gebhart/patrepeval huggingface dataset:
Diabetes-Associated Common Genetic Variation and Its Association With GLP-1 Concentrations and Response to Exogenous GLP-1 (2012)

The mechanisms by which common genetic variation predisposes to type 2 diabetes remain unclear. The disease-associated variants in TCF7L2 (rs7903146) and WFS1 (rs10010131) have been shown to affect response to exogenous glucagon-like peptide 1 (GLP-1), while variants in KCNQ1 (rs151290, rs2237892, and rs2237895) alter endogenous GLP-1 secretion. We set out to validate these observations using a model of GLP-1-induced insulin secretion. We studied healthy individuals using a hyperglycemic clamp and GLP-1 infusion. In addition, we measured active and total GLP-1 in response to an oral challenge in nondiabetic subjects. After genotyping the relevant single nucleotide polymorphisms, generalized linear regression models and repeated-measures ANCOVA models incorporating potential confounders, such as age and BMI, were used to assess the associations, if any, of response with genotype. These variants did not alter GLP-1 concentrations in response to oral intake. No effects on β-cell responsiveness to hyperglycemia and GLP-1 infusion were apparent. Diabetes-associated variation (T allele at rs7903146) in TCF7L2 may impair the ability of hyperglycemia to suppress glucagon (45 ± 2 vs. 47 ± 2 vs. 60 ± 5 ng/L for CC, CT, and TT, respectively, P = 0.02). In nondiabetic subjects, diabetes-associated genetic variation does not alter GLP-1 concentrations after an oral challenge or its effect on insulin secretion.
TIGIT Expression on Activated NK Cells Correlates with Greater Anti-Tumor Activity but Promotes Functional Decline upon Lung Cancer Exposure: Implications for Adoptive Cell Therapy and TIGIT-Targeted Therapies (2023)

Treatments targeting TIGIT have gained a lot of attention due to strong preclinical and early clinical results, particularly with anti-PD-(L)1 therapeutics. However, this combination has failed to meet progression-free survival endpoints in phase III trials. Most of our understanding of TIGIT comes from studies of T cell function. Yet, this inhibitory receptor is often upregulated to the same, or higher, extent on NK cells in cancers. Studies in murine models have demonstrated that TIGIT inhibits NK cells and promotes exhaustion, with its effects on tumor control also being dependent on NK cells. However, there are limited studies assessing the role of TIGIT on the function of human NK cells (hNK), particularly in lung cancer. Most studies used NK cell lines or tested TIGIT blockade to reactivate exhausted cells obtained from cancer patients. For therapeutic advancement, a better understanding of TIGIT in the context of activated hNK cells is crucial, which is different than exhausted NK cells, and critical in the context of adoptive NK cell therapeutics that may be combined with TIGIT blockade. In this study, the effect of TIGIT blockade on the anti-tumor activities of human ex vivo-expanded NK cells was evaluated in vitro in the context of lung cancer. TIGIT expression was higher on activated and/or expanded NK cells compared to resting NK cells. More TIGIT<sup>+</sup> NK cells expressed major activating receptors and exerted anti-tumor response as compared to TIGIT<sup>-</sup> cells, indicating that NK cells with greater anti-tumor function express more TIGIT. However, long-term TIGIT engagement upon exposure to PVR<sup>+</sup> tumors downregulated the cytotoxic function of expanded NK cells while the inclusion of TIGIT blockade increased cytotoxicity, restored the effector functions against PVR-positive targets, and upregulated immune inflammation-related gene sets. These combined results indicate that TIGIT blockade can preserve the activation state of NK cells during exposure to PVR<sup>+</sup> tumors. These results support the notion that a functional NK cell compartment is critical for anti-tumor response and anti-TIGIT/adoptive NK cell combinations have the potential to improve outcomes.
An energy-based optimal control problem for unmanned aircraft systems flight planning (2017)

In this paper, we formulate the flight planning problem for a multirotor Unmanned Aircraft Systems (UAS) as an optimal control problem. The cost optimized is the energy consumption at the cruise phase of a mission. We first present a general formulation, then address a special cases: optimizing flight directions given vehicle speed. The problem was solved numerically on digital elevation models (DEM) with the Ordered Upwind Method (OUM). By combining the optimized path with timestamps, we can generate 4D trajectories typically used in aviation flight planning, and thus maximize the software compatibility between manned and unmanned aviation. Simulation shows that the algorithm can generate energy-optimal paths avoiding obstacles, as well as estimate energy consumption along the entire trajectory.
DISTRICT HEAT PRICE MODEL ANALYSIS : A risk assesment of Mälarenergi's new district heat price model (2019)

Energy efficiency measures in buildings and alternative heating methods have led to a decreased demand for district heating (DH). Furthermore, due to a recent increase in extreme weather events, it is harder for DH providers to maintain a steady production leading to increased costs. These issues have led DH companies to change their price models. This thesis investigated such a price model change, made by Mälarenergi (ME) on the 1st of August 2018. The aim was to compare the old price model (PM1) with the new price model (PM2) by investigating the choice of base and peak loads a customer can make for the upcoming year, and/or if they should let ME choose for them. A prediction method, based on predicting the hourly DH demand, was chosen after a literature study and several method comparisons were made from using weather parameters as independent variables. Consumption data from Mälarenergi for nine customers of different sizes were gathered, and eight weather parameters from 2014 to 2018 were implemented to build up the prediction model. The method comparison results from Unscrambler showed that multilinear regression was the most accurate statistical modelling method, which was later used for all predictions. These predictions from Unscrambler were then used in MATLAB to estimate the total annual cost for each customer and outcome. For PM1, the results showed that the flexible cost for the nine customers stands for 76 to 85 % of the total cost, with the remaining cost as fixed fees. For PM2, the flexible cost for the nine customers stands for 46 to 61 % of the total cost, with the remaining as fixed cost. Regarding the total cost, PM2 is on average 7.5 % cheaper than PM1 for smaller customer, 8.6 % cheaper for medium customers and 15.9 % cheaper for larger customers. By finding the lowest cost case for each customer their optimal base and peaks loads were found and with the use of a statistical inference method (Bootstrapping) a 95 % confidence interval for the base load and the total yearly cost with could be established. The conclusion regarding choices is that the customer should always choose their own base load within the recommended confidence interval, with ME’s choice seen as a recommendation. Moreover, ME should always make the peak load choice because they are willing to pay for an excess fee that the customer themselves must pay otherwise.
The Human Thioesterase II Protein Binds to a Site on HIV-1 Nef Critical for CD4 Down-regulation (2000)

A HIV-1 Nef affinity column was used to purify a 35-kDa Nef-interacting protein from T-cell lysates. The 35-kDa protein was identified by peptide microsequence analysis as the human thioesterase II (hTE) enzyme, an enzyme previously identified in a yeast two-hybrid screen as a potential Nef-interacting protein. Immunofluorescence studies showed that hTE localizes to peroxisomes and that coexpression of Nef and hTE leads to relocalization of Nef to peroxisomes. Interaction of Nef and hTE was abolished by point mutations in Nef at residues Asp(108), Leu(112), Phe(121), Pro(122), and Asp(123). All of these mutations also abrogated the ability of Nef to down-regulate CD4 from the surface of HIV-infected cells. Based on the x-ray and NMR structures of Nef, these residues define a surface on Nef critical for CD4 down-regulation. A subset of these mutations also affected the ability of Nef to down-regulate major histocompatibility complex class I. These results, taken together with previous studies, identify a region on Nef critical for most of its known functions. However, not all Nef alleles bind to hTE with high affinity, so the role of hTE during HIV infection remains uncertain.
Nongenetic Factors Associated With Stress Urinary Incontinence (2011)

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A Review on Host-Leptospira Interactions: What We Know and Future Expectations (2021)

Leptospirosis is a widespread zoonosis caused by pathogenic <i>Leptospira</i> spp. It is considered a neglected infectious disease of human and veterinary concern. Our group has been investigating proteins annotated as hypothetical, predicted to be located on the leptospiral surface. Because of their location, these proteins may have the ability to interact with various host components, which could allow establishment of the infection. These proteins act as adherence factors by binding to host receptor molecules, such as the extracellular matrix (ECM) components laminin and glycosaminoglycans to help bacterial colonization. <i>Leptospira</i> also interacts with the host fibrinolytic system, which has been demonstrated to be a powerful tool for invasion mechanisms. The interaction with fibrinogen and thrombin has been shown to reduce fibrin clot formation. Additionally, the degradation of coagulation cascade components by secreted proteases or by acquired surface plasmin could also play a role in reducing clot formation, hence facilitating dissemination during infection. Interaction with host complement system regulators also plays a role in helping bacteria to evade the immune system, facilitating invasion. Interaction of <i>Leptospira</i> to cell receptors, such as cadherins, can contribute to investigate molecules that participate in virulence. To achieve a better understanding of the host-pathogen interaction, leptospiral mutagenesis tools have been developed and explored. This work presents several proteins that mediate binding to components of the ECM, plasma, components of the complement system and cells, to gather research achievements that can be helpful in better understanding the mechanisms of leptospiral-host interactions and discuss genetic manipulation for <i>Leptospira</i> spp. aimed at protein function validation.
Spectral Analysis of Brillouin Dynamic Grating Based on Heterodyne Detection (2013)

Spectral analysis based on heterodyne detection is used to investigate Brillouin dynamic grating (BDG) in a small-core polarization-maintaining optical fiber. Thanks to direct heterodyning of the readout and diffraction waves, essential BDG properties can be fully investigated. It is experimentally characterized that the BDG diffraction wave has an identical frequency downshift from the readout wave as the pump–probe frequency offset in the BDG generation, which straightforwardly verifies the theoretical estimation of the BDG's phase-matching condition for the first time to our best knowledge. The spectral analysis also confirms that the maximum power of the main peak changes in the same way with the stimulated Brillouin gain and has an exponential (linear) dependence on the pump (probe) power.
Current Density Profile Measurements in the Proto-Cleo Torsatron (1980)

Current density profile measurements were obtained in the Proto-Cleo torsatron (R = 40 cm, a = 5 cm, I = 3, BT = 3 kG, nα ~ 1011 cm-3, Te ~ 20 eV) by using a small back-to-back flat double probe. Three different operating circuits used with this probe are presented, along with experimental results, all showing good agreement. Current is seen to flow only within the separatrix, in channels which follow the magnetic surfaces as they move radially inward with time due to changing vertical magnetic flux.
Polymorphisms and Haplotypes in the Cytochrome P450 17A1, Prolactin, and Catechol-O-Methyltransferase Genes and Non-Hodgkin Lymphoma Risk (2005)

Expression of prolactin and of prolactin and estrogen receptors in lymphocytes, bone marrow, and lymphoma cell lines suggests that hormonal modulation may influence lymphoma risk. Prolactin and estrogen promote the proliferation and survival of B cells, factors that may increase non-Hodgkin lymphoma risk, and effects of estrogen may be modified by catechol-O-methyltransferase (COMT), an enzyme that alters estrogenic activity. Cytochrome P450 17A1 (CYP17A1), a key enzyme in estrogen biosynthesis, has been associated with increased cancer risk and may affect lymphoma susceptibility. We studied the polymorphisms prolactin (PRL) -1149G>T, CYP17A1 -34T>C, and COMT 108/158Val>Met, and predicted haplotypes among a subset of participants (n = 308 cases, n = 684 controls) in a San Francisco Bay Area population-based non-Hodgkin lymphoma study (n = 1,593 cases, n = 2,515 controls) conducted from 1988 to 1995. Oral contraceptive and other hormone use also was analyzed. Odds ratios (OR) for non-Hodgkin lymphoma and follicular lymphoma were reduced for carriers of the PRL -1149TT genotype [OR, 0.64; 95% confidence interval (95% CI), 0.41-1.0; OR, 0.53; 95% CI, 0.26-1.0, respectively]. Diffuse large-cell lymphoma risk was increased for those with CYP17A1 polymorphisms including CYP17A1 -34CC (OR, 2.0; 95% CI, 1.1-3.5). ORs for all non-Hodgkin lymphoma and follicular lymphoma among women were decreased for COMT IVS1 701A>G [rs737865; variant allele: OR, 0.53; 95% CI, 0.34-0.82; OR, 0.42; 95% CI, 0.23-0.78, respectively]. Compared with never users of oral contraceptives, a 35% reduced risk was observed among oral contraceptive users in the total population. Reduced ORs for all non-Hodgkin lymphoma were observed with use of exogenous estrogens among genotyped women although 95% CIs included unity. These results suggest that PRL, CYP17A1, and COMT may be relevant genetic loci for non-Hodgkin lymphoma and indicate a possible role for prolactin and estrogen in lymphoma pathogenesis.
Evaluation of an iterative model–based reconstruction algorithm for low-tube-voltage (80 kVp) computed tomography angiography (2014)

The objective of this study was to investigate the improvement in diagnostic quality of an iterative model-based reconstruction (IMBR) algorithm for low-tube-voltage (80-kVp) and low-tube-current in abdominal computed tomography angiography (CTA). A total of 11 patients were imaged on a 256-slice multidetector computed tomography for visualization of the aorta. For all patients, three different reconstructions from the low-tube-voltage data are generated: filtered backprojection (FBP), IMBR, and a mixture of both [Formula: see text]. To determine the diagnostic value of IMBR-based reconstructions, the image quality was assessed. With IMBR-based reconstructions, image noise could be significantly reduced, which was confirmed by a highly improved contrast-to-noise ratio. In the image quality assessment, radiologists were able to reliably detect more third-order and higher aortic branches in the IMBR reconstructions compared to FBP reconstructions. The effective dose level was, on average, 3.0 mSv for 80-kVp acquisitions. Low-tube-voltage CTAs significantly improve vascular contrast as presented by others; however, this effect in combination with IMBR enabled yet another substantial improvement of diagnostic quality. For IMBR, a significant improvement of image quality and a decreased radiation dose at low-tube-voltage can be reported.
Inkjet printed electronics using copper nanoparticle ink (2010)

Inkjet printing of electrode using copper nanoparticle ink is presented. Electrode was printed on a flexible glass epoxy composite substrate using drop on demand piezoelectric dispenser and was sintered at 200 °C of low temperature in N2 gas condition. The printed electrodes were made with various widths and thickness. In order to control the thickness of the printed electrode, number of printing was varied. Resistivity of printed electrode was calculated from the cross-sectional area measured by a profilometer and resistance measured by a digital multimeter. Surface morphology of electrode was analyzed using scanning electron microscope (SEM) and atomic force microscope (AFM). From the study, it was found that 10 times printed electrode has the most stable grain structure and low resistivity of 36.7 nΩ m.
Figures S1-4 from A Novel, Fully Human Anti–fucosyl-GM1 Antibody Demonstrates Potent <i>In Vitro</i> and <i>In Vivo</i> Antitumor Activity in Preclinical Models of Small Cell Lung Cancer (2023)

&lt;p&gt;4 suppl figures on tumor models&lt;/p&gt;
Can Nutrition Play a Role in Ameliorating Digital Eye Strain? (2022)

Digital eye strain is a complex, multifactorial condition that can be caused by excessive screen time exposure to various electronic devices such as smartphones, tablets, e-readers, and computers. Current literature suggests oxidative damage concomitant with a chronic pro-inflammatory state represent significant etiopathogenic mechanisms. The present review aims to discuss the potential dietary role for micronutrients with nutraceutical properties to ameliorate various ocular and vision-related symptoms associated with digital eye strain. For ocular surface dysfunction, enhanced anti-inflammatory benefits with omega-3 polyunsaturated fatty acids have been well documented for treatment of dry eye disease. The anti-oxidative and immunosuppressive properties of anthocyanin phytochemicals may also confer protective effects against visually induced cognitive stress and digital asthenopia. Meanwhile, nutraceutical strategies involving xanthophyll macular carotenoids demonstrate enhanced cognitive functioning and overall visual performance that aids digital eye strain. Collectively, preliminary findings seem to offer a strong line of evidence to substantiate the need for additional randomized controlled trials aimed at treating digital eye strain with adjunctive nutraceutical strategies. Further RCT and comparisons on commercially available nutritional supplements are needed to quantify the clinical benefits.
Seedborne Fungal Contamination: Consequences in Space-Grown Wheat (1997)

Plants grown in microgravity are subject to many environmental stresses that may promote microbial growth and result in disease symptoms. Wheat (cv. Super Dwarf) recovered from an 8-day mission aboard a NASA (National Aeronautics and Space Administration) space shuttle showed disease symptoms, including girdling of leaf sheaths and chlorosis and necrosis of leaf and root tissues. A Neotyphodium species was isolated from the seed and leaf sheaths of symptomatic wheat used in the spaceflight mission. Certain isozymes of a peroxidase unique to extracts from the microgravity-grown plants were observed in extracts from earth-grown Neotyphodium-infected plants but were not present in noninfected wheat. The endophytic fungus was eliminated from the wheat seed by prolonged heat treatment at 50 degrees C followed by washes with water at 50 degrees C. Plants from wheat seed infected with the Neotyphodium endophyte were symptomless when grown under greenhouse conditions, whereas symptoms appeared after only 4 days of growth in closed containers. Disease spread from an infected plant to noninfected plants in closed containers. Dispersion via spores was found on asymptomatic plants at distances of 7 to 18 cm from infected plants. The size and shape of the conidia, mycelia, and phialide-bearing structures and the ability to grow rapidly on carbohydrates, especially xylose, resembled the characteristics of N. chilense, which is pathogenic on orchard grass, Doctylis glomerati. The Neotyphodium wheat isolate caused disease symptoms on other cereals (wheat cv. Malcolm, orchard grass, barley, and maize) grown in closed containers.
Investigation of the unidirectional spin heat conveyer effect in a 200 nm thin Yttrium Iron Garnet film (2016)

We have investigated the unidirectional spin wave heat conveyer effect in sub-micron thick yttrium iron garnet (YIG) films using lock-in thermography (LIT). Although the effect is small in thin layers this technique allows us to observe asymmetric heat transport by magnons which leads to asymmetric temperature profiles differing by several mK on both sides of the exciting antenna, respectively. Comparison of Damon-Eshbach and backward volume modes shows that the unidirectional heat flow is indeed due to non-reciprocal spin-waves. Because of the finite linewidth, small asymmetries can still be observed when only the uniform mode of ferromagnetic resonance is excited. The latter is of extreme importance for example when measuring the inverse spin-Hall effect because the temperature differences can result in thermovoltages at the contacts. Because of the non-reciprocity these thermovoltages reverse their sign with a reversal of the magnetic field which is typically deemed the signature of the inverse spin-Hall voltage.
Capillary sieving electrophoresis and micellar electrokinetic capillary chromatography produce highly correlated separation of tryptic digests (2010)

We perform 2-D capillary electrophoresis on fluorescently labeled proteins and peptides. Capillary sieving electrophoresis (CSE) was performed in the first dimension and MEKC was performed in the second. A cellular homogenate was labeled with the fluorogenic reagent FQ and separated using the system. This homogenate generated a pair of ridges; the first had essentially constant migration time in the CSE dimension, while the second had essentially constant migration time in the MEKC dimension. In addition, a few spots were scattered through the electropherogram. The same homogenate was digested using trypsin, and then labeled and subjected to the 2-D separation. In this case, the two ridges observed from the original 2-D separation disappeared and were replaced by a set of spots that fell along the diagonal. Those spots were identified using a local-maximum algorithm and each was fit using a 2-D Gaussian surface by an unsupervised nonlinear least squares regression algorithm. The migration times of the tryptic digest components were highly correlated (r=0.862). When the slowest migrating components were eliminated from the analysis, the correlation coefficient improved to r=0.956.
Highly accurate long-read HiFi sequencing data for five complex genomes (2020)

The PacBio<sup>®</sup> HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.