gebhart/patrepeval huggingface dataset:
Isolation and Chronobiological Analysis of a Neuropeptide Pigment-Dispersing Factor Gene in Drosophila melanogaster (1998)

In this article, the authors isolate a gene encoding a neuropeptide in Drosophila melanogaster. The substance is called pigment-dispersing factor (PDF), based on one of the roles it plays in crustaceans (the arthropods in which this factor was initially discovered). The PDF-encoding Drosophila gene (pdf) is intronless and present in a single copy per haploid genome. The cytological location of pdf is 97B on the third chromosome. The putative 102-amino-acid precursor (prepro-PDF) consists of a signal peptide and a PDF-associated peptide, followed by the mature PDF. The PDF-associated peptide region of the precursor is highly diverged from those of the crustacean precursors, whereas the primary structure of the mature PDF is conserved in other members of the pigment-dispersing hormone family. A single pdf transcript (ca. 0.8 kb) is expressed predominantly in the head; the expression levels of pdf mRNA are consistently higher in males than in females. Putative pdf homologous transcripts are present in other Drosophila species, which exhibit similar sexual dimorphic expression patterns. Cyclic expression of pdf over the course of the day and night was assessed, but the mRNA exhibited at best very gentle cycling. The pdf expression in two behaviorally arrhythmic mutants were examined; the expression was intact in a period0 mutant but absent in the disconnected mutant.
Enzyme System for Improving the Detection Limit in Pyrosequencing (2006)

Highly sensitive real-time pyrosequencing seems promising for constructing an inexpensive and small DNA sequencer with a low running cost. A DNA sample of a picomole level is usually used in the conventional pyrosequencing based on a luciferase assay coupled with an APS-ATP surfurylase reaction for producing ATP from pyrophosphate (PPi). Although the luminescence intensity could be increased by increasing the amount of luciferase, it was impossible to reduce the target DNA amount because of a large background luminescence due to the luciferase-APS reaction. In this report, a novel approach using a new conversion reaction of PPi to ATP is proposed. This method has a very low background and can produce high signals in the presence of a large amount of luciferase; thus, the sample amount required for sequencing is significantly reduced. The ATP production from PPi is catalyzed with pyruvate orthophosphate dikinase (PPDK) using AMP and phosphoenolpyruvate as the substrates, which are inactive for the luciferase-catalyzed reaction. All of the components in the AMP-PPDK-based pyrosequencing system are suitable for highly sensitive DNA sequencing in one tube. Real-time DNA sequencing with a readable length up to 70 bases was successfully demonstrated by using this system. By increasing the amount of luciferase, as low as 2.5 fmol of DNA templates was accurately sequenced by the proposed method with a novel simple and inexpensive DNA sequencer having a photodiode array as a sensor instead of a PMT or CCD camera. A sample amount as low as 2 orders of magnitude smaller than that used in the conventional pyrosequencer can be used.
Model Predictive Control Tuning Methods: A Review (2010)

This paper provides a review of the available tuning guidelines for model predictive control, from theoretical and practical perspectives. It covers both popular dynamic matrix control and generalized predictive control implementations, along with the more general state-space representation of model predictive control and other more specialized types, such as max-plus-linear model predictive control. Additionally, a section on state estimation and Kalman filtering is included along with auto (self) tuning. Tuning methods covered range from equations derived from simulation/approximation of the process dynamics to bounds on the region of acceptable tuning parameter values.
Integrin Structure (2000)

The integrins are a family of α,β heterodimeric receptors that mediate dynamic linkages between extracellular adhesion molecules and the intracellular actin cytoskeleton. Integrins are expressed by all multicellular animals, but their diversity varies widely among species; for example, in mammals, 19 α and 8β subunit genes encode polypeptides that combine to form 25 different receptors, whereas the Drosophila and Caenorhabditis genomes encode only five and two integrin a subunits respectively. Thousands of studies over the last two decades have investigated the molecular, cellular and organismal basis of integrin function. Gene deletion has demonstrated essential roles for almost all integrins, with the defects suggesting widespread contributions to both the maintenance of tissue integrity and the promotion of cellular migration. Integrin-ligand interactions are now considered to provide physical support for cells in order to maintain cohesion, to permit the generation of traction forces to enable movement, and to organize signalling complexes to modulate differentiation and cell fate. Animal-model studies have also shown that integrins contribute to the progression of many common diseases, and have implicated them as potential therapeutic targets. The use of anti-integrin monoclonal antibodies and ligand-mimetic peptides has validated this suggestion for inflammatory, neoplastic, traumatic and infectious conditions. Thus, to understand more about the mechanisms underlying tissue organization and cellular trafficking, and to identify approaches for regulating these processes in disease, there is intense interest in determining the molecular basis of integrin function. It is important to state at the outset that the tertiary structure of the integrin dimer is unknown. Our current understanding of the molecular basis of integrin function is therefore compiled from the results of a large number of studies that have employed a wide range of complementary technologies.
GFDM Transceiver using Precoded Data and Low-complexity Multiplication in Time Domain (2015)

Future wireless communication systems are demanding a more flexible physical layer. GFDM is a block filtered multicarrier modulation scheme proposed to add multiple degrees of freedom and cover other waveforms in a single framework. In this paper, GFDM modulation and demodulation will be presented as a frequency-domain circular convolution, allowing for a reduction of the implementation complexity when MF, ZF and MMSE filters are employed in the inner and outer receiver operation. Also, precoding is introduced to further increase GFDM flexibility, addressing a wider set of applications.
Nonionic Detergents Induce Dimerization among Members of the Bcl-2 Family (1997)

Members of the Bcl-2 family (including Bcl-2, Bcl-XL, and Bax) play key roles in the regulation of apoptosis. These proteins are believed to be membrane-associated and have been proposed to regulate apoptosis through both homodimerization and heterodimerization. We have found that whereas Bcl-2 is predominantly membrane-associated as previously reported, significant amounts of Bcl-XL and most of the Bax proteins are not membrane-associated and thus appear in the cytosolic fraction of thymocyte and splenocyte extracts. This finding allows the study of the dimerization properties and conformation of these proteins in the absence of detergent perturbation. For this analysis, we have produced monoclonal antibodies that are specific for known epitopes of Bax, Bcl-2, and Bcl-XL. An antibody to an N-terminal epitope (alpha uBax 6A7) between amino acids 12 and 24 fails to bind the soluble cytosolic form of Bax, indicating that this epitope is normally buried. Nonionic detergents alter the Bax conformation to expose this epitope. In the presence of nonionic detergent, the 6A7 antibody avidly binds the monomeric form of Bax, but not Bax complexed with either Bcl-XL or Bcl-2. In contrast, a monoclonal antibody to an adjacent epitope of Bax (alpha mBax 5B7) within amino acids 3-16 binds the soluble and detergent-altered forms of Bax and also binds the Bax.Bcl-XL or the Bax.Bcl-2 complex. Surprisingly, in the absence of detergent Bax fails to form homodimers or heterodimers with Bcl-XL. These results demonstrate a novel conformational state of members of the Bcl-2 family under a physiological condition that is distinct from the detergent-altered state that forms dimers and is currently believed to regulate apoptosis.
Fatalities From Blood Transfusion (1980)

From April 3, 1976, to Dec 31, 1979, one hundred thirteen fatalities were reported to the Food and Drug Administration as a sequela of the transfusion of blood or blood products. Thirty-three fatalities were due to posttransfusion hepatitis, and three involved plasmapheresis or leukopheresis donors. The remaining 77 cases were of three categories: 47 cases (61%) were due to "clerical errors" such as drawing the wrong blood specimen of giving the wrong unit of blood to the patient; eight cases consisted of genuine errors that occurred in the laboratory; and 22 cases were due to miscellaneous problems, most of which were unpreventable.
Coordination of tilt and touch in one- and two-handed use (2014)

Our goal is to enhance navigation in mobile interfaces with quick command gestures that do not make use of explicit mode-switching actions. TilTouch gestures extend the vocabulary of navigation interfaces by combining motion tilt with directional touch. We consider sixteen directional TilTouch gestures that rely on tilt and touch movements along the four main compass directions. An experiment explores their effectiveness for both one-handed and two-handed use. Results identify the best combinations of TilTouch gestures in terms of performance, motor coordination, and user preferences.
Histone Deacetylase Inhibitor Romidepsin Has Differential Activity in Core Binding Factor Acute Myeloid Leukemia (2008)

Romidepsin has differential antileukemic and molecular activity in CBF AML. Development of this agent in CBF AML should focus on combinations that target related mechanisms of gene silencing such as DNA methylation.
Functional correlation between cell adhesive properties and some cell surface proteins. (1977)

The adhesive properties of Chinese hamster V79 cells were analyzed and characterized by various cell dissociation treatments. The comparisons of aggregability among cells dissociated with EDTA, trypsin + Ca2+, and trypsin + EDTA, revealed that these cells have two adhesion mechanisms, a Ca2+-independent and a Ca2+-dependent one. The former did not depend on temperature, whereas the latter occurred only at physiological temperatures. Both mechanisms were trypsin sensitive, but the Ca2+-dependent one was protected by Ca2+ against trypsinization. In morphological studies, the Ca2+-independent adhesion appeared to be a simple agglutination or flocculation of cells, whereas the Ca2+-dependent adhesion seemed to be more physiological, being accompanied by cell deformation resulting in the increase of contact area between adjacent cells. Lactoperoxidase-catalyzed iodination of cell surface proteins revealed that several proteins are more intensely labeled in cells with Ca2+-independent adhesiveness than in cells without that property. It was also found that a cell surface protein with a molecular weight of approximately 150,000 is present only in cells with Ca2+-dependent adhesiveness. The iodination and trypsinization of this protein were protected by Ca2+, suggesting its reactivity to Ca2+. Possible mechanisms for each adhesion property are discussed, taking into account the correlation of these proteins with cell adhesiveness.
Saponin and sapogenol. XXXVI. Chemical constituents of astragali radix, the root of Astragalus membranaceus Bunge. (3). Astragalosides III,V, and VI. (1983)

Based on chemical and physicochemical investigations including carbon-13 nuclear magnetic resonance (13C-NMR) examinations and methylation analyses, the structures of three astragalosides, which were isolated from Astragali Radix, the root of Korean Astragalus membranaceus BUNGE (Leguminosae), were elucidated : astragaloside III is 3-O-[β-D-glucopyranosyl (1→2)-β-D-xylopyranosyl] cycloastragenol (3), astragaloside V is 3-O-[β-D-glucopyranosyl (1→2)-β-D-xylopyranosyl]-25-O-β-D-glucopyranosyl-cycloastragenol (5) and astragaloside VI is 3-O-[β-D-glucopyranosyl (1→2)-β-D-xylopyranosyl]-6-O-β-D-glucopyranosyl-cycloastragenol (6).
[Effect of poloxamer 407 on the middle ear and inner ear after regional perfusion in guinea pigs]. (2007)

Poloxamer 407 can be biodagraded in vivo or discharged via eustachian tube, and causes no inflammation on the middle ear cavity. There are temporary changes on auditory function of inner ear after topical perfusion with poloxamer 407 in round window can cause, but no irreversible damage on function and morphology of cochlear and vestibular organs.
Efficient and accurate spline-based time delay estimation (2005)

We have previously presented a highly accurate, spline-based time delay estimator (TDE) that directly determines sub-sample time delay estimates from sampled data. The algorithm uses cubic splines to produce a continuous time representation of a reference signal and then computes an analytical matching function between this reference and a delayed signal. The location of the minima of this function yields estimates of the time delay. In this paper we present a more computationally efficient formulation of this algorithm, which is based on FIR filtering to determine the cubic spline coefficients, polynomial approximation to determine the time delay estimates, and adaptive search of the delay estimate. The proposed algorithm is particularly useful in applications such as blood flow estimation and tissue elasticity estimation since it can include companding with little additional computational cost.
Synthesis of Linear and Star-Shaped Block Copolymers of Isobutylene and Methacrylates by Combination of Living Cationic and Anionic Polymerizations (1998)

A new synthetic route for the preparation of polyisobutylene (PIB)-based linear and star-shaped block copolymers was developed by combining living carbocationic and anionic polymerizations. Living PIB chains were quantitatively endcapped with 1,1-diphenylethylene, leading to 1,1-diphenyl-1-methoxy (DPOMe) or 2,2-diphenylvinyl (DPV) termini, or both. Both the DPOMe- and DPV-terminated PIBs, and the mixtures of both endgroups were quantitatively metalated with K/Na alloy, Cs metal, or Li dispersion in THF at room temperature. The resulting stable macrocarbanion obtained by metalation with K/Na alloy was used to initiate living anionic polymerization of tert-butyl methacrylate (tBMA) yielding PIB-b-PtBMA block copolymers with nearly quantitative blocking efficiency. Hydrolysis of the ester groups by HCl in dioxane resulted in amphiphilic polyisobutylene-block-poly(methacrylic acid) block copolymers. Replacing K+ with Li+ by excess LiCl gave a PIB macroinitiator suitable for anionic polymerization of methyl methacrylate (MMA). A series of linear PMMA-b-PIB-b-PMMA block copolymers and of star-shaped PIB-b-(PMMA)3 block copolymers were successfully synthesized by telechelic PIB macroanions with high blocking efficiencies. Characterizations of these new thermoplastic elastomers were carried out by SEC, DSC, dynamic−mechanical, and stress−strain measurements.
Corn trypsin inhibitor decreases tissue-type plasminogen activator-mediated fibrinolysis of human plasma (2009)

Corn trypsin inhibitor (CTI) has been considered the molecule of choice to inhibit activated factor XII (FXIIa) during the conduct of experimentation focusing on tissue factor-initiated coagulation. However, CTI-mediated attenuation of fibrinolysis following celite activation of coagulation was observed in pilot studies with the clot lifespan model. The goal of the present study was thus to characterize the mechanism(s) responsible for CTI-mediated hypofibrinolysis. Normal plasma was exposed to 0 or 49.6 microg/ml CTI, with coagulation initiated with celite or tissue factor. Fibrinolysis was initiated with tissue-type plasminogen activator (tPA). Additional experiments utilized plasminogen activator inhibitor 1 deficient or alpha2-antiplasmin-deficient plasma. Coagulation/fibrinolysis kinetics were monitored with the thrombelastography-based clot lifespan model. In addition to delaying the initiation of coagulation, CTI prolonged clot growth time, delayed the onset of lysis, and prolonged clot lysis time in normal plasma after celite activation. Conversely, CTI increased the speed of clot growth, clot strength, and prolonged clot lysis time after tissue factor activation. Experiments with plasma deficient in antifibrinolytic proteins supported a primary inhibition of tPA by CTI. In addition to anti-FXIIa effects following celite activation, CTI likely exerts an anti-tPA effect, which contributed to hypofibrinolysis in this model.
Welcome and Opening Remarks Work/Life Conflict in the Legal Profession (2006)

At a symposium sponsored by the Women’s Rights Law Reporter, Professor Tanya Hernandez introduces the keynote speaker, Professor Joan Williams, a law professor at the American Law School, Washington College of Law in Washington,D.C. where she teaches Property, Women's Legal History, Feminist Jurist Prudence, and a Jurist Prudence seminar. The topic of the symposium is Work/Life Conflict in the Legal Profession.
Cisandtrans-actingelements involved in the activation ofArabidopsis thalianaAl gene encoding the translation elongation factor EF-lα (1991)

In A. thaliana the translation elongation factor EF-1 alpha is encoded by a small multigenic family of four members (A1-A4). The A1 gene promoter has been dissected and examined in a transient expression system using the GUS reporter gene. Deletion analysis has shown that several elements are involved in the activation process. One cis-acting domain, the TEF 1 box, has been accurately mapped 100 bp upstream of the transcription initiation site. This domain is the target for trans-acting factors identified in nuclear extracts prepared from A. thaliana. Homologies are found between the TEF 1 box and sequences present at the same location within the A2, A3 and A4 promoters. This observation, together with those obtained from gel retardation assays performed using DNA fragments from the A4 promoter, suggest that the activation process mediated by the TEF 1 element is conserved among the A. thaliana EF-1 alpha genes. Analysis of nearly full length cDNA clones has shown that in addition to a single intron located within the coding region, the A1 gene contains a second intron located within the 5' non coding region. Such an intron is also present within the A2, A3 and A4 genes. This 5' intervening sequence appears to be essential to obtain a maximum GUS activity driven by the A1 gene promoter.
Origin and Reduction of 1=f Magnetic Flux Noise in Superconducting Devices (2016)

Magnetic flux noise is a dominant source of dephasing and energy relaxation in superconducting qubits. The noise power spectral density varies with frequency as 1/fα, with α1, and spans 13 orders of magnitude. Recent work indicates that the noise is from unpaired magnetic defects on the surfaces of the superconducting devices. Here, we demonstrate that adsorbed molecular O2 is the dominant contributor to magnetism in superconducting thin films. We show that this magnetism can be reduced by appropriate surface treatment or improvement in the sample vacuum environment. We observe a suppression of static spin susceptibility by more than an order of magnitude and a suppression of 1/f magnetic flux noise power spectral density of up to a factor of 5. These advances open the door to the realization of superconducting qubits with improved quantum coherence.
Bacteriorhodopsin: a biological material for information processing (1991)

Technology which makes use of biological materials has advanced dramatically in the last few decades. Production of specific biochemicals by selected microbial strains, the use of enzymes for stereospecific biosynthesis of materials and gene technological production of biologically important macromolecules are a few examples of these developments.
Microbial ecosystems therapeutics: a new paradigm in medicine? (2012)

Increasing evidence indicates that the complex microbial ecosystem of the human intestine plays a critical role in protecting the host against disease. This review discusses gut dysbiosis (here defined as a state of imbalance in the gut microbial ecosystem, including overgrowth of some organisms and loss of others) as the foundation for several diseases, and the applicability of refined microbial ecosystem replacement therapies as a future treatment modality. Consistent with the concept of a 'core' microbiome encompassing key functions required for normal intestinal homeostasis, 'Microbial Ecosystem Therapeutics' (MET) would entail replacing a dysfunctional, damaged ecosystem with a fully developed and healthy ecosystem of 'native' intestinal bacteria. Its application in treating Clostridium difficile infection is discussed and possible applications to other diseases such as ulcerative colitis, obesity, necrotising enterocolitis, and regressive-type autism are reviewed. Unlike conventional probiotic therapies that are generally limited to a single strain or at most a few strains of bacteria 'Microbial Ecosystem Therapeutics' would utilise whole bacterial communities derived directly from the human gastrointestinal tract. By taking into account the intrinsic needs of the entire microbial ecosystem, MET would emphasise the rational design of healthy, resilient and robust microbial communities that could be used to maintain or restore human health. More than simply a new probiotic treatment, this emerging paradigm in medicine may lead to novel strategies in treating and managing a wide variety of human diseases.
ApoB-containing lipoproteins promote infectivity of chlamydial species in human hepatoma cell line (2010)

A productive infection caused by C. trachomatis and C. pneumoniae may take place in human-derived hepatocytes revealing hepatic cells as possible target in chlamydial infection. Obtained results may suggest the participation of lipoprotein receptors in the mechanism of attachment and/or entry of chlamydial particles into target cells.
Development of the Proteasome Inhibitor Velcade™ (Bortezomib) (2004)

The dipeptide boronic acid analogue VELCADE (Bortezomib; formerly known as PS-341, LDP-341 and MLM341) is a potent and selective inhibitor of the proteasome, a multicatalytic enzyme that mediates many cellular regulatory signals by degrading regulatory proteins or their inhibitors. The proteasome is, thus, a potential target for pharmacological agents. Bortezomib, the first proteasome inhibitor to reach clinical trials, has shown in vitro and in vivo activity against a variety of malignancies, including myeloma, chronic lymphocytic leukemia, prostate cancer, pancreatic cancer, and colon cancer. The drug is rapidly cleared from the vascular compartment, but a novel pharmacodynamic assay has shown that bortezomib--mediated proteasome blockade is dose-dependent and reversible. Based on phase I studies demonstrating that bortezomib has manageable toxicities in patients with advanced cancers, phase II trials have been initiated for both solid and hematological malignancies.