gebhart/patrepeval huggingface dataset:
cAMP-dependent protein kinase phosphorylation of the acid-sensing ion channel-1 regulates its binding to the protein interacting with C-kinase-1 (2003)

The acid-sensing ion channel-1 (ASIC1) contributes to synaptic plasticity and may influence the response to cerebral ischemia and acidosis. We found that cAMP-dependent protein kinase phosphorylated heterologously expressed ASIC1 and endogenous ASIC1 in brain slices. ASIC1 also showed significant phosphorylation under basal conditions. Previous studies showed that the extreme C-terminal residues of ASIC1 bind the PDZ domain of the protein interacting with C-kinase-1 (PICK1). We found that protein kinase A phosphorylation of Ser-479 in the ASIC1 C terminus interfered with PICK1 binding. In contrast, minimizing phosphorylation or mutating Ser-479 to Ala enhanced PICK1 binding. Phosphorylation-dependent disruption of PICK1 binding reduced the cellular colocalization of ASIC1 and PICK1. Thus, the ASIC1 C terminus contains two sites that influence its binding to PICK1. Regulation of this interaction by phosphorylation provides a mechanism to control the cellular localization of ASIC1.
An Integrin-Targeted, Highly Diffusive Construct for Photodynamic Therapy (2017)

Targeted antineoplastic agents show great promise in the treatment of cancer, having the ability to impart cytotoxicity only to specific tumor types. However, these therapies do not experience uniform uptake throughout tumors, leading to sub-lethal cell killing that can impart treatment resistance, and cause problematic off-target effects. Here we demonstrate a photodynamic therapy construct that integrates both a cyclic RGD moiety for integrin-targeting, as well as a 5 kDa PEG chain that passivates the construct and enables its rapid diffusion throughout tumors. PEGylation of the photosensitizer construct was found to prevent photosensitizer aggregation, boost the generation of cytotoxic reactive radical species, and enable the rapid uptake of the construct into cells throughout large (>500 µm diameter) 3D tumor spheroids. Replacing the cyclic RGD with the generic RAD peptide led to the loss of cellular uptake in 3D culture, demonstrating the specificity of the construct. Photodynamic therapy with the construct was successful in inducing cytotoxicity, which could be competitively blocked by a tenfold concentration of free cyclic RGD. This construct is a first-of-its kind theranostic that may serve as a new approach in our growing therapeutic toolbox.
Laser slice thinning of GaN-on-GaN high electron mobility transistors (2022)

As a newly developed technique to slice GaN substrates, which are currently very expensive, with less loss, we previously reported a laser slicing technique in this journal. In the previous report, from the perspective of GaN substrate processing, we could only show that the GaN substrate could be sliced by a laser and that the sliced GaN substrate could be reused. In this study, we newly investigated the applicability of this method as a device fabrication process. We demonstrated the thinning of GaN-on-GaN high-electron-mobility transistors (HEMTs) using a laser slicing technique. Even when the HEMTs were thinned by laser slicing to a thickness of 50 mm after completing the fabrication process, no significant fracture was observed in these devices, and no adverse effects of laser-induced damage were observed on electrical characteristics. This means that the laser slicing process can be applied even after device fabrication. It can also be used as a completely new semiconductor process for fabricating thin devices with thicknesses on the order of 10 mm, while significantly reducing the consumption of GaN substrates.
Role of Localized Network Damage in Block Copolymer Toughened Epoxies (2012)

The underlying mechanisms responsible for the toughening of block copolymer modified thermoset epoxies are not completely understood. A current theory targets cavitation of the rubbery cores in dispersed micelles as the key event that triggers shear yielding, resulting in enhanced toughness. To evaluate this hypothesis, we prepared spherical micelle forming block copolymers with rubbery cores (prone to cavitation) and glassy cores (unable to cavitate). Surprisingly, both systems enhance fracture toughness, although the rubbery core micelles outperform the glassy core counterparts. This finding challenges previous deductions regarding the toughening mechanism. We propose that the mechanical integrity of the region immediately surrounding the micelle core is compromised by the presence of the corona blocks, facilitating local deformation of the matrix. We speculate that the compliant nature of the rubber amplifies this effect.
Impaired development of HIV-1 gp160-specific CD8+ cytotoxic T cells by a delayed switch from Th1 to Th2 cytokine phenotype in mice withHelicobacter pylori infection (2001)

Th1 and Th2 cells play a central role in immunoregulation during infection. We show that Helicobacter pylori induces Th1 cytokine responses early (2 weeks) but predominantly Th2 responses later (6 weeks) in infection. The switch is principally mediated by urease-specific CD4(+) T cells, and correlates with a loss of urease-specific high-avidity JNK(+) Th1 and gain of low-avidity JNK(-) (possibly Th2) cells at the later stage of infection, concomitant with a 100-fold higher colonization level of H. pylori at 6 weeks than at 2 weeks that might tolerize high-avidity Th1 cells. Furthermore, differentiation of HIV gp160-specific CD4(+) Th and CD8(+) cytotoxic T lymphocytes (CTL) into effector cells is impaired in 6-week H. pylori-infected mice immunized with vaccinia expressing gp160, and serum IL-12 stimulated by vaccinia infection is barely detectable. Adoptive transfer of urease-specific Th2 cells to mice infected only with gp160-expressing vaccinia abrogates Th1 polarization of the gp120 response, down-modulates virus-specific CTL responses, and delays virus clearance. Therefore, the H. pylori urease-mediated immunoregulation in the switch from JNK(+) Th1 to JNK(-) Th2 phenotype, and the preceding low IL-12 response, are likely critical steps in the impairment of antiviral immunity.
dnaB analog function associated with plasmid R100drd-1 (1983)

Plasmid R100 and a number of its derivatives were able to suppress the temperature sensitivity of strains carrying different alleles of the dnaB gene of Escherichia coli K-12. R100drd-l and pAR132 were able to rescue a strain carrying the dnaB266(Am) mutation in the absence of any known amber suppressors. This was taken as evidence for the existence of an R100drd-l dnaB analog function. The R100drd-l dnaB analog was different from those of bacteriophages P1 and P7 in that it was able to support the growth of bacteriophage lambda in a dnaB266(Am) background. The dnaB analog was also shown to be thermosensitive. The structural gene for this protein lies within the EcoRI fragment D of R100drd-l.
Anthocyanin-rich fruits and mental health outcomes in an Italian cohort (2022)

BACKGROUND: Evidence suggests that diets rich in flavonoids affect human health. Among flavonoids, anthocyanins have been demonstrated to exert beneficial effects toward brain through modulation of neuroinflammation, neurogenesis, neuronal signaling and by modulating gut microbiota. OBJECTIVE: This study aimed to investigate the association between consumption of anthocyanin-rich fruits (strawberries, berries, cherries, prickly pears, grapes, blood oranges) and mental health in an Italian cohort study. METHODS: Dietary information was collected using a validated food frequency questionnaire. Mental health outcomes were assessed using the Pittsburgh Sleep Quality Index (PSQI), the Perceived Stress Scale (PSS), the 10-item Center for the Epidemiological Studies of Depression Short Form (CES-D-10) as a screening tool for sleep quality, perceived stress and depressive symptoms, respectively. RESULTS: A significant inverse association between higher anthocyanin-rich fruits intake and occurrence of poor sleep quality, high perceived stress, and depressive symptoms was found. In the most adjusted model, individuals in the highest tertile of anthocyanin-rich fruits were less likely to have poor sleep quality (OR = 0.63, 95% CI: 0.47–0.86), high perceived stress (OR = 0.68, 95% CI: 0.51–0.92), and depressive symptoms (OR = 0.67, 95% CI: 0.49–0.90). CONCLUSIONS: Diets including fruits rich in anthocyanins may result in positive mental health outcomes.
Liquid Microjunction Surface Sampling Coupled with High-Pressure Liquid Chromatography−Electrospray Ionization-Mass Spectrometry for Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections (2010)

In this work, a commercially available autosampler was adapted to perform direct liquid microjunction (LMJ) surface sampling followed by a high-pressure liquid chromatography (HPLC) separation of the extract components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the utility of coupling a separation with this direct liquid extraction based surface sampling approach, four different organs (brain, lung, kidney, and liver) from whole-body thin tissue sections of propranolol dosed and control mice were examined. The parent drug was observed in the chromatograms of the surface sampling extracts from all the organs of the dosed mouse examined. In addition, two isomeric phase II metabolites of propranolol (an aliphatic and an aromatic hydroxypropranolol glucuronide) were observed in the chromatograms of the extracts from lung, kidney, and liver. Confirming the presence of one or the other or both of these glucuronides in the extract from the various organs was not possible without the separation. These drug and metabolite data obtained using the LMJ surface sampling/HPLC-MS method and the results achieved by analyzing similar samples by conventional extraction of the tissues and subsequent HPLC-MS analysis were consistent. The ability to directly and efficiently sample from thin tissue sections via a liquid extraction and then perform a subsequent liquid phase separation increases the utility of this liquid extraction surface sampling approach.
Molecular Clones from a Non-Acutely Pathogenic Derivative of SIV smmPBj14 : Characterization and Comparison to Acutely Pathogenic Clones (1992)

Molecularly cloned simian immunodeficiency viruses capable of inducing acute, fatal disease in pig-tailed macaques had been derived previously from a biological clone (bcl-3) of the PBj14 isolate of SIV from sooty mangabey monkeys (SIVsmmPBj14). The present study was undertaken in order to characterize virus from a second biological clone of SIVsmmPBj14, bcl-1, which fails to induce acute or fatal disease. Polymerase chain reaction was used to amplify 5' and 3' viral genome halves. The DNA sequence of two 3' halves was determined, and an infectious recombinant generated using a bcl-3-derived 5' half and a bcl-1-derived 3' half. Overall, bcl-1- and bcl-3-derived viruses displayed close homology, differing by a total of 2% at the DNA level and 1-6% at the amino acid level within the 8 open reading frames examined. In contrast to the bcl-3-derived viruses, the bcl-1-derived viruses encode a truncated transmembrane envelope glycoprotein. Another consistent difference was the presence of a 22 bp duplication in the U3 portion of the long terminal repeat (LTR) of bcl-3-derived viruses that includes the NF-kappa B transcriptional enhancer binding site. To assess the importance of this duplication, virus chimeras were generated which removed the duplication from the 3'-LTR or from both LTRs of a bcl-3 clone. The former virus was unstable, reacquiring the duplication through recombination with the 5' LTR. No consistent difference were observed, however, between viruses with or without the duplication in the in vitro studies conducted to date.(ABSTRACT TRUNCATED AT 250 WORDS)
ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech Recognition (2001)

A challenging, unsolved problem in the speech recognition community is recognizing speech signals that are corrupted by loud, highly nonstationary noise. One approach to noisy speech recognition is to automatically remove the noise from the cepstrum sequence before feeding it in to a clean speech recognizer. In previous work published in Eurospeech, we showed how a probability model trained on clean speech and a separate probability model trained on noise could be combined for the purpose of estimating the noisefree speech from the noisy speech. We showed how an iterative 2nd order vector Taylor series approximation could be used for probabilistic inference in this model. In many circumstances, it is not possible to obtain examples of noise without speech. Noise statistics may change significantly during an utterance, so that speechfree frames are not sucient for estimating the noise model. In this paper, we show how the noise model can be learned even when the data contains speech. In particular, the noise model can be learned from the test utterance and then used to denoise the test utterance. The approximate inference technique is used as an approximate E step in a generalized EM algorithm that learns the parameters of the noise model from a test utterance. For both Wall Street Journal data with added noise samples and the Aurora benchmark, we show that the new noise adaptive technique performs as well as or significantly better than the non-adaptive algorithm, without the need for a separate training set of noise examples.
Interfacial rheology and direct imaging reveal domain-templated network formation in phospholipid monolayers penetrated by fibrinogen (2019)

Phospholipids are found throughout the natural world, including the lung surfactant (LS) layer that reduces pulmonary surface tension and enables breathing. Fibrinogen, a protein involved in the blood clotting process, is implicated in LS inactivation and the progression of disorders such as acute respiratory distress syndrome. However, the interaction between fibrinogen and LS at the air-water interface is poorly understood. Through a combined microrheological, confocal and epifluorescence microscopy approach we quantify the interfacial shear response and directly image the morphological evolution when a model LS monolayer is penetrated by fibrinogen. When injected into the subphase beneath a monolayer of the phospholipid dipalmitoylphosphatidylcholine (DPPC, the majority component of LS), fibrinogen preferentially penetrates disordered liquid expanded (LE) regions and accumulates on the boundaries between LE DPPC and liquid condensed (LC) DPPC domains. Thus, fibrinogen is line active. Aggregates grow from the LC domain boundaries, ultimately forming a percolating network. This network stiffens the interface compared to pure DPPC and imparts the penetrated monolayer with a viscoelastic character reminiscent of a weak gel. When the DPPC monolayer is initially compressed beyond LE-LC coexistence, stiffening is significantly more modest and the penetrated monolayer retains a viscous-dominated, DPPC-like character.
Psychosocial Factors Affecting Adherence to Medical Regimens in a Group of Hemodialysis Patients (1982)

The present research was designed to identify psychosocial correlates of adherence among patients receiving hemodialysis at two outpatient clinics. The 116 participants were interviewed concerning their knowledge of treatment, health beliefs, treatment history, social support, personal characteristics, and adherence to the medication, diet and fluid-intake aspects of the regimen. In addition, medical record data were obtained on serum phosphorus and serum potassium levels, and on between-dialysis weight gains. The magnitude of relationships between predictors and adherence measures varied, depending on the method used to measure adherence. For the self-report measures, beliefs concerning the efficacy of the behavior and barriers to the behavior, along with reported family problems, proved to be consistent predictors. Other beliefs and characteristics did not contribute significantly. For the medical chart information, however, the predictive factors were less consistent. In general, situational factors seem to be the major contributors to patient adherence, and adherence itself is seen as a complex and multidimensional phenomenon.
COVID-19 inflammation results in urine cytokine elevation and causes COVID-19 associated cystitis (CAC) (2020)

Coronavirus disease 2019 (COVID-19) causes a wide range of symptoms, including several unexpected symptoms such as loss of taste, skin changes, and eye problems. We recently observed patients with documented COVID-19 develop de novo severe genitourinary symptoms, most notably urinary frequency of ≥ 13 episodes/24 h and nocturia ≥ 4 episodes/night. We call these associated urinary symptoms COVID-19 associate cystitis (CAC). COVID-19 severity is associated with inflammation. We collected urine samples from COVID-19 patients, including patients with CAC, and found elevation of proinflammatory cytokines also in the urine. It has been previously shown that patients with urinary incontinence and ulcerative interstitial cystitis/bladder pain syndrome have elevated urinary inflammatory cytokines compared to normal controls. We therefore hypothesize that CAC, with presentation of de novo severe urinary symptoms, can occur in COVID-19 and is caused by increased inflammatory cytokines that are released into the urine and/or expressed in the bladder. The most important implications of our hypothesis are: 1) Physician caring for COVID-19 patients should be aware of COVID-19 associate cystitis (CAC); 2) De novo urinary symptoms should be included in the symptom complex associated with COVID-19; and 3) COVID-19 inflammation may result in bladder dysfunction.
Preparation and Characterization of Group A Meningococcal Capsular Polysaccharide Conjugates and Evaluation of Their Immunogenicity in Mice (2003)

Epidemic and endemic meningitis caused by group A Neisseria meningitidis remains a problem in sub-Saharan Africa. Although group A meningococcal capsular polysaccharide (GAMP) vaccine confers immunity at all ages, the improved immunogenicity of a conjugate and its compatibility with the World Health Organization's Extended Program on Immunization offers advantages over GAMP alone. Conjugates of GAMP bound to bovine serum albumin (BSA) were synthesized, characterized, and evaluated for their immunogenicities in mice. Two methods, involving adipic acid dihydrazide (ADH) as a linker, were used. First, ADH was bound to GAMP activated with cyanogen bromide (CNBr) or with 1-cyano-4(dimethylamino)-pyridinium tetrafluoroborate (CDAP) to form GAMP(CNBr)AH and GAMP(CDAP)AH. These derivatives were bound to BSA by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to form GAMP(CNBr)AH-BSA and GAMP(CDAP)AH-BSA. Second, ADH was bound to BSA with EDC to form AHBSA. AHBSA was bound to activated GAMP to form GAMP(CNBr)-AHBSA and GAMP(CDAP)-AHBSA. The yield of GAMP(CDAP)-AHBSA (35 to 40%) was higher than those of the other conjugates (5 to 20%). GAMP conjugates elicited immunoglobulin G (IgG) anti-GAMP in all mice after three injections of 2.5 or 5.0 microg of GAMP: the geometric mean (GM) was highest in recipients of GAMP(CDAP)-AHBSA (11.40 enzyme-linked immunosorbent assay units). Although the difference was not statistically significant, the 5.0- microg dose elicited a higher GM IgG anti-GAMP than the 2.5- microg dose. Low levels of anti-GAMP were elicited by GAMP alone. GAMP(CDAP)-AHBSA elicited bactericidal activity roughly proportional to the level of IgG anti-GAMP.
Computational See-Through Near-Eye Displays (2019)

See-through near-eye displays with the form factor and field of view of eyeglasses are a natural choice for augmented reality systems: the non-encumbering size enables casual and extended use and large field of view enables general-purpose spatially registered applications. However, designing displays with these attributes is currently an open problem. Support for enhanced realism through mutual occlusion and the focal depth cues is also not found in eyeglasses-like displays. This dissertation provides a new strategy for eyeglasses-like displays that follows the principles of computational displays, devices that rely on software as a fundamental part of image formation. Such devices allow more hardware simplicity and flexibility, showing greater promise of meeting form factor and field of view goals while enhancing realism. This computational approach is realized in two novel and complementary see-through near-eye display designs. The first subtractive approach filters omnidirectional light through a set of optimized patterns displayed on a stack of spatial light modulators, reproducing a light field corresponding to in-focus imagery. The design is thin and scales to wide fields of view; see-through is achieved with transparent components placed directly in front of the eye. Preliminary support for focal cues and environment occlusion is also demonstrated. The second additive approach uses structured point light illumination to form an image with a minimal set of rays. Each of an array of defocused point light sources is modulated by a region of a spatial light modulator, essentially encoding an image in the focal blur. See-through is also achieved with transparent components and thin form factors and wide fields of view (>= 100 degrees) are demonstrated. The designs are examined in theoretical terms, in simulation, and through prototype hardware with public demonstrations. This analysis shows that the proposed computational near-eye display designs offer a significantly different set of trade-offs than conventional optical designs. Several challenges remain to make the designs practical, most notably addressing diffraction limits.
A value based approach to determine optimal phytase dose: A case study in turkey poults (2016)

There is a recent trend to increase phytase dose from the traditional 500 FTU/kg to 750 or 1000 FTU/kg in poultry feed formulations, driven by high inorganic phosphorus prices and more bioefficacious phytases. This paper outlines a method for calculating optimum phytase dose, based on the replacement of inorganic phosphorus through the application of the marginal decision rule. In this 21 day digestibility study 768 male BUT 6 turkey poults were assigned to 8 treatments (6 replications/treatment): a negative control diet based on corn/soy, meeting the nutritional requirements of turkey poults except in phosphorus (0.26% ret P) and calcium (0.8%), 4 graded levels of phytase over the negative control (345, 690, 1035, 1380 FTU/kg), and 3 graded levels of supplemental MCP (0.6, 1.2, 1.8 g P/kg). Significance was determined using ANOVA and means separation for all parameters was achieved using Tukey’s HSD. Bodyweight gain was maximised at the 1035 FTU/kg dose, with all levels of phytase supplementations significantly increasing BWG compared to the negative control (P < 0.05). Non-linear regression was conducted on ileal phosphorus digestibility, and optimum phytase dose was determined using the as the point where the incremental value of P release was equal to the incremental phytase cost, assuming the value of incremental P from phytase was equal to the value of the same amount of digestible P from an inorganic source. The optimum dose of phytase under typical 2014 US market price conditions was calculated to be 996 FTU/kg. At 996 FTU/kg, 100% of the potential value of inorganic P replacement was captured, compared to 70% of the value at 500 FTU/kg. Under different phytase and inorganic P price conditions, the optimum dose varied between 762 FTU/kg and 1231 FTU/kg. In conclusion, this study highlights a method that provides a rational justification for use of targeted phytase doses greater than 500 FTU/kg.