gebhart/patrepeval huggingface dataset:
Adenylate Cyclases of Trypanosoma brucei Inhibit the Innate Immune Response of the Host (2012)

The parasite Trypanosoma brucei possesses a large family of transmembrane receptor-like adenylate cyclases. Activation of these enzymes requires the dimerization of the catalytic domain and typically occurs under stress. Using a dominant-negative strategy, we found that reducing adenylate cyclase activity by about 50% allowed trypanosome growth but reduced the parasite's ability to control the early innate immune defense of the host. Specifically, activation of trypanosome adenylate cyclase resulting from parasite phagocytosis by liver myeloid cells inhibited the synthesis of the trypanosome-controlling cytokine tumor necrosis factor-α through activation of protein kinase A in these cells. Thus, adenylate cyclase activity of lyzed trypanosomes favors early host colonization by live parasites. The role of adenylate cyclases at the host-parasite interface could explain the expansion and polymorphism of this gene family.
Discovery of Two Novel Antiplatelet Clinical Candidates (BMS-986120 and BMS-986141) That Antagonize Protease-Activated Receptor 4 (2022)

Protease-activated receptor 4 (PAR4) is a G-protein coupled receptor that is expressed on human platelets and activated by the coagulation enzyme thrombin. PAR4 plays a key role in blood coagulation, and its importance in pathological thrombosis has been increasingly recognized in recent years. Herein, we describe the optimization of a series of imidazothiadiazole PAR4 antagonists to a first-in-class clinical candidate, BMS-986120 (<b>43</b>), and a backup clinical candidate, BMS-986141 (<b>49</b>). Both compounds demonstrated excellent antithrombotic efficacy and minimal bleeding time prolongation in monkey models relative to the clinically important antiplatelet agent clopidogrel and provide a potential opportunity to improve the standard of care in the treatment of arterial thrombosis.
Characterization of a novel phosphatidylinositol 3-phosphate-binding protein containing two FYVE fingers in tandem that is targeted to the Golgi (2001)

We have identified a novel protein of predicted molecular mass 40kDa that contains two FYVE domains in tandem and has therefore been named TAFF1 (TAndem FYVE Fingers-1). The protein is expressed predominantly in heart and binds to PtdIns3P specifically, even though the FYVE domains in TAFF1 lacks the first Arg of the consensus sequence R(K/R)HHCR, critical for the PtdIns3P binding of other FYVE domains identified so far. The first Arg is replaced by a Thr and Ser in the N-terminal and C-terminal FYVE domains of TAFF1 respectively. Mutational analysis indicates that both FYVE domains are required for high affinity binding to PtdIns3P. Cell localization studies using a green fluorescent protein fusion show that TAFF1 is localized to the Golgi, and that the Golgi targeting sequence is located within the N-terminal 187 residues and not in either FYVE domain. The sequence of TAFF1has been deposited with the GenBank®, EMBL, DDBJ and GSDB Nucleotide Sequence Databases under accession number AF311602.
Multi-Omics Approach: New Potential Key Mechanisms Implicated in Cardiorenal Syndromes (2019)

Cardiorenal syndromes (CRS) include a scenario of clinical interactions characterized by the heart and kidney dysfunction. The crosstalk between cardiac and renal systems is clearly evidenced but not completely understood. Multi-factorial mechanisms leading to CRS do not involve only hemodynamic parameters. In fact, in recent works on organ crosstalk endothelial injury, the alteration of normal immunologic balance, cell death, inflammatory cascades, cell adhesion molecules, cytokine and chemokine overexpression, neutrophil migration, leukocyte trafficking, caspase-mediated induction of apoptotic mechanisms and oxidative stress has been demonstrated to induce distant organ dysfunction. Furthermore, new alternative mechanisms using the multi-omics approach may be implicated in the pathogenesis of cardiorenal crosstalk. The study of "omics" modifications in the setting of cardiovascular and renal disease represents an emerging area of research. Over the last years, indeed, many studies have elucidated the exact mechanisms involved in gene expression and regulation, cellular communication and organ crosstalk. In this review, we analyze epigenetics, gene expression, small non-coding RNAs, extracellular vesicles, proteomics, and metabolomics in the setting of CRS.
[Home ventilatory support--retrospective view and perspectives]. (1990)

Mechanical home ventilation is a child of this centuries polio epidemics. The tank respirator, or iron lung, signaled the beginning of the new era. Improved techniques like positive pressure ventilation via tracheostoma followed soon. Hypoventilation syndromes of various origin are more and more encountered thanks to better detection methods. They benefit from a new, efficient and noninvasive technique, the positive pressure ventilation via nasal mask.
Hard x-ray nanoprobe of beamline P06 at PETRA III (2016)

The hard x-ray scanning microscope at beamline P06 of PETRA III at DESY in Hamburg serves a large user community, from physics, chemistry, and nanotechnology to the bio-medical, materials, environmental, and geosciences. It has been in user operation since 2012, and is mainly based on nanofocusing refractive x-ray lenses. Using refractive optics, nearly Gaussian-limited nanobeams in the range from 50 to 100 nm can be generated in the hard x-ray energy range from 8 to 30 keV. The degree of coherence can be traded off against the flux in the nanobeam by a two-stage focusing scheme. We give a brief overview on published results from this instrument and describe its most important components and parameters.
New High‐Permittivity AgNb1‐xTaxO3 Microwave Ceramics: Part II, Dielectric Characteristics (1999)

Ceramic samples with the AgNb 1− x Ta x O 3 (0.46 &lt; x &lt; 0.54) composition were synthesized and analyzed, with respect to their dielectric properties, in a microwave‐frequency range and at radio frequencies. The permittivity over the compositional range 0.46 lessthan equal to x lessthan equal to 0.52 was &gt;410, whereas the Q × f value, measured at 2 GHz, reaches values of 640–900 GHz. Dependence of the resonant frequency on temperature was not linear but did display a minimum at a particular temperature, which was dependent on the composition of the ceramic. Samples that were measured at radio frequencies displayed low dissipation factors ( tg δ= 7 ×10 −4 −18 × 10 −4 ), a low aging rate (0.2% per time decade), and good dielectric strength (8 V/μm at a thickness of 0.6 mm). Microstructural investigations revealed the presence of precipitates and transformation twins that should be eliminated during additional processing optimization.
Polyfluorinated Amino Acids for Sensitive 19F NMR-Based Screening and Kinetic Measurements (2007)

Two novel series of polyfluorinated amino acids (PFAs) were designed and synthesized according to a very short and scalable synthetic sequence. The advantages and limitations of these moieties for screening purposes are presented and discussed. The potential applications of these PFAs were tested with their incorporation into small arginine-containing peptides that represent suitable substrates for the enzyme trypsin. The enzymatic reactions were monitored by 19F NMR spectroscopy, using the 3-FABS (three fluorine atoms for biochemical screening) technique. The high sensitivity achieved with these PFAs permits a reduction in substrate concentration required for 3-FABS. This is relevant in the utilization of 3-FABS in fragment-based screening for identification of small scaffolds that bind weakly to the receptor of interest. The large dispersion of 19F isotropic chemical shifts allows the simultaneous measurement of the efficiency of the different substrates, thus identifying the best substrate for screening purposes. Furthermore, the knowledge of KM and Kcat for the different substrates allows the identification of the structural motifs responsible for the binding affinity to the receptor and those affecting the chemical steps in enzymatic catalysis. This enables the construction of suitable pharmacophores that can be used for designing nonpeptidic inhibitors with high affinity for the enzyme or molecules that mimic the transition state. The novel PFAs can also find useful application in the FAXS (fluorine chemical shift anisotropy and exchange for screening) experiment, a 19F-based competition binding assay for the detection of molecules that inhibit the interaction between two proteins.
Vascular niche for adult hippocampal neurogenesis (2000)

The thin lamina between the hippocampal hilus and granule cell layer, or subgranule zone (SGZ), is an area of active proliferation within the adult hippocampus known to generate new neurons throughout adult life. Although the neuronal fate of many dividing cells is well documented, little information is available about the phenotypes of cells in S-phase or how the dividing cells might interact with neighboring cells in the process of neurogenesis. Here, we make the unexpected observation that dividing cells are found in dense clusters associated with the vasculature and roughly 37% of all dividing cells are immunoreactive for endothelial markers. Most of the newborn endothelial cells disappear over several weeks, suggesting that neurogenesis is intimately associated with a process of active vascular recruitment and subsequent remodeling. The present data provide the first evidence that adult neurogenesis occurs within an angiogenic niche. This environment may provide a novel interface where mesenchyme-derived cells and circulating factors influence plasticity in the adult central nervous system.
A major role for intestinal epithelial nucleotide oligomerization domain 1 (NOD1) in eliciting host bactericidal immune responses to Campylobacter jejuni (2007)

Campylobacter jejuni is the foremost cause of bacterial-induced diarrhoeal disease worldwide. Although it is well established that C. jejuni infection of intestinal epithelia triggers host innate immune responses, the mechanism(s) involved remain poorly defined. Innate immunity can be initiated by families of structurally related pattern-recognition receptors (PRRs) that recognize specific microbial signature motifs. Here, we demonstrated maximal induction of epithelial innate responses during infection with live C. jejuni cells. In contrast when intestinal epithelial cells (IECs) were exposed to paraformaldehyde-fixed bacteria, host responses were minimal and a marked reduction in the number of intracellular bacteria was noted in parallel. These findings suggested a role for intracellular host-C. jejuni interactions in eliciting early innate immunity. We therefore investigated the potential involvement of a family of intracellular, cytoplasmic PRRs, the nucleotide-binding oligomerization domain (NOD) proteins in C. jejuni recognition. We identified NOD1, but not NOD2, as a major PRR for C. jejuni in IEC. We also found that targeting intestinal epithelial NOD1 with small interfering RNA resulted in an increase in number of intracellular C. jejuni, thus highlighting a critical role for NOD1-mediated antimicrobial defence mechanism(s) in combating this infection at the gastrointestinal mucosal surface.
Implementing and optimizing real-time Java (2004)

The Real-time Java Experts Group has defined the real-time specification for Java (RTSJ), which provides the following capabilities: (1) new memory management models that can be used in lieu of garbage collection, (2) access to raw physical memory. (3) a higher resolution time granularity suitable for real-time systems, and (4) stronger guarantees on thread semantics when compared to regular Java, i.e., the most eligible runnable thread is always run.
Immunoglobulin and dextran losses during peritoneal dialysis. (1974)

Losses of immunoglobulins were measured in ten patients undergoing peritoneal dialysis. Mean immunoglobulin losses per 80 liter dialysis were as follows: IgG 17.9 gm, IgA 3.8 gm, and IgM 0.78 gm. Bleeding during dialysis generally accounted for less than 10% of these losses. lgA/lgG and lgM/lgG ratios in dialysate and serum were similar suggesting that the peritoneal membrane is permeable to higher molecular weight molecules. This was confirmed by the demonstration of peritoneal permeability to dextrans of greater than 150,000 molecular weight. In the absence of compensatory increases in synthesis, losses of immunoglobulins of the magnitude described in patients on chronic peritoneal dialysis programs could result in hypoglobulinemia and altered host resistance.
Impact of nitrogen ion-implantation on deep submicron SALICIDE process (1997)

In this paper, key issues of salicide process are studied for a variety of additional nitrogen (N) implantation step. As devices are scaled down to deep sub-micron level, transformation of TiSi2 from the high resistivity metastable C49-phase to fmal C54-phase is retarded. Different techniques had been developed to enhance the silicidation process, including PAT (pre-amorphization implant) to enhance C54-phase TiSi2 nucleation, and ITM (Jmplant through metal) to iniroduce Ti/Si interface-mixing. It is of great interest to thrther improve the process such that the use of self-aligned TiSi2 process can be further extended down to deep sub-micron devices without switching to other materials. Impact of incorporating N implantation into the conventional self-aligned TiSi2 sub-micron CMOS devices is presented. Silicidation reaction is found to be enhanced by N implantation. As a result, lower sheet resistance is achieved on narrow polysilicon line. Low energy and dosage ion-implantation conditions are preferred in order to minimise the gate to source/drain leakage. p+ and n+ junction leakage will be further discussed in this article. This is the very first study on the effect of N ion-implantation on silicidation reaction. SEM and AFM were used to study the impact of N incorporation, cross-section TEM were perfonned to study the defects generated after N implantation. Keywords: N ion-implantation, RTA, TiSi2, sheet resistance, gate to source/drain leakage, junction leakage, salicide process, defects
Complex Proteolytic Processing Acts on Delta, a Transmembrane Ligand for Notch, duringDrosophilaDevelopment (1998)

Delta functions as a cell nonautonomous membrane-bound ligand that binds to Notch, a cell-autonomous receptor, during cell fate specification. Interaction between Delta and Notch leads to signal transduction and elicitation of cellular responses. During our investigations to further understand the biochemical mechanism by which Delta signaling is regulated, we have identified four Delta isoforms in Drosophila embryonic and larval extracts. We have demonstrated that at least one of the smaller isoforms, Delta S, results from proteolysis. Using antibodies to the Delta extracellular and intracellular domains in colocalization experiments, we have found that at least three Delta isoforms exist in vivo, providing the first evidence that multiple forms of Delta exist during development. Finally, we demonstrate that Delta is a transmembrane ligand that can be taken up by Notch-expressing Drosophila cultured cells. Cell culture experiments imply that full-length Delta is taken up by Notch-expressing cells. We present evidence that suggests this uptake occurs by a nonphagocytic mechanism.
Method of creating microscale prototypes using SLM based holographic lithography (2013)

A method of generating arbitrary structures using spatial light modulator (SLM) based holograms with multiphoton absorption is presented. Current methodologies for designing 3D prototyping, such as G-code, are not ideally suited for holographic lithography and therefore limit its functionality or requires additional complex processing. The process outlined here allows a microstructure to be fabricated based on designs from commercially available CAD software. CAD software enables the microstructures to be designed and then realized using dynamic holographic lithography methods enabling designers a simple, quick, and robust method of fabricating novel microstructures. Holographic patterning routines such as raster scans of one or multiple focal points, holograms encoded with two or three dimensional spatial information, or a combination of both techniques may be utilized with this methodology. The process described allows for the development of complex structures that would be difficult to otherwise program using traditional methods. No limitations are placed on the form or function of the designed components, enabling undercut and interlocking features to be fabricated. This methodology also enables the location and orientation of the structures to be controlled dynamically simplifying the process of creating multi-scaled structures or complex arrays of arbitrary structures. As a proof of concept demonstration, a simple cantilever beam was modeled and fabricated.
The Choline Requirement of Broiler Chicks During the Seventh Week of Life (1976)

Male crossbred chicks were used to quantify the choline requirement and choline-sparing value of methionine and betaine for broiler chicks during the seventh week of life. The sulfur amino acid (SAA) requirement of male and female chicks was also determined. In all assays a crystalline amino acid diet containing 14.9% protein equivalent and 3400 kcal. M.E./kg, was employed. Increasing increments (0.08%) of SAA (equal mixture of DL-methionine and L-cystine) were fed from 0.38 to 0.70% of the diet. Least squares analysis indicated SAA requirements for maximal weight gain of 0.61 and 0.62% of the diet for males and females, respectively. The choline requirement was determined by feeding six levels of choline in the presence of 0.62% SAA. Gain but not gain/feed responded linearly to choline addition. Least squares analysis of gain indicated a dietary choline requirement of 358 p.p.m. of 30.6 mg./day. The choline-replacement value of methionine and betaine was found to be minimal.
Active Control of the Acoustic Boundary Conditions of Combustion Test Rigs: Extension to Actuators With Non-Linear Response (2009)

In the design process, new burners are generally tested in combustion test rigs. With these experiments, as well as with CFD, finite element calculations, and low-order network models, the burner’s performance in the full-scale engine is sought to be predicted. Especially, information about the thermoacoustic behaviour and the emissions is very important. As the thermoacoustics strongly depend on the acoustic boundary conditions of the system, it is obvious that test rig conditions should match or be close to those of the full-scale engine. This is, however, generally not the case. Hence, if the combustion process in the test rig is stable at certain operating conditions, it may show unfavourable dynamics at the same conditions in the engine. In previous works, the authors introduced an active control scheme which is able to mimic almost arbitrary acoustic boundary conditions. Thus, the test rig properties can be tuned to correspond to those of the full-scale engine. The acoustic boundary conditions were manipulated using woofers. In the present study, an actuator with higher control authority is investigated, which could be used to apply the control scheme in industrial test rigs. The actuator modulates an air mass flow to generate an acoustic excitation. However, in contrast to the woofers, it exhibits a strong non-linear response regarding amplitude and frequency. Thus, the control scheme is further developed to account for these non-linear transfer characteristics. This modified control scheme is then applied to change the acoustic boundary conditions of an atmospheric swirl-stabilized combustion test rig. Excellent results were obtained in terms of changing the reflection coefficient to different levels. By manipulating its phase, different resonance frequencies could be imposed without any hardware changes. The non-linear control approach is not restricted to the actuator used in this study and might therefore be of use for other actuators as well.
MindNet (1998)

As a lexical knowledge base constructed automatically from the definitions and example sentences in two machine-readable dictionaries (MRDs), MindNet embodies several features that distinguish it from prior work with MRDs. It is, however, more than this static resource alone. MindNet represents a general methodology for acquiring, structuring, accessing, and exploiting semantic information from natural language text. This paper provides an overview of the distinguishing characteristics of MindNet, the steps involved in its creation, and its extension beyond dictionary text.
Fully integrated dual-band power amplifiers with on-chip baluns in 65nm CMOS for an 802.11n MIMO WLAN SoC (2009)

Fully integrated dual-band power amplifiers with on-chip baluns for 802.11 n MIMO WLAN applications are presented. With a 3.3 v supply, the PAs produce a saturated output power of 28.3 dBm and 26.7 dBm with peak drain efficiency of 35.3% and 25.3% for the 2.4 GHz and 5 GHz bands, respectively. By utilizing multiple fully self-contained linearization algorithms, an EVM of -25 dB is achieved at 22.4 dBm for the 2.4 GHz band and 20.5dBm for the 5 GHz band while transmitting 54 Mbs OFDM. The chip is fabricated in standard 65 nm CMOS and the PAs occupy 0.31 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (2.4 G) and 0.27 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (5G) area.
RETRACTED: Amitriptyline-Based Biodegradable PEG-PLGA Self-Assembled Nanoparticles Accelerate Cutaneous Wound Healing in Diabetic Rats (2022)

The aim of this work was to study the healing activity of amitriptyline (Amitrip) in rat diabetic wounds. A nanoformula of the drug was prepared as Amitrip-based biodegradable PEG-PLGA self-assembled nanoparticles (Amitrip-NPs) with a mean particle size of 67.4 nm. An in vivo investigation was conducted to evaluate the wound-healing process of Amitrip-NPs in streptozotocin-induced diabetic rats. Wound contraction was accelerated in rats treated with Amitrip-NPs. Histological examinations confirmed these findings, with expedited remodeling and collagen deposition in the NPs-treated animals. The formula showed anti-inflammatory activities as demonstrated by inhibition of interleukin-6 (IL-6) expression and tumor necrosis factor-α (TNF-α) expression, as well as enhanced expression of interleukin-10 (IL-10). In addition, Amitrip-NPs protected against malondialdehyde (MDA) buildup and superoxide dismutase (SOD) and glutathione peroxidase (GPx) enzymatic exhaustion. The pro-collagen activity of Amitrip-NPs was confirmed by the observed enhancement of hydroxyproline wounded skin content, upregulation of Col 1A1 mRNA expression and immune expression of collagen type IV expression. Further, Amitrip-NPs significantly increased expression transforming growth factor-β1 (TGF-β1), vascular endothelial growth factor-A (VEGF-A), platelet-derived growth factor-B (PDGF-B) and cluster of differentiation 31 (CD31). In conclusion, the developed Amitrip-NPs expedited wound healing in diabetic rats. This involves anti-inflammatory, antioxidant, pro-collagen and angiogenic activities of the prepared NPs. This opens the gate for evaluating the usefulness of other structurally related tricyclic antidepressants in diabetic wounds.