gebhart/patrepeval huggingface dataset:
Epitope Mapping of Monoclonal Antibodies againstBordetella pertussisAdenylate Cyclase Toxin (1999)

Adenylate cyclase (AC) toxin from Bordetella pertussis is a 177-kDa repeats-in-toxin (RTX) family protein that consists of four principal domains; the catalytic domain, the hydrophobic domain, the glycine/aspartate-rich repeat domain, and the secretion signal domain. Epitope mapping of 12 monoclonal antibodies (MAbs) directed against AC toxin was conducted to identify regions important for the functional activities of this toxin. A previously developed panel of in-frame deletion mutants of AC toxin was used to localize MAb-specific epitopes on the toxin. The epitopes of these 12 MAbs were located throughout the toxin molecule, recognizing all major domains. Two MAbs recognized a single epitope on the distal portion of the catalytic domain, two reacted with the C-terminal 217 amino acids, one bound to the hydrophobic domain, and one bound to either the hydrophobic domain or the functionally unidentified region adjacent to it. The remaining six MAbs recognized the glycine/aspartate-rich repeat region. To localize these six MAbs, different peptides derived from the repeat region were constructed. Two of the six MAbs appeared to react with the repetitive motif and exhibited cross-reactivity with Escherichia coli hemolysin. The remaining four MAbs appeared to interact with unique epitopes within the repeat region. To evaluate the roles of these epitopes on toxin function, each MAb was screened for its effect on intoxication (cyclic AMP accumulation) and hemolytic activity. The two MAbs recognizing the distal portion of the catalytic domain blocked intoxication of Jurkat cells by AC toxin but had no effect on hemolysis. On the other hand, a MAb directed against a portion of the repeat region caused partial inhibition of AC toxin-induced hemolysis without affecting intoxication. In addition, the MAb recognizing either the hydrophobic domain or the unidentified region adjacent to it inhibited both intoxication and hemolytic activity of AC toxin. These findings extend our understanding of the regions necessary for the complex events required for the biological activities of AC toxin and provide a set of reagents for further study of this novel virulence factor.
Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study (2013)

This is the first study showing that type 1 diabetes is associated with compositional changes in gut microbiota. The significant differences in the number of Bifidobacterium, Lactobacillus and Clostridium and in the Firmicutes to Bacteroidetes ratio observed between the two groups could be related to the glycemic level in the group with diabetes. Moreover, the quantity of bacteria essential to maintain gut integrity was significantly lower in the children with diabetes than the healthy children. These findings could be useful for developing strategies to control the development of type 1 diabetes by modifying the gut microbiota.
Grb-IR: a SH2-domain-containing protein that binds to the insulin receptor and inhibits its function. (1995)

To identify potential signaling molecules involved in mediating insulin-induced biological responses, a yeast two-hybrid screen was performed with the cytoplasmic domain of the human insulin receptor (IR) as bait to trap high-affinity interacting proteins encoded by human liver or HeLa cDNA libraries. A SH2-domain-containing protein was identified that binds with high affinity in vitro to the autophosphorylated IR. The mRNA for this protein was found by Northern blot analyses to be highest in skeletal muscle and was also detected in fat by PCR. To study the role of this protein in insulin signaling, a full-length cDNA encoding this protein (called Grb-IR) was isolated and stably expressed in Chinese hamster ovary cells overexpressing the human IR. Insulin treatment of these cells resulted in the in situ formation of a complex of the IR and the 60-kDa Grb-IR. Although almost 75% of the Grb-IR protein was bound to the IR, it was only weakly tyrosine-phosphorylated. The formation of this complex appeared to inhibit the insulin-induced increase in tyrosine phosphorylation of two endogenous substrates, a 60-kDa GTPase-activating-protein-associated protein and, to a lesser extent, IR substrate 1. The subsequent association of this latter protein with phosphatidylinositol 3-kinase also appeared to be inhibited. These findings raise the possibility that Grb-IR is a SH2-domain-containing protein that directly complexes with the IR and serves to inhibit signaling or redirect the IR signaling pathway.
The Proposition Bank: An Annotated Corpus of Semantic Roles (2005)

The Proposition Bank project takes a practical approach to semantic representation, adding a layer of predicate-argument information, or semantic role labels, to the syntactic structures of the Penn Treebank. The resulting resource can be thought of as shallow, in that it does not represent coreference, quantification, and many other higher-order phenomena, but also broad, in that it covers every instance of every verb in the corpus and allows representative statistics to be calculated. We discuss the criteria used to define the sets of semantic roles used in the annotation process and to analyze the frequency of syntactic/semantic alternations in the corpus. We describe an automatic system for semantic role tagging trained on the corpus and discuss the effect on its performance of various types of information, including a comparison of full syntactic parsing with a flat representation and the contribution of the empty “trace” categories of the treebank.
A class AB monolithic mixer for 900-MHz applications (1997)

A class AB downconversion mixer for 900-MHz applications is presented. The circuit is implemented in a 25-GHz f/sub T/ bipolar process and consumes 10.2 mA total current from a 3-V supply. The design has a power gain of 7.5 dB and operates with supply voltages from 2.7 to 5 V. A single-sideband noise figure of 7.5 dB is achieved by design simplicity, use of bond-wire degeneration in the common-emitter driver stage, and optimization of the device sizes and bias currents. An input 1-dB compression point of -1.5 dBm is achieved by exploiting the class AB behavior of the common-emitter driver stage.
Assembly of Designed Oligonucleotides as an Efficient Method for Gene Recombination: A New Tool in Directed Evolution (2003)

A new and practical method for gene recombination with formation of libraries of mutant genes is presented. The method is based on the assembly of appropriately prepared oligonucleotides whose design is guided by sequence information. High recombination frequency with formation of full-length products is achieved by controlled overlapping of the designed oligomers. This process (ADO) minimizes self-hybridization of parental genes, which constitutes a significant advantage over conventional family shuffling as used in the directed evolution of functional enzymes. ADO was applied to the recombination of two lipase family genes from Bacillus subtilis (LipA and LipB). In a library of 3000 lipase variants created by this method, several were found that display increased enantioselectivity in a model reaction involving the hydrolysis of a meso-diacetate.
Processing and utilization of by‐products from soy oil processing (1981)

Abstract Crude soybean oil contains a number of materials which must be removed to produce a neutral, bland‐flavored and light‐colored refined oil. While at times these materials may have been considered waste constituting a disposal problem, they are, in fact, valuable byproducts when efficiently recovered and processed. Methods of recovery and processing lecithin, soapstock and deodorizer distillate at the refinery level are reviewed. Process and analytical control are discussed. Some of the important end uses are listed.
The Onco-Embryonic Antigen ROR1 Is Expressed by a Variety of Human Cancers (2012)

ROR1 is an orphan-receptor tyrosine-kinase-like surface antigen that is expressed by many tissues during embryogenesis, some B-cell malignancies, and various cancer cell lines but not by virtually all normal adult tissues. Here, we report that large proportions of many different human cancers also express ROR1, particularly those cancers that have high-grade histology. Primary cancers that expressed ROR1 more commonly expressed high levels of phosphorylated AKT (p-AKT) and phosphorylated cAMP response element binding-factor (p-CREB) than similar cancers that lacked expression of ROR1. Induced expression of ROR1 could enhance basal p-AKT and p-CREB levels and could promote the growth of a cancer cell line, MEC1. Conversely, silencing ROR1 resulted in lower levels of p-AKT and p-CREB, which was associated with impaired tumor cell growth. In summary, this study found that many different human cancers express ROR1 and that ROR1 may play a functional role in promoting tumor cell growth, suggesting that this orphan-receptor tyrosine-kinase-like protein may be a potential target for therapy directed against a variety of human cancers.
FBG Sensing Glove for Monitoring Hand Posture (2011)

A wearable sensing glove for monitoring hand gestures and posture has been developed. The glove sensing capability is based on optical fiber Bragg gratings (FBGs) sensors. These sensors, due to their inherent self-referencing and multiplexing capability, are a value-added choice for this application. A single optical fiber would cross all the hand with Bragg structures in specific spots, as the finger joints. The functionality and performance of the glove was fully evaluated. The sensor response was linear to the hand movements for opening and closing down. Through the sensor response, it was possible to retrieve information about the joint angles from which other set of information like finger force can be estimated. The developed glove was able to provide numerical data about the angles of the hand posture in real time. The simplicity of the system and performance makes it well suitable for physical therapy applications, study of the human kinematics during sport activity, virtual reality or even remote control applications, among others.
The One Hour Yeast Proteome (2013)

We describe the comprehensive analysis of the yeast proteome in just over one hour of optimized analysis. We achieve this expedited proteome characterization with improved sample preparation, chromatographic separations, and by using a new Orbitrap hybrid mass spectrometer equipped with a mass filter, a collision cell, a high-field Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT, Orbitrap Fusion). This system offers high MS(2) acquisition speed of 20 Hz and detects up to 19 peptide sequences within a single second of operation. Over a 1.3 h chromatographic method, the Q-OT-qIT hybrid collected an average of 13,447 MS(1) and 80,460 MS(2) scans (per run) to produce 43,400 (x) peptide spectral matches and 34,255 (x) peptides with unique amino acid sequences (1% false discovery rate (FDR)). On average, each one hour analysis achieved detection of 3,977 proteins (1% FDR). We conclude that further improvements in mass spectrometer scan rate could render comprehensive analysis of the human proteome within a few hours.
A 52 $\mu$W Wake-Up Receiver With $-$72 dBm Sensitivity Using an Uncertain-IF Architecture (2009)

A dedicated wake-up receiver may be used in wireless sensor nodes to control duty cycle and reduce network latency. However, its power dissipation must be extremely low to minimize the power consumption of the overall link. This paper describes the design of a 2 GHz receiver using a novel ldquouncertain-IFrdquo architecture, which combines MEMS-based high-Q filtering and a free-running CMOS ring oscillator as the RF LO. The receiver prototype, implemented in 90 nm CMOS technology, achieves a sensitivity of -72 dBm at 100 kbps (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> bit error rate) while consuming just 52 muW from the 0.5 V supply.
In vivo induction of cytotoxic T cell response by a free synthetic peptide requires CD4+ T cell help (1991)

Most attempts to induce CTL responses by in vivo priming with free synthetic peptides have been unsuccessful so far. However, two separate studies have recently succeeded in inducing antiviral CTL responses by immunizing mice with unmodified free synthetic peptides derived from nucleoproteins from either lymphocytic choriomeningitis virus or Sendai virus. In the present study, we have analyzed the cellular mechanisms by which the lymphocytic choriomeningitis virus synthetic peptide induced CTL responses. We demonstrated that this peptide, which was previously shown to be recognized by CD8+ T cells, also contains a helper CD4+ T cell epitope. It stimulates in vivo both CD4+ T cell-mediated CTL response. The in vivo elimination of CD4+ T cells by treatment with a mAb was shown to strongly reduce the antipeptide CTL response. This study therefore demonstrates that to be able to induce CTL responses, a peptide has to stimulate both CD4+ and CD8+ T cell subset.
A small molecule inhibitor of β-catenin/cyclic AMP response element-binding protein transcription (2004)

Inherited and somatic mutations in the adenomatous polyposis coli occur in most colon cancers, leading to activation of beta-catenin-responsive genes. To identify small molecule antagonists of this pathway, we challenged transformed colorectal cells with a secondary structure-templated chemical library, looking for compounds that inhibit a beta-catenin-responsive reporter. We identified ICG-001, a small molecule that down-regulates beta-catenin/T cell factor signaling by specifically binding to cyclic AMP response element-binding protein. ICG-001 selectively induces apoptosis in transformed cells but not in normal colon cells, reduces in vitro growth of colon carcinoma cells, and is efficacious in the Min mouse and nude mouse xenograft models of colon cancer.
Electronic markets and electronic hierarchies (1987)

By reducing the costs of coordination, information technology will lead to an overall shift toward proportionately more use of markets—rather than hierarchies—to coordinate economic activity.
Extracellular Signal-Regulated Kinase 5 in the Cerebrospinal Fluid-Contacting Nucleus Contributes to Neuropathic Pain in Rats. (2015)

These findings suggest activation of ERK5 in CSF-CN might contribute to the onset and development of neuropathic pain and its role might be partly accomplished by p-CREB.
Dried Blood Spots as a Sample Collection Technique for the Determination of Pharmacokinetics in Clinical Studies: Considerations for the Validation of a Quantitative Bioanalytical Method (2009)

A novel approach has been developed for the quantitative determination of circulating drug concentrations in clinical studies using dried blood spots (DBS) on paper, rather than conventional plasma samples. A quantitative bioanalytical HPLC-MS/MS assay requiring small blood volumes (15 microL) has been validated using acetaminophen as a tool compound (range 25 to 5000 ng/mL human blood). The assay employed simple solvent extraction of a punch taken from the DBS sample, followed by reversed phase HPLC separation, combined with selected reaction monitoring mass spectrometric detection. In addition to performing routine experiments to establish the validity of the assay to internationally accepted criteria (precision, accuracy, linearity, sensitivity, selectivity), a number of experiments were performed to specifically demonstrate the quality of the quantitative data generated using this novel sample format, namely, stability of the analyte and metabolites in whole human blood and in DBS samples; effect of the volume of blood spotted, the device used to spot the blood, or the temperature of blood spotted. The validated DBS approach was successfully applied to a clinical study (single oral dose of 500 mg or 1 g acetaminophen).
Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries (1997)

One of the problems encountered in handling computer representations of combinatorial libraries (especially “virtual libraries”) is the extremely large number of compounds which may be covered by even quite simple libraries. This paper discusses work on the generation of structure fingerprints for the compounds in a library, which avoids the need to enumerate the compounds themselves by utilizing techniques originally developed for handling Markush structures in chemical patents.
Increased Amygdala and Insula Activation During Emotion Processing in Anxiety-Prone Subjects (2007)

Increased amygdala and insula reactivity to certain types of emotional processing is seen in young adults with increased anxiety-related temperamental traits. Therefore, this brain emotion-processing profile may be a functional endophenotype for proneness to (certain kinds of) anxiety disorders.
Scoring the Severity of Atopic Dermatitis: Three Item Severity Score as a Rough System for Daily Practice and as a Pre-screening Tool for Studies (1999)

Different scoring systems have been developed to determine the severity of atopic dermatitis. The SCORAD (SCORing Atopic Dermatitis), one of the best validated systems, is suited for clinical trials, but is too complicated and time consuming for routine clinical use. The TIS score (Three Item Severity score), a simplified system, is based on the evaluation of erythema, oedema/papulation and excoriation on a scale from 0 to 3. In order to determine the value of the TIS score we conducted a prospective study in 126 children with mild to severe atopic dermatitis. Both the TIS score and the SCORAD were assessed by trained investigators. Interobserver agreement was investigated in 20 children by comparing the independently performed scores of three investigators. A positive correlation was found between the TIS score and the SCORAD (Rank Spearman r(s)=0.86; p<0.0005). The item which correlated best with the SCORAD was excoriation (r(s)=0.72; p<0.0005) followed by oedema/papulations (r(s)=0.66; p<0.0005). Interobserver agreement which was calculated by Cohen's kappa (kappa) was "excellent" for SCORAD (kappa=0.82; p<0.001) and "fair" for TIS score (kappa=0.58; p<0.01). We conclude that the TIS score is a rough, though reliable and simple system for scoring atopic dermatitis. It is particularly suitable in general practice, for routine clinical use and for screening purposes in clinical trials. For research purposes, the objective SCORAD offers a more detailed and comprehensive assessment.
24‐hour 51Cr post‐transfusion survival, 51Cr life span and haemolysis of red blood cells stored at 4 °C for 56 days in AS‐3 (2001)

Whether collected manually or by apheresis, the outcomes were similar for RBC stored at 4 degrees C for 56 days in CP2D/AS-3.
Myocyte Death, Growth, and Regeneration in Cardiac Hypertrophy and Failure (2003)

The accepted paradigm considers the adult mammalian heart as a postmitotic organ, which possesses a relatively constant number of myocytes from shortly after birth to adulthood and senescence. This notion is questioned by the demonstration that although most adult myocytes are terminally differentiated, there is a small and continuously renewed subpopulation of cycling myocytes produced by the differentiation of cardiac stem-like cells. Myocyte death and myocyte regeneration are introduced as major determinants of cardiac homeostasis and alterations of ventricular anatomy and function in physiological and pathological states. The possibility of reconstituting dead myocardium by stem-like cells is advanced and proposed as a major area of future research.
Oscillatory Breathing Patterns During Wakefulness in Patients With Chronic Heart Failure (1999)

An oscillatory breathing pattern during the daytime is a marker of impaired autonomic regulation and poor outcome. Augmented activity of peripheral chemoreceptors may be involved in the genesis of this respiratory pattern. Modulation of peripheral chemosensitivity can reduce or abolish abnormal respiratory patterns and may be an option in the management of CHF patients with oscillatory breathing.
Signal space diversity: a power- and bandwidth-efficient diversity technique for the Rayleigh fading channel (1998)

The increasing need for high data-rate transmissions over time- or frequency-selective fading channels has drawn attention to modulation schemes with high spectral efficiency such as QAM. With the aim of increasing the "diversity order" of the signal set we consider multidimensional rotated QAM constellations. Very high diversity orders can be achieved and this results in an almost Gaussian performance over the fading channel, This multidimensional modulation scheme is essentially uncoded and enables one to trade diversity for system complexity, at no power or bandwidth expense.
A transmitting and receiving method for CDMA communications over indoor electrical power lines (2002)

Transmitting and receiving methods for CDMA communications through 2-wire or 3-wire power line cord over indoor power lines are proposed. The key idea for transmitting method is to use a fundamental model of a coupling transformer-less transmitting circuit including the influence of the distribution transformer and to find out the combinations of model parameters giving the acceptable distortion of the transmitted waveforms for CDMA communications. The receiving method is to use a filtering method that separates arbitrary waveforms of transmitted data signal from the superposition waveforms of the sinusoidal high power signal and transmitted data signal without distorting arbitrary waveforms of transmitting signal at all. These methods are experimentally confirmed to be effective.