gebhart/patrepeval huggingface dataset:
On the expressiveness of rule-based systems for reasoning with uncertainty (1987)

We demonstrate that classes of dependencies among beliefs held with uncertainty cannot be represented in rule-based systems in a natural or efficient manner. We trace these limitations to a fundamental difference between certain and uncertain reasoning. In particular, we show that beliefs held with certainty are more modular than uncertain beliefs. We argue that the limitations of the rule-based approach for expressing dependencies are a consequence of forcing nonmodular knowledge into a representation scheme originally c!esigtrect to represent modular beliefs. Finally, we describe cl representation technique that is related.to the rule-based framework yet is not limited in the types of dependencies that it can represent. I
Biochemical and Structural Characteristics, Gene Regulation, Physiological, Pathological and Clinical Features of Lipocalin-Type Prostaglandin D2 Synthase as a Multifunctional Lipocalin (2021)

Lipocalin-type prostaglandin (PG) D<sub>2</sub> synthase (L-PGDS) catalyzes the isomerization of PGH<sub>2</sub>, a common precursor of the two series of PGs, to produce PGD<sub>2</sub>. PGD<sub>2</sub> stimulates three distinct types of G protein-coupled receptors: (1) D type of prostanoid (DP) receptors involved in the regulation of sleep, pain, food intake, and others; (2) chemoattractant receptor-homologous molecule expressed on T helper type 2 cells (CRTH2) receptors, in myelination of peripheral nervous system, adipocyte differentiation, inhibition of hair follicle neogenesis, and others; and (3) F type of prostanoid (FP) receptors, in dexamethasone-induced cardioprotection. L-PGDS is the same protein as β-trace, a major protein in human cerebrospinal fluid (CSF). L-PGDS exists in the central nervous system and male genital organs of various mammals, and human heart; and is secreted into the CSF, seminal plasma, and plasma, respectively. L-PGDS binds retinoic acids and retinal with high affinities (Kd < 100 nM) and diverse small lipophilic substances, such as thyroids, gangliosides, bilirubin and biliverdin, heme, NAD(P)H, and PGD<sub>2</sub>, acting as an extracellular carrier of these substances. L-PGDS also binds amyloid β peptides, prevents their fibril formation, and disaggregates amyloid β fibrils, acting as a major amyloid β chaperone in human CSF. Here, I summarize the recent progress of the research on PGD<sub>2</sub> and L-PGDS, in terms of its "molecular properties," "cell culture studies," "animal experiments," and "clinical studies," all of which should help to understand the pathophysiological role of L-PGDS and inspire the future research of this multifunctional lipocalin.
Real-time decoding of brain activity by embedded Spiking Neural Networks using OxRAM synapses (2016)

An innovative approach for decoding of brain signals based on Spiking Neural Networks is presented in this paper. Synapses are implemented by BEOL compatible oxide resistive RAM (OxRAM) devices providing low programming voltages (<;2.5V) and currents (~30μA). Spike-timing-dependent plasticity enables the network for autonomous online spike sorting of measured biological signals. Ultra-low synaptic power consumption in the range of 10nW, recognition rates around 90% and real-time functionality bear high potential for future healthcare applications.
The acceleration of OfSoftSwitch (2017)

The emerging trend of network devices with configurable data planes is pushing software switches as convenient playgrounds for experimenting novel programming paradigms and abstractions. OfSoftSwitch is a popular tool for carrying on such experimentation, as it provides a straightforward implementation of a pipeline of match-action tables. Unfortunately, OfSoftSwitch is not performance oriented and it is therefore limited only to functional experimentation of new abstractions. In this paper, we present our work to make OfSoftSwitch faster, while keeping it simple. The core of the work revolves around the use of the PFQ framework to expedite packet I/O operations as well as to enable multi-core parallel processing. In addition, other well-known techniques have also been applied to modify the original code of OfSoftSwitch. We demonstrate that our acceleration is effective by measuring a 96× performance speed-up, with more than 4 Mpps on a single core, when OfSoftSwitch performs OpenFlow forwarding. Likewise, we demonstrate that our approach is effective in keeping the simple programming model of OfSoftSwitch. In fact, we are able to effortlessly port OpenState, a stateful forwarding dataplane abstraction, to our accelerated OfSoftSwitch implementation.
Effects of potent VEGF blockade on experimental Wilms tumor and its persisting vasculature (2004)

We characterized the effect of potent vascular endothelial growth factor (VEGF) blockade on early-stage Wilms tumor xenograft growth, vasculature and metastasis. VEGF is a key mediator of both physiologic and tumor angiogenesis. We recently described that potent VEGF blockade induces regression of established Wilms tumor xenografts and vessels, also reducing the size but not the incidence of pre-existing metastases. In these studies, we examined the effects of potent VEGF blockade on earlier stages of experimental Wilms tumors, focusing on tumor growth, vasculature and metastasis. Athymic mice received intrarenal human Wilms tumor cell implants. Biweekly treatment with vehicle or the VEGF-Trap, a high-affinity soluble decoy receptor incorporating regions of VEGFR1 and VEGFR2, was begun 1 week later (100 or 500 micrograms/dose, n=20 in each group). Mice were euthanized at week 6 to examine tumor weight, incidence of lung metastases, vascularity and expression of angiogenic factors. A cohort of mice was examined 2 weeks after cessation of treatment. Compared to controls, VEGF-Trap treated tumors were significantly smaller (100 micrograms/dose: 92.7% smaller, p=0.0017; 500 micro g/dose: 99.0% smaller, p=0.0009). The incidence of lung metastasis also decreased significantly (p<0.0055). VEGF-Trap nearly eradicated tumor vasculature. Rare persisting vessels were characterized by large caliber, quiescence (lacking proliferation/apoptosis) and arterialization (both phenotypic and molecular). Potent VEGF blockade caused near-arrest of experimental Wilms tumor growth, resulted in nearly avascular tumors, and also decreased the incidence and size of metastases. Persistent vessels in tumors treated with VEGF-Trap displayed specific morphologic and molecular features, suggestive of arterialization. Future strategies that target these persisting vessels may enhance the efficacy of VEGF blockade therapy.
Increased Expression of Cathepsins and Obesity-Induced Proinflammatory Cytokines in Lacrimal Glands of Male NOD Mouse (2010)

Expression of CATS and CATH increases in parallel with proinflammatory cytokines during the development of autoimmune inflammatory disease in the NOD mouse disease model. Tear CATS may represent a biomarker for diagnosis of dacryoadenitis in SjS.
Development and characterization of a novel nano-liposomal formulation of Alendronate Sodium loaded with biodegradable polymer (2018)

ABSTRACT Background: Alendronate Sodium (ALDS) is the drug of choice for treatment of osteoporosis. However, 50% of the osteoporotic patients ceased the treatment within the first year due to its potential side effect on the gastrointestinal tract (GIT). Objective: The current study aimed to utilize nanotechnology to develop a nano-oral liposomal preparation containing biodegradable polymer (Starch) that enhance the drug prosperities. Methods: Nanoliposomes of ALDS were prepared using different concentrations of solubilized starch (0.1 - 0.5 g) by thin film hydration method. A new method of alendronate quantitative determination was used to overcome the obstacle of its determination by using a new highly sensitive derivatization method. The selected formula was visualized using TEM, in vitro release studies and Stability study was also carried out. Furthermore, ulcerogenicity studies were performed to compare between the optimum prepared formula and a standard nonliposomal ALDS. Results: Six nano-oral liposomal formulations were prepared with zeta potentials ranging from -12 mV to -39 mV and a particle size ranging from 94 nm to 298 nm. The encapsulation efficiency studies demonstrated that the amount of ALDS entrapped within liposomes increased with increasing starch concentration. The stability studies confirmed the role of starch in increasing the stability of the prepared liposomes. In vitro release studies have demonstrated a relative delay in ALDS releases from the liposome core. Ulcerogenicity studies proofed that the prepared formula has a significant gastric tolerance. Conclusion: a novel liposomal formula of ALDS was developed with better tolerability. However, further clinical investigations are necessary to evaluate its therapeutic effectiveness.
Design, implementation and testing of an implantable impedance-based feedback-controlled neural gastric stimulator (2011)

Functional neural gastrointestinal electrical stimulation (NGES) is a methodology of gastric electrical stimulation that can be applied as a possible treatment for disorders such as obesity and gastroparesis. NGES is capable of generating strong lumen-occluding local contractions that can produce retrograde or antegrade movement of gastric content. A feedback-controlled implantable NGES system has been designed, implemented and tested both in laboratory conditions and in an acute animal setting. The feedback system, based on gastric tissue impedance change, is aimed at reducing battery energy requirements and managing the phenomenon of gastric tissue accommodation. Acute animal testing was undertaken in four mongrel dogs (2 M, 2 F, weight 25.53 ± 7.3 kg) that underwent subserosal two-channel electrode implantation. Three force transducers sutured serosally along the gastric axis and a wireless signal acquisition system were utilized to record stimulation-generated contractions and tissue impedance variations respectively. Mechanically induced contractions in the stomach were utilized to indirectly generate a tissue impedance change that was detected by the feedback system. Results showed that increasing or decreasing impedance changes were detected by the implantable stimulator and that therapy can be triggered as a result. The implantable feedback system brings NGES one step closer to long term treatment of burdening gastric motility disorders in humans.
Smart optics in ast (2003)

Smart optics means much more than adaptive optics on telescopes: these new technologies are changing the way space instruments are built and operated and are bringing new technologies into everyday life in the form of cheaper, lighter and more robust optical systems.
Mild, Fast, and Stereoselective Epoxide Opening by Ketone Enolate Anions. Application to Synthesis of the Norlignan Curculigine (2003)

We report here that (1) enolate anions of five- to seven-membered cycloalkanones nucleophilically open cyclopentene and cyclohexene oxides in 57-76% yields and with 4-8:1 diastereoselectivity; (2) enolate anions formed regiospecifically via kinetic deprotonation of 2-cyclohexenone and 2-cycloheptenone open cyclohexene oxide in 60-62% yields and with 32-95:1 diastereoselectivity; and (3) an aryl methyl ketone enolate anion opens a monosubstituted epoxide as the key step in a short synthesis of the gamma-hydroxyketone (GHK) aglycon of the natural product curculigine.
Mapping of the influenza virus genome. III. Identification of genes coding for nucleoprotein, membrane protein, and nonstructural protein (1976)

In previous communications we reported that the eight RNA segments of influenza A/PR/8/34 (HON1) virus could be distinguished from corresponding segments of influenza A/Hong Kong/8/68 (H3N2) virus by migration on polyacrylamide-urea gels. Examination of the RNA patterns of the two parent viruses and recombinants derived from them in concert with serological identification of surface proteins and analysis of the other proteins on sodium dodecyl sulfate gradient gels permitted the identification of the genes coding for hemagglutinin, neuraminidase, and the P1, P2, and P3 proteins (Palese and Schulman, 1976; P. Palese et al., Virology, in press). In the present report we have extended these observations using similar techniques to examine other recombinants and have identified the genes coding for the remaining virus-specific moving RNA segment as 1) and segment 6 of Hong Kong virus coding for the respective nucleoproteins, and that segment 7 of both viruses codes for the membtane protein and RNA segment 8 codes for the nonstructural protein. This completes the mapping of the influenza A virus genome.
miR‐34a is upregulated in AIP‐mutated somatotropinomas and promotes octreotide resistance (2020)

Pituitary adenomas (PAs) are intracranial tumors associated with significant morbidity due to hormonal dysregulation, mass effects and have a heavy treatment burden. Growth hormone (GH)-secreting PAs (somatotropinomas) cause acromegaly-gigantism. Genetic forms of somatotropinomas due to germline AIP mutations (AIPmut+) have an early onset and are aggressive and resistant to treatment with somatostatin analogs (SSAs), including octreotide. The molecular underpinnings of these clinical features remain unclear. We investigated the role of miRNA dysregulation in AIPmut+ vs AIPmut- PA samples by array analysis. miR-34a and miR-145 were highly expressed in AIPmut+ vs AIPmut- somatotropinomas. Ectopic expression of AIPmut (p.R271W) in Aip<sup>-/-</sup> mouse embryonic fibroblasts (MEFs) upregulated miR-34a and miR-145, establishing a causal link between AIPmut and miRNA expression. In PA cells (GH3), miR-34a overexpression promoted proliferation, clonogenicity, migration and suppressed apoptosis, whereas miR-145 moderately affected proliferation and apoptosis. Moreover, high miR-34a expression increased intracellular cAMP, a critical mitogenic factor in PAs. Crucially, high miR-34a expression significantly blunted octreotide-mediated GH inhibition and antiproliferative effects. miR-34a directly targets Gnai2 encoding Gαi2, a G protein subunit inhibiting cAMP production. Accordingly, Gαi2 levels were significantly lower in AIPmut+ vs AIPmut- PA. Taken together, somatotropinomas with AIP mutations overexpress miR-34a, which in turn downregulates Gαi2 expression, increases cAMP concentration and ultimately promotes cell growth. Upregulation of miR-34a also impairs the hormonal and antiproliferative response of PA cells to octreotide. Thus, miR-34a is a novel downstream target of mutant AIP that promotes a cellular phenotype mirroring the aggressive clinical features of AIPmut+ acromegaly.
Manufacturing Mechatronics Using Thermal Spray Shape Deposition (2018)

A new technology for manufacturing mechatronics is described. The technique is based on recursive&#13;\nmasking and deposition of thermally sprayed materials. Using these methods, mechanical structures&#13;\ncan be created that embed and interconnect electronic components. This results in highly integrated&#13;\nmechatronic devices. A simple, electromechanical artifact was designed and produced to assess the&#13;\nfeasibility of these techniques. The details and limitations of this project will be discussed. Areas of&#13;\nfuture research are identified which are aimed at realizing the full potential of this emerging manufacturing&#13;\nprocess.
Toward sclera-force-based robotic assistance for safe micromanipulation in vitreoretinal surgery (2017)

In vitreoretinal surgery instruments are inserted through the sclera to perform precise surgical maneuvers inside the eyeball, which exceeds typical human capabilities. Robotic assistance can enhance the skills of a novice surgeon, provide guidance during tool manipulation based on the desired behavior defined by expert surgeons' maneuvers, and consequently improve the surgical outcome. This paper presents an experimental study characterizing the safe/desired magnitude of forces between the surgical instrument and the sclera insertion port as a function of the tool insertion depth. We explore two types of regressions, a polynomial and a sum of sines fit, to describe the observed user behavior during our one-user pilot study, based on which a variable admittance control scheme can be implemented to robotically guide other users towards this desired behavior for a safe operation.
The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato (2021)

Abstract Cucurbit downy mildew (DM), caused by the obligate biotroph Pseudoperonospora cubensis , is a destructive disease in cucumber. A valuable source of DM resistance is the Indian cucumber accession PI 197088, which harbours several quantitative trait loci (QTLs) contributing to quantitatively inherited DM resistance. With a combination of fine‐mapping and transcriptomics, we identified Amino Acid Permease 2A ( CsAAP2A ) as a candidate gene for QTL DM4.1.3. Whole‐genome and Sanger sequencing revealed the insertion of a Cucumis Mu‐like element (CUMULE) transposon in the allele of the resistant near‐isogenic line DM4.1.3. To confirm whether loss of CsAAP2A contributes to partial DM resistance, we performed targeting induced local lesions in genomes on a DM‐susceptible cucumber genotype to identify an additional csaap2a mutant, which indeed was partially DM resistant. In view of the loss of the putative function as amino acid transporter, we measured amino acids in leaves. We found that DM‐inoculated leaves of line DM4.1.3 (with the csaap2a mutation) contained significantly fewer amino acids than wild‐type cucumber. The decreased flow of amino acids towards infected leaves in csaap2a plants compared to the wild type might explain the resistant phenotype of the mutant, as this would limit the available nutrients for the pathogen and thereby its fitness. To examine whether AAP genes play a conserved role as susceptibility factors in plant–oomycete interactions, we made targeted mutations in two AAP genes from tomato and studied the effect on susceptibility to Phytophthora infestans . We conclude that not only CsAAP2A but also SlAAP5A/SlAAP5B are susceptibility genes for oomycete pathogens.
Effect of Pentoxifylline on the Intrinsic Swimming Forces of Human Sperm Assessed by Optical Tweezers (2000)

It is still controversial whether in vitro exposure of sperm to pentoxifylline increases sperm motility and force, which is defined as the product of velocity by beat frequency of the tail. Laser optical tweezers have been successfully used in the past to evaluate sperm force in basal conditions. The aim of this prospective study was to determine whether exposure of human sperm to pentoxifylline has any effect on sperm intrinsic forces. Twelve healthy subjects undergoing routine semen analysis were enrolled in the study. Ten exhibited normal semen parameters, 2 exhibited asthenozoospermia. Each semen specimen was washed and, after swim-up, resuspended in human tubal fluid (HTF) and divided into 2 aliquots. One aliquot was incubated with pentoxifylline for 30 minutes (final concentration = 3.6 mM); the second aliquot, without pentoxifylline, served as a control. After 30 minutes the pentoxifylline-treated aliquot was divided into 2 portions, 1 of which was washed to remove the pentoxifylline, the other was left in prolonged coincubation with the chemical. The main outcome was the measurement of sperm intrinsic force in milliwatts (mW), which was assessed by means of a noninvasive infrared laser optical trap created by a continuous wave, 1064-nm Nd:YAG laser beam directed in an inverted microscope. Exposure of sperm to pentoxifylline consistently increased sperm relative escape force from the laser optical trap. The increase ranged from 33% to 154% over baseline force compared with controls. The average absolute increase in sperm force rose from 37 mW to 79 mW (P < .05). Specimens with sperm having an initial low relative escape force gained the highest relative increase. The effect of pentoxifylline on sperm force, already apparent after 5 minutes, reached a peak at 30 minutes and persisted for up to 3 hours in sperm that were left in coincubation and in those on which the pentoxifylline had been washed off. In conclusion, pentoxifylline significantly increases sperm intrinsic relative force in normozoospermic and asthenozoospermic samples. This experiment confirms that optical tweezers can provide an accurate determination of sperm force in in vitro conditions. Clinical data must now establish whether a documented increase in sperm force is an important parameter for assessing sperm fertilizing capacity.
Circadian clock component REV-ERBα controls homeostatic regulation of pulmonary inflammation (2018)

Recent studies reveal that airway epithelial cells are critical pulmonary circadian pacemaker cells, mediating rhythmic inflammatory responses. Using mouse models, we now identify the rhythmic circadian repressor REV-ERBα as essential to the mechanism coupling the pulmonary clock to innate immunity, involving both myeloid and bronchial epithelial cells in temporal gating and determining amplitude of response to inhaled endotoxin. Dual mutation of REV-ERBα and its paralog REV-ERBβ in bronchial epithelia further augmented inflammatory responses and chemokine activation, but also initiated a basal inflammatory state, revealing a critical homeostatic role for REV-ERB proteins in the suppression of the endogenous proinflammatory mechanism in unchallenged cells. However, REV-ERBα plays the dominant role, as deletion of REV-ERBβ alone had no impact on inflammatory responses. In turn, inflammatory challenges cause striking changes in stability and degradation of REV-ERBα protein, driven by SUMOylation and ubiquitination. We developed a novel selective oxazole-based inverse agonist of REV-ERB, which protects REV-ERBα protein from degradation, and used this to reveal how proinflammatory cytokines trigger rapid degradation of REV-ERBα in the elaboration of an inflammatory response. Thus, dynamic changes in stability of REV-ERBα protein couple the core clock to innate immunity.
Unusually Conductive Organic–Inorganic Hybrid Nanostructures Derived from Bio-Inspired Mineralization of Peptide/Pi-Electron Assemblies (2020)

Supramolecular materials derived from pi-conjugated peptidic macromolecules are well-established to self-assemble into 1D nanostructures. In the presence of KOH, which was used to more fully dissolve the peptide macromolecules prior to triggering the self-assembly by way of exposure to HCl vapor, we report here an unexpected mineralization of KCl as templated presumably by the glutamic acid residues that were present along the backbone of the peptide macromolecules. In order to decouple the peptidic side chains from the central pi-electron unit, three-carbon spacers were added between them on both sides. The assembled structures that resulted from the collective formation of β-sheets, π-orbital overlaps, and mineralization resulted in highly interconnected dendritic structures under suitable KOH concentrations. Electrical measurements indicated that when well-interconnected, these dendritic structures maintained conductivities comparable to those of metals at around 1800 S/cm. About 50 mA current was measured for 0.5 V/37.5 μm. Varying the gate voltage in a transistor configuration had no effect on the current levels, indicating a conductive instead of a semiconducting pathway. Control experiments without the peptide, measurements of conductivity over time, and conductivity quenching by ammonia suggested the conductivity of these dendritic networks was derived from proton doping of the central π-electron units in a strong acid environment and was facilitated by closely spaced chromophores, as suggested in the literature, leading to facile π-electron transfer along the interconnected dendritic pathways. Our findings suggest that mineralization templated by appropriate amino acids combined with peptide/π-electron self-assembly can lead to highly conductive dendritic macrostructures as well as control of nanowire growth in specific directions.