gebhart/patrepeval huggingface dataset:
Abstract B17: Validation of targeted gene expression profiling panel for identifying biomarker signatures of immunotherapy responders (2017)

Abstract Cancer immunotherapy has led to an unprecedented, long-lasting response in populations susceptible to the therapies. Despite the therapeutic potential, identifying biomarkers and stratifying populations that are likely to respond has been a challenge. Gene expression profiling has previously been successfully used to stratify individuals based on survival and treatment characteristics, but there exist limitations with the prevalent technologies. In particular, full transcriptome gene expression estimates use limited biological material to measure the concentrations of tens of thousands uninformative genes and often lack the depth required to accurately measure expression levels of lowly-expressed genes. These genes may be critical to the identification of a signature associated with immunotherapy responders. To efficiently measure the expression of the key genes potentially informative of an immunotherapy response, we developed a high-throughput targeted gene expression solution measured by our RNA Ion Oncomine Immune Response Profiling panel* containing 395 genes. This panel provides information about the expression of genes involved in tumor checkpoint inhibition (including CTLA4, PD-1, PD-L1, OX-40, 4-1BB, TIM3, LAG3) and other targets such as CSF1R, and IDO1, as well as additional markers of T cell signaling pathway, interferon signaling, and markers of tumor infiltrating lymphocytes (TIL). We used publicly available TCGA data to demonstrate the need and develop a solution for a new normalization procedure that allows for accurate comparisons of samples within various cancer types. Furthermore, we verified a linear and unbiased estimate of fold change in our assays across mixing concentrations of a cell-line titration experiment. Finally, by achieving a high correlation (r &amp;gt; .99) of technical replicates, along with robust expression estimation even at low input amounts (10 ng RNA), our panel offers a valuable solution for biomarker research in cancer immunotherapy. *For research use only. Not for use in diagnostic procedures. Citation Format: Aleksandr Pankov, Yongming Sun, Yuan-Chieh Ku, Warren Tom, Jianping Zheng, Timothy Looney, Janice Au-Yong, Fiona Hyland, Ann Mongan. Validation of targeted gene expression profiling panel for identifying biomarker signatures of immunotherapy responders. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr B17.
Dopage laser en microélectronique (2006)

Les procds de recuit et de dopage laser du silicium ont t tudis de manire intensive au cours des prcdentes dcennies. Ces tudes ont d'ores et dj permis un transfert technologique pour la fabrication des semiconducteurs. Cependant les futures gnrations CMOS vont ncessiter des techniques de dopage encore plus fines, capable de fabriquer les jonctions ultra-minces dcrites dans la "roadmap" de l'ITRS (International Technology Roadmap for Semiconductors). Ce papier dcrit des rsultats rcents obtenus dans le cadre du RMNT DOLAMI consacr au dopage laser de jonctions ultra-minces, ainsi que des applications du dopage laser pour les microtechnologies lies la fabrication de MEMS.
Functional Site in α-Lactalbumin Encompasses a Region Corresponding to a Subsite in Lysozyme and Parts of Two Adjacent Flexible Substructures (1996)

Aromatic cluster 1 of alpha-lactalbumin (LA), a substructure adjacent to the cleft, is important for its interaction with galactosyltransferase (GT) and effects on glucose binding in the lactose synthase complex [Grobler, J. A., Wang, M., Pike, A. K., & Brew, K. (1994) J. Biol. Chem. 269, 5106-5114]. The full extent of the functional region in LA has been probed by mutagenesis of residues that are near aromatic cluster 1 or within the cleft that corresponds to the active site in the homologous type c lysozymes. The conserved residues Val42, Gln54, and Ile59, which correspond to residues of lysozyme that act in substrate binding in subsites C to E, together with residues adjacent to aromatic cluster 1, were found to be not required for activity. In contrast, replacing Leu110, a component of the region corresponding to lysozyme subsite F, with His or Glu greatly reduces the affinity of LA for GT while the introduction of Arg lowers the synergism of LA and glucose binding to GT and also reduces the affinity of LA for GT. Substitutions for Ala106, which is adjacent to Leu110 in the structure, also perturb activity. The region of the cleft corresponding to subsite F is important for function in LA as well as in lysozyme since other components of this subsite, His32 and Phe31, are also crucial for LA activity. The qualitatively different effects of various substitutions for Leu110 may be mediated by their influence on His32 or by changes in the structure of the lactose synthase complex.
Quantitative Precipitation Estimation of the Epic 2013 Colorado Flood Event: Polarization Radar-Based Variational Scheme (2016)

Abstract The accuracy of rain-rate estimation using polarimetric radar measurements has been improved as a result of better characterization of radar measurement quality and rain microphysics. In the literature, a variety of power-law relations between polarimetric radar measurements and rain rate are described because of the dynamic or varying nature of rain microphysics. A variational technique that concurrently takes into account radar observational error and dynamically varying rain microphysics is proposed in this study. Rain-rate estimation using the variational algorithm that uses event-based observational error and background rain climatological values is evaluated using observing system simulation experiments (OSSE), and its performance is demonstrated in the case of an epic Colorado flood event. The rain event occurred between 11 and 12 September 2013. The results from OSSE show that the variational algorithm with event-based observational error consistently estimates more accurate rain rate than does the “ R ( Z HH , Z DR )” power-law algorithm. On the contrary, the usage of ad hoc or improper observational error degrades the performance of the variational method. Furthermore, the variational algorithm is less sensitive to the observational error of differential reflectivity Z DR than is the R ( Z HH , Z DR ) algorithm. The variational quantitative precipitation estimation (QPE) retrieved more accurate rainfall estimation than did the power-law dual-polarization QPE in this particular event, despite the fact that both algorithms used the same dual-polarization radar measurements from the Next Generation Weather Radar (NEXRAD).
Riboregulation in Escherichia coli : DsrA RNA acts by RNA:RNA interactions at multiple loci (1998)

DsrA is an 87-nt untranslated RNA that regulates both the global transcriptional silencer and nucleoid protein H-NS and the stationary phase and stress response sigma factor RpoS (σ s ). We demonstrate that DsrA acts via specific RNA:RNA base pairing interactions at the hns locus to antagonize H-NS translation. We also give evidence that supports a role for RNA:RNA interactions at the rpoS locus to enhance RpoS translation. Negative regulation of hns by DsrA is achieved by the RNA:RNA interaction blocking translation of hns RNA. In contrast, results suggest that positive regulation of rpoS by DsrA occurs by formation of an RNA structure that activates a cis -acting translational operator. Sequences within DsrA complementary to three additional genes, argR , ilvIH , and rbsD , suggest that DsrA is a riboregulator of gene expression that acts coordinately via RNA:RNA interactions at multiple loci.
Eszopiclone Treatment for Insomnia (2012)

Eszopiclone 3 mg is an effective treatment for insomnia across 5 clinically diverse patient populations; however, magnitude of effect is mediated by underlying comorbidity and their treatments, with largest measures of effect seen in primary insomnia and lowest in MDD and GAD. These consistent results, and the fact that clinical trials were conducted in patients being treated as appropriate for their comorbid clinical conditions, support the results' real-world generalizability and utility to clinical practice.
Supplementary Notes from Classification of Proliferative Pulmonary Lesions of the Mouse (2023)

Supplementary Notes from Classification of Proliferative Pulmonary Lesions of the Mouse
Structured Mo/Si multilayers for IR-suppression in laser-produced EUV light sources (2013)

Laser produced plasma sources are considered attractive for high-volume extreme-ultraviolet (EUV) lithography because of their high power at the target wavelength 13.5 nm. However, besides the required EUV light, a large amount of infrared (IR) light from the CO<sub>2</sub> drive laser is scattered and reflected from the plasma as well as from the EUV mirrors in the optical system. Since these mirrors typically consist of molybdenum and silicon, the reflectance at IR wavelengths is even higher than in the EUV, which leads to high energy loads in the optical system. One option to reduce this is to structure the EUV multilayer, in particular the collector mirror, with an IR grating that has a high IR-suppression in the zeroth order. In this paper, the characterization of such an optical element is reported, including the IR-diffraction efficiency, the EUV performance (reflectance and scattering), and the relevant surface roughness. The measurement results are directly linked to the individual manufacturing steps.
Multi-institutional randomized control study of haemolysis in stored red cell units prepared manually or by an automated system (2010)

The data reported in this study suggest a link between the specific whole blood donor and the haemolysis levels observed in red-blood-cell units stored refrigerated for 42 days. Additional research to identify possible donor characteristics associated with haemolysis during storage is warranted.
Discrete tracking system for slow FH. I. Algorithms with distributed synchronization group (1991)

A novel approach to slow frequency hopping (FH) spread-spectrum signal tracking is presented and analyzed. This approach is based on utilization of additional synchronization data carrying information for FH signal tracking purposes which is added to the digital data stream. Using a renewal process model, the steady-state probability mass function for the phase error process is derived, along with expressions for the tracking error variance, and the mean time to lose lock. Results are presented for several different tracking algorithms and a rough comparison with a standard early-late gate tracking loop is made.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Physical Activity in Elderly Subjects with Impaired Glucose Tolerance and Newly Diagnosed Diabetes Mellitus (1999)

The authors carried out a study to investigate the association between different indicators of physical activity and the prevalence of impaired glucose tolerance (IGT) and newly diagnosed diabetes (nDM) in a population-based cohort of elderly men and women in the Netherlands. A sample of participants of the Rotterdam Study (n = 1,016) aged 55-75 years who were not known to have diabetes mellitus underwent an oral glucose tolerance test. Physical activity was assessed by means of a self-administered questionnaire and expressed as time spent on activities per week. Associations with the prevalence of IGT and nDM were assessed by logistic regression analysis after adjustment for age, body mass index, waist-hip ratio, family history of diabetes, and smoking. A total of 745 subjects had normal glucose tolerance, 153 IGT, and 118 nDM. The total amount of time spent on physical activity decreased with increasing glucose intolerance. Adjusted for main confounders, vigorous activities such as bicycling (men: odds ratio (OR) = 0.26, 95% confidence interval (CI) 0.14-0.49; women: OR = 0.37, 95% CI 0.18-0.78) and sports (men: OR = 0.28, 95% CI 0.11-0.74) showed an inverse association with the presence of nDM. For IGT, the associations pointed in the same direction but did not reach statistical significance. These results indicate that physical inactivity and glucose intolerance are associated among older adults similar to the way they are associated among middle-aged adults.
ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions -- V. Hierarchical fragmentation and gas dynamics in IRDC G034.43+00.24 (2021)

We present new 3-mm continuum and molecular lines observations from the ATOMS survey towards the massive protostellar clump, MM1, located in the filamentary infrared dark cloud (IRDC), G034.43+00.24 (G34). The lines observed are the tracers of either dense gas (e.g. HCO+/H13CO+ J = 1-0) or outflows (e.g. CS J = 2-1). The most complete picture to date of seven cores in MM1 is revealed by dust continuum emission. These cores are found to be gravitationally bound, with virial parameter, $\alpha_{vir}<2$. At least four outflows are identified in MM1 with a total outflowing mass of $\sim 45 M_\odot$, and a total energy of $\sim 1\times 10^{47}$ erg, typical of outflows from a B0-type star. Evidence of hierarchical fragmentation, where turbulence dominates over thermal pressure, is observed at both the cloud and the clump scales. This could be linked to the scale-dependent, dynamical mass inflow/accretion on clump and core scales. We therefore suggest that the G34 cloud could be undergoing a dynamical mass inflow/accretion process linked to the multiscale fragmentation, which leads to the sequential formation of fragments of the initial cloud, clumps, and ultimately dense cores, the sites of star formation.
Stimulatory effect ofCeriops tagalon hexose uptake in L6 muscle cells in culture (2008)

The ethanolic extracts of a mangrove plant Ceriops tagal (Family Rhizophoraceae) and its sequential fractions thereof were studied for their effect on 3H-2-deoxyglucose uptake by L6 rat muscle cells cultured to the myotube stage. Among these, the n-hexane soluble fraction of ethanolic extract of the leaves of C. tagal enhanced 3H-2-deoxyglucose uptake even at 2 microg mL(-1) concentration with half maximum activity at 10 microg mL(-1), comparable with insulin (1 microM) and metformin (400 microM). This enhancement in glucose uptake was found to be insulin independent and in contrast to insulin, its effect was also prevalent in undifferentiated myoblasts. It may be concluded from the results that n-hexane soluble fraction of ethanolic extract of C. tagal have the property to stimulate the glucose uptake, which might be a useful source for the isolation of new antihyperglycemic compounds.
Stilbenes as κ-Selective, Non-nitrogenous Opioid Receptor Antagonists (2014)

The natural stilbene pawhuskin A has been shown to function as an opioid receptor antagonist, with preferential binding to the κ receptor. This finding encouraged assembly of a set of analogues to probe the importance of key structural features. Assays on these compounds determined that one (compound 29) shows potent opioid receptor binding activity and significantly improved selectivity for the κ receptor. These studies begin to illuminate the structural features of these non-nitrogenous opioid receptor antagonists that are required for activity.
Purification and properties of geranylgeranyl-diphosphate synthase from bovine brain. (1994)

Geranylgeranyl-diphosphate synthase was purified to homogeneity from bovine brain in a one-step procedure employing an affinity column. For the construction of the affinity column, a farnesyl diphosphate analog, O-(6-amino-1-hexyl)-P-farnesylmethyl phosphonophosphate, was synthesized and linked to the spacer of the matrix of Affi-Gel 10 via the amino group. The native enzyme appeared to be a homooligomer (150-195 kDa) with a molecular mass of the monomer of 37.5 kDa. The pI for the enzyme was 6.2. The Km values for dimethylallyl diphosphate, geranyl diphosphate, and farnesyl diphosphate were estimated to be 33, 0.80, and 0.74 microM, respectively. The Km value for isopentenyl diphosphate in the reaction with isopentenyl diphosphate and farnesyl diphosphate was 2 microM. The reaction velocities for the formation of geranylgeranyl diphosphate from dimethylallyl diphosphate, geranyl diphosphate, and farnesyl diphosphate were in the ratio of 0.004:0.145:1. The intermediate farnesyl diphosphate was formed in the reaction with geranyl diphosphate as an allylic primer. Geranylgeranyl diphosphate acted as a competitive inhibitor against farnesyl diphosphate with an approximate Ki value of 1.2 microM in the condensation reaction of farnesyl diphosphate with isopentenyl diphosphate. Farnesyl-diphosphate synthase catalyzing the formation of farnesyl diphosphate from dimethylallyl diphosphate and isopentenyl diphosphate was also purified to homogeneity from the same organ by similar affinity chromatography using a geranyl diphosphate analog, O-(6-amino-1-hexyl)-P-geranylmethyl phosphonophosphate, as a ligand. This enzyme was a homodimer with a monomeric molecular mass of 40.0 kDa. These results indicate that geranylgeranyl diphosphate, a lipid precursor for the biosynthesis of a majority of prenylated proteins, is synthesized from dimethylallyl diphosphate and isopentenyl diphosphate by the action of farnesyl-diphosphate synthase catalyzing the reaction of C5-->C15, followed by the action of geranylgeranyl-diphosphate synthase catalyzing a single reaction of C15-->C20, and that geranylgeranyl diphosphate can down-regulate its own synthesis through the inhibition of the geranylgeranyldiphosphate synthase action.
On dynamic malware payloads aimed at programmable logic controllers (2011)

With the discovery of the Stuxnet attack, increasing at-tention is being paid to the potential for malware to target Programmable Logic Controllers (PLCs). Despite much speculation about threats from PLC malware, the popu-lar opinion is that automated attacks against PLCs are not practical without having a priori knowledge of the target physical process. In this paper, we explore the problem of designing PLC malware that can generate a dynamic payload based on observations of the process taken from inside the control system. This significantly lowers the bar for attacks against PLCs. We evaluate how PLC mal-ware may infer the structure of the physical plant and how it can use this information to construct a dynamic payload to achieve an adversary’s end goal. We find that at the very least, a dynamic payload can be constructed that causes unsafe behavior for an arbitrary process defi-nition. 1
ATOMIC SPECTROSCOPY WITH OPTOGALVANIC DETECTION (1983)

This paper deals with the application of the optogalvanic effect (the impedance change in a feebly electrically excited gas or metal vapour due to the absorption of an irradiating light) in atomic spectroscopy. This impedance change is easily recorded and provides a simple non-optical detector to measure the modification of the atomic level populations under the radiative absorption process. Associated with the advent of the tunable dye laser, the optogalvanic detection provides a valuable spectroscopic tool to investigate the atomic structure properties from the excited levels, mainly for high lying Rydberg level studies. Use of the hollow-cathode lamp as a sputtering device to generate atomic vapours, opens the future to this method for studying refractory elements.
Health Monitoring Method for Load Assessment and Cooling Performance Degradation of Printed Circuit Boards (2010)

Health monitoring technologies, which can evaluate the performance degradation, load history and degree of fatigue, have the potential to improve the maintenance, the reliability design method and the availability in improper use conditions of electronic equipment. In this paper, we propose a method to assess the cooling performance degradation and load history of printed circuit boards in electronic equipment by use of a hierarchical Bayes model based on CAE (Computer Aided Engineering) results of thermal stress simulation and experiment data from actual measurements. We applied this method to a notebook PC that can monitor the device load factor and revolution number of cooling fan. It is shown that this method can estimate the temperature and deformation distribution of the printed circuit board from monitoring variables through latent variables such as thermal dissipation of the device and thermal boundary condition by use of the hierarchical Bayes model. And it is confirmed that the statistical load assessment concerning thermal cyclic load and the maximum load distribution can be conducted using the estimated temperature and deformation data. We verified that the cooling performance degradation can be assessed, if the temperature difference per unit thermal value between two suitable points on the printed circuit board can be obtained. Furthermore, we attempted the estimation method based on the hierarchical Bayes model to dynamic load assessment such as cyclic drop impact for PCB. The assessment method for the strain range distribution of the solder joints on the PCB was conducted to lead to the conservative results for reliability design. It is concluded that the proposed method can be effective to assess the field load history and cooling performance degradation.
The Patient’s Point of View: COVID-19 and Neuroendocrine Tumor Disease (2022)

The assessment of cancer patient care during the COVID-19 pandemic has been mainly reported from a physician's perspective. Patients with rare tumor entities such as neuroendocrine tumors (NET), which require a complex and specialized care infrastructure, were highly affected by the COVID-19 crisis. Using a structured questionnaire consisting of a general section on the disease and a special COVID-19 section to record medical care, vaccination behavior as well as social and psycho-emotional parameters were collected from NET patients. The survey was distributed via direct medical contact and via the patient organization NETZWERK NeT. A total of 684 patients participated in the survey and 79.2% (<i>n</i> = 542) of the participants answered the questionnaire completely (54 questions). Patient characteristics were comparable to those in large NET registries. The majority of participants were patients with pancreatic and small bowel NET on somatostatin analogue (SSA) therapy. Medical care under COVID-19 was adequate and appointment cancellations and postponements were not common. Nevertheless, the majority of patients were worried about adequate treatment for their tumor disease during the crisis. Most of the participants considered themselves to be at risk of severe COVID-19 infection and were therefore very concerned. This was accompanied by an extremely high vaccination readiness rate of 90%. Increased distress in the social and psycho-emotional domains in the course of the crisis reflected a need for optimization in the medical care of NET patients, although the rate of COVID-19 positive participants was low (3.7%). Therefore, patient-reported measurements are required to identify and address all areas of medical care. Overall, our survey provides an essential contribution to the care of NET patients during the COVID-19 pandemic from the patient's perspective.