liposomes prepared from pure lipids and Forssman hapten (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComplement-dependent damage to liposomes prepared from pure lipids and Forssman haptenStephen C. Kinsky, James A. Haxby, David A. Zopf, Carl R. Alving, and Constance B. KinskyCite this: Biochemistry 1969, 8, 10, 4149–4158Publication Date (Print):October 1, 1969Publication History Published online1 May 2002Published inissue 1 October 1969https://pubs.acs.org/doi/10.1021/bi00838a036https://doi.org/10.1021/bi00838a036research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations151LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Slug Flow: Occurrence, Consequences, and Prediction (1994)

Abstract BP Exploration currently has an interest in hundreds of kilometres of operating multiphase flowlines. Most of the company's proposed field developments also involve multiphase flowlines. A large number of these do or will experience slug flow, either as the normal flow regime, or as a result of transient behaviour. Data on flow regime and slug flow characteristics have been collected from many lines over the past 8 years. Information on slug characteristics from a number of different systems is presented in this paper, including velocity, length and holdup. Some unfavourable consequences of slug flow on both process performance and system integrity are highlighted, including plant shutdowns and mechanical damage. The need to be able to predict slug flow for the design of future systems, and to advise the operators of existing systems, remains a high priority for R&amp;D activities, as ever longer and more complex multiphase systems are proposed. BP's latest slug frequency method is described, followed by guidelines for pipework layout, and comments on current R&amp;D on corrosion in multiphase flow.
An approach to the structure determination of nucleic acid analogues hybridized to RNA. NMR studies of a duplex between 2′-OMe RNA and an oligonucleotide containing a single amide backbone modification (1994)

The backbone modification amide-3, in which -CH2-NH-CO-CH2- replaces -C5'H2-O5'-PO2-O3'-, is studied in the duplex d(G1-C2-G3-T4.T5-G6-C7-G8)*mr(C9-G10-C11-A12-A13-C14-G15+ ++-C16) where . indicates the backbone modification and mr indicates the 2'-OMe RNA strand. The majority of the exchangeable and non-exchangeable resonances have been assigned. The assignment procedure differs from standard methods. The methyl substituent of the 2'-OMe position of the RNA strand can be used as a tool in the interpretation. The duplex structure is a right-handed double helix. The sugar conformations of the 2'-OMe RNA strand are predominantly N-type and the 2'-OMe is positioned at the surface of the minor groove. In the complementary strand, only the sugar of residue T4 is found exclusively in N-type conformation. The incorporation of the amide modification does not effect very strongly the duplex structure. All bases are involved in Watson-Crick base pairs.
Immunogenic Tumor Cell Death for Optimal Anticancer Therapy: The Calreticulin Exposure Pathway (2010)

In response to some chemotherapeutic agents such as anthracyclines and oxaliplatin, cancer cells undergo immunogenic apoptosis, meaning that their corpses are engulfed by dendritic cells and that tumor cell antigens are presented to tumor-specific CD8(+) T cells, which then control residual tumor cells. One of the peculiarities of immunogenic apoptosis is the early cell surface exposure of calreticulin (CRT), a protein that usually resides in the lumen of the endoplasmic reticulum (ER). When elicited by anthracyclines or oxaliplatin, the CRT exposure pathway is activated by pre-apoptotic ER stress and the phosphorylation of the eukaryotic translation initiation factor eIF2alpha by the kinase PERK, followed by caspase-8-mediated proteolysis of the ER-sessile protein BAP31, activation of the pro-apoptotic proteins Bax and Bak, anterograde transport of CRT from the ER to the Golgi apparatus and exocytosis of CRT-containing vesicles, finally resulting in CRT translocation onto the plasma membrane surface. Interruption of this complex pathway abolishes CRT exposure, annihilates the immunogenicity of apoptosis, and reduces the immune response elicited by anticancer chemotherapies. We speculate that human cancers that are incapable of activating the CRT exposure pathway are refractory to the immune-mediated component of anticancer therapies.
Area routing oriented hierarchical corner stitching with partial bin (2000)

Article Free Access Share on Area routing oriented hierarchical corner stitching with partial bin Authors: Zhang Yan Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. China Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. ChinaView Profile , Wang Baohua Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. China Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. ChinaView Profile , Cai Yici Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. China Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. ChinaView Profile , Hong Xianlong Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. China Department of Computer Science and Technology, Tsinghua University, Beijing 100084, P.R. ChinaView Profile Authors Info & Claims ASP-DAC '00: Proceedings of the 2000 Asia and South Pacific Design Automation ConferenceJanuary 2000Pages 105–110https://doi.org/10.1145/368434.368587Published:28 January 2000Publication History 0citation220DownloadsMetricsTotal Citations0Total Downloads220Last 12 Months45Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Analysis of chromosome 6 markers in eight Utah schizophrenia pedigrees (1998)

Eight multiplex Utah schizophrenia pedigrees were screened for linkage by applying a non-parametric linkage program, GENEHUNTER, using 30 chromosome 6 DNA markers. The overall maximum NPL score of the combined pedigrees was 1.50 (P = 0.079) at marker D6s281, located near the q terminus. The highest overall maximum NPL score for an individual pedigree was 2.81 (P = 0.043). In the chromosome 6p region, where numerous positive findings have been reported, we obtained no positive results.
The Parietal Reach Region Codes the Next Planned Movement in a Sequential Reach Task (2001)

Distinct subregions of the posterior parietal cortex contribute to planning different movements. The parietal reach region (PRR) is active during the delay period of a memory-guided reach task but generally not active during a memory-guided saccade task. We explored whether the reach planning activity in PRR is related to remembering targets for reaches or if it is related to specifying the reach that the monkey is about to perform. Monkeys were required to remember two target locations and then reach to them in sequence. Before the movements were executed, PRR neurons predominantly represented the reach about to be performed and only rarely represented the remembered target for the second reach. This indicates the area plays a role in specifying the target for the impending reach and may not contribute to storing the memory of subsequent reach targets.
Identification of the cydC locus required for expression of the functional form of the cytochrome d terminal oxidase complex in Escherichia coli (1987)

The aerobic respiratory chain of Escherichia coli contains two terminal oxidases which are differentially regulated. The cytochrome o complex predominates under growth conditions of high aeration, whereas the cytochrome d complex predominates when the oxygen tension is low. Either terminal oxidase will support aerobic growth. The goal of the work presented in this paper was to identify genes required for the expression of the functional form of the cytochrome d complex, other than the genes encoding the polypeptide components of the oxidase complex (cyd locus). A strain lacking the cytochrome o complex (cyo mutant strain) was mutagenized by using a lambda-Mu hybrid hopper bacteriophage, lambda placMu53, which inserts randomly into the chromosome and carries a kanamycin resistance marker. Strains were isolated and examined which were unable to grow aerobically, i.e., which lacked functional cytochrome d complex, and which could not be complemented by introduction of the cyd gene on F-prime episomes. One strain was selected for characterization. The phage insert was mapped to min 18.9 on the genetic linkage map, defining a new genetic locus, cydC. Evidence described in the text suggests that the gene product is probably required for the synthesis of the unique heme d component of the cytochrome d complex.
Unlocking Clinical Data from Narrative Reports: A Study of Natural Language Processing (1995)

Physicians disagreed on the interpretation of narrative reports, but this was not caused by outlier physicians or a consistent difference in the way internists and radiologists read reports. The natural language processor was not distinguishable from the physicians and was superior to all other comparison subjects. Although the domain of this study was restricted (six clinical conditions in chest radiographs), natural language processing seems to have the potential to extract clinical information from narrative reports in a manner that will support automated decision-support and clinical research.