gebhart/patrepeval huggingface dataset:
Core cysteine residues in the PAN domain are critical for HGF/c-MET signaling (2021)

Abstract The Plasminogen-Apple-Nematode (PAN) domain, with a core of four to six cysteine residues, is found in &gt; 28,000 proteins across 959 genera but its role in protein function is not fully understood. The PAN domain was initially characterized to be present in numerous proteins including hepatocyte growth factor (HGF). Dysregulation of HGF-mediated signaling results in numerous deadly cancers. All biological impacts of HGF in cell proliferation are triggered by binding of HGF to its cell surface receptor, cellular mesenchymal-epidermal transition (c-MET). Here, we show that four PAN domain cysteine residues are essential for HGF/c-MET signaling. Mutating these residues resulted in retardation of perinuclear localization, cellular internalization of HGF and its receptor, c-MET, and c-MET ubiquitination. Our observations indicate that the PAN domain of HGF is required for the c-MET binding and subsequent c-MET autophosphorylation and phosphorylation of its downstream targets, protein kinase B (AKT), extracellular signal-regulated kinase (ERK), and signal transducer and activator of transcription 3 (STAT3). Furthermore, transcriptional activation of HGF/c-MET signaling-related genes including matrix metalloproteinase-9 (MMP9), ETS translocation variant 1, 4, and 5 (ETV1, ETV4, ETV5), and early growth response 1 (EGR1) was impaired and cell proliferation was attenuated. These results suggest that core cysteine residues in the PAN domain are critical for HGF/c-MET interaction, c-MET mediated signal transduction, and cell survival. Thus, targeting the PAN domain of HGF may represent a mechanism for selectively regulating the binding and activation of the c-MET pathway. Significance HGF/c-MET signaling induces multifunctional cellular responses. Dysregulation of HGF/c-MET signaling cascade can lead to tumorigenesis by transforming normal cells to tumor cells. This work defines the importance of core cysteine residues in the PAN domain of HGF in downstream activation of HGF/c-MET signaling. To understand the role of cysteines in the PAN domain, PAN mutants of HGF were used to stimulate c-MET signaling in cells and the impact was delineated by determining phosphorylation and transcription of downstream targets. Mutations in core cysteines in the HGF-PAN domain completely blocked downstream phosphorylation and perinuclear accumulation of c-MET. These results suggest an indispensable role for the cysteine-rich PAN domain in HGF/c-MET interaction and could set the stage for future therapies that selectively disrupt the MET signaling cascade with limited off-target effects in tumors overexpressing HGF/c-MET.
A compact 31-input programmable majority gate based on capacitive threshold logic (2002)

An improved, modular realization of the capacitive threshold logic (CTL) gates is presented which offers significant advantages in terms of silicon area and speed in certain applications. The general architecture and building blocks of the new modular CTL gates is introduced and the operation of the circuit is discussed. The main advantages of the CTL design concept include a very large fan-in capability, compact design, small logic depth and compatibility with conventional CMOS gates. These advantages are illustrated by the design of a 31-input majority gate. The CTL realization of the majority gate is almost three times faster than a full custom standard CMOS realization and occupies approximately one third of the area which results in a performance increase of nearly an order of magnitude.
Cardiac troponin I predicts clinical outcome of patients with cancer at emergency department (2020)

Abstract Background Cardiac troponin I has been shown its prognostic ability in general population or cardiovascular disease but not yet in cancer patients. This study aimed to investigate the prognostic implication of cardiac troponin in cancer patients visiting emergency department. Methods In this retrospective cohort study, cancer patients visiting emergency department were enrolled. Patients with previously known coronary artery disease or clinically indicated coronary angiography were not included. The maximal value of Siemens ADVIA Centaur troponin I Ultra assay (TnI) within 24 hour were assessed. Primary endpoint was 180-day all-cause death that included cardiovascular and non-cardiovascular death. Results A total of 9,135 patients (mean age 63 year, male gender 60%) were enrolled. The lowest (0.006 ng/ml), assay-specific &lt;99 percentile (0.007-0.039 ng/ml), below median of ≥99 percentile (0.040-0.129 ng/ml), and above median of ≥99 percentile (≥0.130 ng/ml) TnI were found in 4,487 (49.1%), 3,158 (34.6%), 852 (9.3%), and 638 (7.0%) patients. There was 3,192 (34.9%) all-cause death including 137 (1.5%) cardiovascular and 3,047 (33.4%) non-cardiovascular death in the 180-day follow-up period. The risks of all-cause, cardiovascular, and non-cardiovascular death increased across higher TnI strata (hazard ratio (HR)=1.3 to 2.9; 2.1 to 9.3; 1.3 to 1.8; p&lt;0.001, all). These findings were consistent in clinical subgroups including solid and hematologic cancer. Conclusions Cancer patients visiting emergency department with elevated troponin I were at increased risk of 180-day death. Cancer patients with elevated TnI may need additional evaluation or careful follow-up even without diagnosis of cardiovascular disease.
Poor Adherence to Placebo or Amiodarone Therapy Predicts Mortality (1999)

Poor adherence is associated with a greater risk of mortality. The relationship between adherence and social activities suggests a higher motivation to adhere to treatment in individuals more engaged in enjoyable activities.
Joint <scp>time‐frequency</scp> analysis of visible laser reflections in a sheep heart (2021)

Limited methods exist to confirm the position of cardiovascular devices in the superior vena cava or right atrium of the heart. The aim of this study was to design, test and validate the feasibility of whether an optical fiber-based instrument could accurately distinguish when a cardiovascular catheter was located in the superior vena cava vs in the right atrium. An optical fiber was placed in a cardiovascular catheter which was inserted into a living sheep and guided to the vicinity of the heart where diode laser-based reflection intensity data were simultaneously gathered from two visible wavelengths of light reflected from the venous and atrial tissue surfaces near the cavoatrial junction. The time series data were postoperatively analyzed using methods of joint time-frequency analysis and validated against catheter positions determined with fluoroscopy and ECG. The system was successful in distinguishing the location of the superior vena cava from the right atrium.
Clinical Staging in Bipolar Disorder (2014)

This study showed progressive functional changes from stage I to stage IV of bipolar disorder, with a greater impairment in patients in later stages of the illness. FAST scores seem to have a good discriminant ability to distinguish between patients in early versus late stages of bipolar disorder and could therefore contribute to the development of a bipolar disorder staging system.
The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle (2016)

Microorganisms are the foundation of the marine carbon cycle. Photosynthetic cyanobacteria and eukaryotic phytoplankton in the surface ocean use solar energy to convert carbon dioxide into energy-rich organic compounds (“carbon fixation”) that are then released when the organisms are grazed or lysed. This in turn fuels a dynamic community of heterotrophic bacteria in both the surface and deep oceans. Over a year, oceanic phytoplankton species fix as much carbon as do land plants.
Crystal structure of methyl-2-phthalimido-3- methylbut-2-enoate, C<sub>14</sub>H<sub>13</sub>N<sub>1</sub>O<sub>4</sub> (1992)

Article Crystal structure of methyl-2-phthalimido-3- methylbut-2-enoate, C14H13N1O4 was published on July 1, 1992 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 198, issue 1-4).
Mass Die-Off of Caspian Seals Caused by Canine Distemper Virus (2000)

Thousands of Caspian seals (Phoca caspica) died in the Caspian Sea from April to August 2000. Lesions characteristic of morbillivirus infection were found in tissue specimens from dead seals. Canine distemper virus infection was identified by serologic examination, reverse transcriptase- polymerase chain reaction, and sequencing of selected P gene fragments. These results implicate canine distemper virus infection as the primary cause of death.
Langmuir–Blodgett Films of Polyacrylic Acid Modified with Perfluoroalkyl Groups (1991)

Abstract Long chain perfluoroalkyl groups were introduced to polyacrylic acid, and Langmuir–Blodgett films of the polymers were successfully prepared. The preparation of the polymer LB films containing metal ions was achieved by spreading the polymer solution on the aqueous solution of metal salt. Characterization of the films was attempted.
ChemInform Abstract: The High‐Pressure Cadmium Borate Cd<sub>6</sub>B<sub>22</sub>O<sub>39</sub>·H<sub>2</sub>O. (2015)

Abstract Colorless crystals of the new title compound are synthesized from a 1:2 molar mixture of CdO and partially hydrolyzed B 2 O 3 using a Walker‐type multianvil apparatus (Pt capsule, 4.7 GPa, 1000 °C, 10 min).
Avaliação da situação de risco devido à erosão hídrica em trecho do córrego Afonso XIII em Tupã / SP – Causas e solução / Risk situation assessment due to water erosion in a stream section of Afonso XIII in Tupã / SP - Causes and Solution (2020)

Em muitas cidades brasileiras vem ocorrendo graves problemas relacionados à erosão hídrica que se inicia dentro do perímetro urbano, através de perda de solos, degradação de áreas urbanas ou em urbanização. No estado de São Paulo, a maior parte das cidades que estão instaladas em terrenos constituídos por solos de textura arenosa e relativamente profundos, apresenta erosão em suas áreas urbanas e de expansão urbana. O presente trabalho pretende evidenciar os efeitos da erosão hídrica, a influência das características geomorfológicas, pedológicas e pluviométricas de um trecho do córrego Afonso XIII, que se inicia dentro do perímetro urbano, no município de Tupã, localizado na região oeste do estado de São Paulo. O trecho analisado recebe grande parte da carga pluviométrica da porção sul e oeste da cidade e apresentam erosão hídrica nas margens do córrego.
HSPC300 and its role in neuronal connectivity (2007)

Present data provide the first evidence for HSPC300 playing a role in nervous system development and demonstrate in vivo that this small protein works in the context of the WAVE/SCAR complex.
Locally-adaptive slip prediction for planetary rovers using Gaussian processes (2017)

This paper presents a method for predicting slip using Gaussian process regression. Slip models are learned for visually classified terrain types as a function of terrain geometry. Spatial correlations between terrain properties are leveraged for on-line slip model adaptation. Results show that regression-based modeling using in-situ rover data outperforms the state-of-practice, terrestrially-calibrated slip curves in both mean prediction and uncertainty bounds. Local adaptation improves slip prediction results, particularly in high-slip sand areas that pose the greatest threat to rovers. Slip estimates made using a visual classifier to identify terrain type are compared to estimates using on-line model selection with only proprioceptive slip measurements as inputs. The proprioceptive results nearly match the visual results, showing that this approach could work even when a visual classifier is not available.
Post-translational control of genetic circuits using<i>Potyvirus</i>proteases (2016)

Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
High Efficiency Silicon Solar Cells (1987)

The early chapters comprehensively review the optical and transport properties of silicon. Light trapping is described in detail. Limits on the efficiency of silicon cells are discussed as well as material requirements necessary to approach these limits. The status of current approaches to passifying surfaces, contacts and bulk regions is reviewed. The final section of the book describes the most practical approaches to the fabrication of high-efficiency cells capable of meeting the efficiency targets for both concentrated and non-concentrated sunlight, including a discussion of design and processing approaches for non-crystalline silicon.
RF Circuit Linearity Optimization Using a General Weak Nonlinearity Model (2012)

This paper focuses on optimizing the linearity in known RF circuits, by exploring the circuit design space that is usually available in today's deep submicron CMOS technologies. Instead of using brute force numerical optimizers we apply a generalized weak nonlinearity model that only involves AC transfer functions to derive simple equations for obtaining design insights.
HiBiT-SpyTag: A Minimal Tag for Covalent Protein Capture and Degrader Development (2023)

The ability to rapidly and selectively modulate cellular protein levels using small molecules is essential for studying complex biological systems. Degradation tags, such as dTAG, allow for selective protein removal with a specific degrader molecule, but their utility is limited by the large tag size (>12 kDa) and the low efficiency of fusion product gene knock-in. Here, we describe the development of a short 24 amino acid peptide tag that enables cell-based quantification and covalent functionalization of proteins to which it is fused. The minimalistic peptide, termed HiBiT-SpyTag, incorporates the HiBiT peptide for protein level quantification and SpyTag, which forms a spontaneous isopeptide bond in the presence of the SpyCatcher protein. Transient expression of dTAG-SpyCatcher efficiently labels HiBiT-SpyTag-modified BRD4 or IRE1α in cells, and subsequent treatment with the dTAG13 degrader results in efficient protein removal without the need for full dTAG knock-in. We also demonstrate the utility of HiBiT-SpyTag for validating the degradation of the endoplasmic reticulum (ER) stress sensor IRE1α, which led to the development of the first PROTAC degrader of the protein. Our modular HiBiT-SpyTag system represents a valuable tool for the efficient development of degraders and for studying other proximity-induced pharmacology.
The Decline of Glutamate‐Stimulated Norepinephrine Release in Aging Rat Brain (2019)

Unravelling and understanding the molecular and neurochemical changes of the aging brain is key to early intervention strategies. Glutamate (Glu) neurotransmission, the major excitatory neurotransmitter in the brain, is mechanistically involved in memory, learning performance, and other aspects of cognition. Moreover, as the brain ages, the glutamatergic signaling system mediated through brain N‐methyl‐D‐aspartate (NMDA) receptors becomes hypofunctional, and this decline may be associated with cognitive dysfunction in normal aging and in disease states. We have developed an in vitro assay that measures Glu‐stimulated release of neurotransmitters in rat brain slices. Using this assay, we compared changes in Glu‐stimulated release of [ 3 H]‐norepinephrine (NE) from the cerebral cortex and hippocampus in young (2–3 months old) versus old (21–23 months old) Fischer F344 rats. Our findings demonstrate that that there is a pronounced deficit (approximately 30–40%) of Glu‐stimulated [ 3 H]‐NE release in the aged rat brain in comparison to younger controls. In the same tissues, potassium (K + ) stimulated‐NE release is similar in brains from young and old rats, suggesting that the age‐related decline in in Glu‐stimulated NE release is related to a change in NMDA receptors. Notably, the deficit in Glu‐stimulated [ 3 H]‐NE release in both brain regions was completely rescued by the addition of 1 uM d‐amphetamine sulfate to the tissue slices. Overall, these findings reveal an important deficit in NE release in the aging brain, which may have important implications for cognitive dysfunction in aging. Moreover, this deficit can be reversed with amphetamine and possibly with similar drugs. These studies have clear clinical implications for the use of CNS stimulants as a therapeutic intervention for early cognitive impairment. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Interleukin-6 and Tumor Necrosis Factor-α Are Associated with Quality of Life–Related Symptoms in Pulmonary Arterial Hypertension (2015)

IL-6 and tumor necrosis factor-α levels are associated with certain quality of life domains in patients with pulmonary arterial hypertension. Clinical trial registered with www.clinicaltrials.gov (NCT00384865).
Reinforcement Learning Based Dynamic Resource Allocation for Massive MTC in Sliced Mobile Networks (2022)

With the rapid development of the Internet of Things (IoT) systems, the low latency requirement of massive Machine Type Communication (mMTC) in the IoT is an urgent problem to be solved for future mobile communication networks. In this paper, we use a reasonable resource allocation strategy and set priority parameters for each slice according to the average access delay of each slice. We propose a dynamic resource allocation strategy based on Markov Decision Process (MDP) modeling of mMTC random access process and using Actor-Critic (AC) algorithm in reinforcement learning. Simulations show that the proposed resource block resource allocation algorithm can reasonably allocate resources for each mMTC access slice to ensure the Quality-of-Service (QoS) requirements of mMTC applications.
Prognostic Significance of FRA Expression in Epithelial Cancers using AQUA <sup>®</sup> technology (2013)

These studies confirm the prognostic value of FRA in multiple indications. The opposing prognostic effects observed may suggest differential biology.
Engineering Model For Enterprise Command and Control in Federated Systems (2004)

Enterprises are increasingly complex; especially those found in National Defense. They are dynamic systems, geographically and operationally distributed, and faced with operating with increased agility in always conditions under greater regulatory scrutiny within highly volatile market conditions where continuous quality improvements are expected. This situation requires continuous improvements in the conduct of enterprise operations, with a corresponding increase in the efficacy of decision (command) and control applied to all facets of enterprise management. To address this challenge we introduce and engineering model supporting advances in both the concept and implementation of enterprise command and control (EC2) systems. We characterize the objectives of EC2 in terms of units of value production (VPU) that function at the intersection of enterprise supply and asset chains. Enterprise governance is consequently focused on the continuous optimization of performance of value production processes linked by these two value chains. VPUs range in size and function from low level tactical, to mid-level operational, to high level strategic activities, all of which must interact effectively in order to sustain enterprise viability. This paper provides a summary of our work in the application of our VPU model to the EC2 requirements of complex federated enterprise systems.
Effect of Annealing on the Rheological and Thermal Properties of Aliphatic Hyperbranched Polyester Based on 2,2-Bis(methylol)propionic Acid (2005)

We investigated the effects of annealing on the rearrangement of H-bonding structure and its influence on the thermal and rheological properties of a fourth-generation hyperbranched polyester polyol based on 2,2-bis(methylol)propionic acid (Boltorn H40). With increasing annealing time and decreasing temperature, the enthalpy of the endothermic transition in the DSC thermograms of Boltorn H40 increases, whereas the viscoelastic response shows a considerable elastic contribution. During annealing of amorphous Boltorn H40, its structure becomes more ordered as a consequence of formation of multiple intermolecular H-bonds (−OH...OC〈 and/or −OH...−OH) between long linear sequences in the hyperbranched structure. DSC, FTIR, and XRD results of the individual fractions of Boltorn H40 and an ideally structured dendrimer analogue show that the ordering of the structure is highest in the case of low molar mass hyperbranched species with an open structure and low degree of branching. Such species have the longest average length of linear sequences between branch points and therefore the highest possibility for multiple H-bond interactions.
ChemInform Abstract: Charge Separation in Metallomacrocycle Complexes Linked with Electron Acceptors by Axial Coordination (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
In vivo porcine liver radiofrequency ablation with simultaneous MR temperature imaging (2006)

The feasibility of performing RF ablation with a modified commercial RF generator simultaneously with MRI was demonstrated. Interference-free MR temperature maps were produced with both variable respiratory motion and mechanical ventilation, and showed the extent of heating as the ablation progressed.
Concise Synthesis, Preparative Resolution, Absolute Configuration Determination, and Applications of an Atropisomeric Biaryl Catalyst for Asymmetric Acylation (2003)

A new three-step synthesis and resolution of nucleophilic catalyst 1 suitable for large-scale preparation has been developed, and this catalyst has been shown to be effective for the kinetic resolution and asymmetric desymmetrization of a range of sec-alcohol substrates.