gebhart/patrepeval huggingface dataset:
Susceptibility Loci Associated with Prostate Cancer Progression and Mortality (2010)

Abstract Purpose: Prostate cancer is a heterogenous disease with a variable natural history that is not accurately predicted by currently used prognostic tools. Experimental Design: We genotyped 798 prostate cancer cases of Ashkenazi Jewish ancestry treated for localized prostate cancer between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to clinical data. The survival analysis was adjusted for Gleason score and prostate-specific antigen. We investigated associations between 29 single nucleotide polymorphisms (SNP) and biochemical recurrence, castration-resistant metastasis, and prostate cancer–specific survival. Subsequently, we did an independent analysis using a high-resolution panel of 13 SNPs. Results: On univariate analysis, two SNPs were associated (P &amp;lt; 0.05) with biochemical recurrence, three SNPs were associated with clinical metastases, and one SNP was associated with prostate cancer–specific mortality. Applying a Bonferroni correction (P &amp;lt; 0.0017), one association with biochemical recurrence (P = 0.0007) was significant. Three SNPs showed associations on multivariable analysis, although not after correcting for multiple testing. The secondary analysis identified an additional association with prostate cancer–specific mortality in KLK3 (P &amp;lt; 0.0005 by both univariate and multivariable analysis). Conclusions: We identified associations between prostate cancer susceptibility SNPs and clinical end points. The rs61752561 in KLK3 and rs2735839 in the KLK2-KLK3 intergenic region were strongly associated with prostate cancer–specific survival, and rs10486567 in the 7JAZF1 gene were associated with biochemical recurrence. A larger study will be required to independently validate these findings and determine the role of these SNPs in prognostic models. Clin Cancer Res; 16(10); 2819–32. ©2010 AACR.
Joint Channel Estimation and Data Transmission: Achievable Rates (2007)

A formulation for a joint communication and estimation problem is proposed: simultaneous communication over a noisy channel and estimation of certain channel parameters are desired. We are interested in quantifying the tradeoff between the achievable rate and distortion in estimating the channel parameters. Two particular sample channels are considered and achievable rates for these channels are determined. First, the binary symmetric channel is examined; an achievable capacity-distortion tradeoff is derived for both joint and time-orthogonal protocols. For the flat fading, additive, white, Gaussian noise channel, a novel joint communication and estimation scheme using low correlation sequences is presented. It is observed that in most situations, joint communication and estimation performs better than a scheme where communication and estimation are performed individually, furthermore, the gains of joint communication and estimation over individual communication and estimation can be significant as the distortion tolerance increases. Finally, it is observed that even a slight tolerance to errors in the channel parameters close to the theoretical lower bounds yield significant improvements in the rate at which reliable communication is achievable.
Resonant Behavior and Selective Switching of Stop Bands in Three-Dimensional Photonic Crystals with Inhomogeneous Components (2007)

We demonstrate that, in contrast with the well-studied photonic crystals consisting of two homogeneous components, photonic crystals comprised of inhomogeneous or multiple (three or more) components may bring new opportunities to photonics due to the discovered quasiperiodic resonant behavior of their (hkl) stop bands as a function of the reciprocal lattice vector. A resonant stop band cannot be switched off for any permittivity of structural components. Tuning the permittivity or structural parameters allows the selective on-off switching of nonresonant (hkl) stop bands. This independent manipulation of light at different Bragg wavelengths provides a new degree of freedom to design selective optical switches and waveguides. Transmission experiments performed on synthetic opals confirmed the theoretical predictions.
Acute radiation esophagitis in a phase I dose-escalation trial evaluating helical tomotherapy for inoperable non-small cell lung cancer (NSCLC) (2007)

7694 Background: In an attempt to improve the poor local control in patients with locally advanced and medically inoperable lung cancer we investigated helical tomotherapy as a means to decrease radiation dose to critical normal structures while escalating tumor dose. Methods: Thirty-six patients with Stage I-IV NSCLC requiring definitive radiotherapy and judged not to be surgical candidates due to medical comorbidities or advanced tumor stage were enrolled in this phase I trial. Chemotherapy was given sequentially but not allowed concurrently. Pts were placed in 1 of 4 dose-per-fraction bins, all treated for 25 fractions, with dose per fraction ranging from 2.28 to 3.22 Gy. Bins were calculated to yield normalized total dose (NTD) equivalents in 2 Gy fractions of 60–100 Gy. Dose escalation limiting constraints included esophageal maximum NTD, lung NTD mean, and esophageal effective volume (V eff ). Radiotherapy was limited to the primary site and clinically proven or suspicious nodal regions. Elective nodal irradiation (ENI) was not performed. A graded-response logistic regression analysis was performed to identify dosimetric and clinical factors associated with esophagitis. Results: No grade 3 (CTCAE v3.0 and RTOG) acute esophageal toxicities were observed. Only 6 patients (16.7%) required narcotic analgesia (RTOG gr. 2 toxicity). Average mean NTD dose to the esophagus (D mean )=15.3 Gy. Average volume of the esophagus receiving NTD 55 Gy (V 55 )=3.65%. Both D mean and V 55 were significantly associated with the grade of esophagitis, with P- values of 0.018 and 0.010, respectively. In this limited series, there was no significant effect of sequential chemotherapy, in agreement with previous studies. Conclusions: 1) Acute esophageal toxicity was minimal despite dose escalation via helical tomotherapy for inoperable NSCLC cancer. 2) The observed significant associations between V 55 , D mean , and grade of esophagitis validate improved dose distribution as a strategy to permit radiation dose escalation. Pending acceptable rates of radiation pneumonitis the addition of concurrent chemotherapy is anticipated. Supported by NIH Grant CA-88960. No significant financial relationships to disclose.
Aggregation, pretransitional behavior, and optical properties in the isotropic phase of lyotropic chromonic liquid crystals studied in high magnetic fields (2013)

We report results on the high-field magneto-optical response of four aqueous, lyotropic, chromonic liquid crystal formulations in the isotropic phase. Measurements of the field-induced birefringence at temperatures above the isotropic-nematic coexistence region at high magnetic fields reveal qualitative differences in different materials; these differences can be attributed to the nature of aggregation and are discussed within the context of competing aggregation models. Extending these measurements to very high fields and large optical phase differences reveals the presence of an unexpected optical phenomenon: magnetic field-induced circular birefringence, measured in the Voigt geometry, in a system containing no molecularly chiral species. Possible origins of this effect are discussed.
Synthesis of a Novel Zeolite through a Pressure‐Induced Reconstructive Phase Transition Process (2013)

Durch Druckeinwirkung auf den herkömmlichen Zeolith ITQ-29 gelang erstmals die druckinduzierte Festphasensynthese eines Zeoliths (siehe Schema; Si gelb, O rot): Das Produkt, ITQ-50, hat eine einzigartige mikroporöse Struktur und ist leistungsfähiger in der Propen-Propan-Trennung als das Ausgangsmaterial ITQ-29. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Synthesis and Structure—Activity Relationships of Isoxazole Carboxamides as Growth Hormone Secretagogue Receptor Antagonists. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Clinical Characterization of Familial Isolated Pituitary Adenomas (2006)

Homogeneous and heterogeneous expression of prolactinomas, somatotropinomas, NS, and Cushing's disease can occur within families in the absence of MEN1/CNC. FIPA and sporadic cases have differing clinical characteristics. FIPA may represent a novel endocrine neoplasia classification that requires further genetic characterization.
Decoding in hyperbolic spaces: quantum LDPC codes with linear rate and efficient error correction (2014)

We analyze the four dimensional toric code in a hyperbolic space and show that it has a classical error correction procedure which runs in almost linear time and can be parallelized to almost constant time, giving an example of a quantum LDPC code with linear rate and efficient error correction.
ChemInform Abstract: ELECTRONIC STRUCTURES AND SPECTRA OF TRINUCLEAR CARBONYL COMPLEXES (1979)

Abstract Genaue experimentelle Untersuchungen der Elektronenspektren der dreikernigen Metallcarbonyle M3(CO)12, M: Ru, 0s, Fe; FeRu 2 (CO) 12 , Ru3(CO)9L3, L: PPh 3 , PEtPh 2 , FeM 2 (CO) 14 , M: Mn, Re und MnFeRe(CO) 14 werden angestellt.
Retrofit device to improve vapor compression cooling system performance by dynamic blower speed modulation (2023)

A device and method are provided to improve performance of a vapor compression system using a retrofittable control board to start up the vapor compression system with the evaporator blower initially set to a high speed. A baseline evaporator operating temperature with the evaporator blower operating at the high speed is recorded, and then the device detects if a predetermined acceptable change in evaporator temperature has occurred. The evaporator blower speed is reduced from the initially set high speed as long as there is only a negligible change in the measured evaporator temperature and therefore a negligible difference in the compressor's power consumption so as to obtain a net increase in the Coefficient of Performance.
MP71-12 GENOMIC CHARACTERIZATION OF SARCOMATOID TRANSFORMATION IN CLEAR CELL RENAL CELL CARCINOMA (2016)

site (p0.0205). Table
Density Functional Theory Study of the Adsorption of Nitrogen and Sulfur Atoms on Gold (111), (100), and (211) Surfaces (2011)

Nitrogen and sulfur atom adsorption on flat and stepped gold surfaces are examined by density functional theory. With detailed investigation of adatom location on the (111), (100), and (211) gold surfaces, nitrogen and sulfur atom adsorption are compared with reference to previous work on the oxygen/gold system. Sulfur adsorbed most strongly, followed by oxygen and nitrogen. The results demonstrate the preference for 3-fold over 2-fold and single-fold adatom coordination as well as the role of low coordinated gold surface atoms in increasing the adsorption energy for nitrogen, sulfur, and oxygen atoms. Pseudopotential curves, calculated adsorption energy as a function of surface position, and nudged-elastic band calculations explored adatom diffusion along the surface. The results indicated limited diffusion on the (111) and (211) surfaces. On the other hand, while nitrogen and sulfur atoms remained localized on the (100) surface, oxygen atoms showed facile diffusion. These results provide a reference for the interaction of nitrogen, sulfur, and oxygen adatoms with gold nanoparticles that project faces similar to the surfaces studied here.
Regolith and Environment Science and Oxygen and Lunar Volatile Extraction (RESOLVE): Lunar Advanced Volatile Analysis (LAVA) Capillary Fluid Dynamic Restriction Effects on Gas Chromatography (2015)

The Resource Prospector (RP) mission with the Regolith and Environment Science and Oxygen Lunar Volatile Extraction (RESOLVE) payload aims to show the presence of water in lunar regolith, and establish a proving ground for NASAs mission to Mars. One of the analysis is performed by the Lunar Advanced Volatiles Analysis (LAVA) subsystem, which consists of a fluid network that facilitates the transport of volatile samples to a gas chromatograph and mass spectrometer (GC-MS) instrument. The understanding of fluid dynamics directed from the GC to the MS is important due to the influence of flow rates and pressures that affect the accuracy of and prevent the damage to the overall GC-MS instrument. The micro-scale capillary fluid network within the GC alone has various lengths and inner-diameters; therefore, determination of pressure differentials and flow rates are difficult to model computationally, with additional complexity from the vacuum conditions in space and lack of a lunar atmosphere. A series of tests were performed on an experimental set-up of the system where the inner diameters of the GC transfer line connecting to the MS were varied. The effect on chromatography readings were also studied by applying these lines onto a GC instrument. It was found that a smaller inner diameter transfer line resulted in a lower flow rate, as well as a lower pressure differential across the thermal conductivity detector (TCD) unit of the GC and a negligible pressure drop across the mock-up capillary column. The chromatography was affected with longer retention times and broader peak integrations. It was concluded that a 0.050 mm inner diameter line still proved most suitable for the systems flow rate preferences. In addition, it was evident that this small transfer line portrayed some expense to GC signal characteristics and the wait time for steady-state operation.
Measuring KS0K± interactions using Pb–Pb collisions at sNN=2.76 TeV (2017)

We present the first ever measurements of femtoscopic correlations between the KS0 and K± particles. The analysis was performed on the data from Pb–Pb collisions at sNN=2.76 TeV measured by the ALICE experiment. The observed femtoscopic correlations are consistent with final-state interactions proceeding via the a0(980) resonance. The extracted kaon source radius and correlation strength parameters for KS0K− are found to be equal within the experimental uncertainties to those for KS0K+. Comparing the results of the present study with those from published identical-kaon femtoscopic studies by ALICE, mass and coupling parameters for the a0 resonance are tested. Our results are also compatible with the interpretation of the a0 having a tetraquark structure instead of that of a diquark.
Rollover Crash Sensing and Safety Overview (2004)

&lt;div class="htmlview paragraph"&gt;This paper provides an overview of rollover crash safety, including field crash statistics, pre- and rollover dynamics, test procedures and dummy responses as well as a bibliography of pertinent literature. Based on the 2001 Traffic Safety Facts published by NHTSA, rollovers account for 10.5% of the first harmful events in fatal crashes; but, 19.5% of vehicles in fatal crashes had a rollover in the impact sequence. Based on an analysis of the 1993-2001 NASS for non-ejected occupants, 10.5% of occupants are exposed to rollovers, but these occupants experience a high proportion of AIS 3-6 injury (16.1% for belted and 23.9% for unbelted occupants). The head and thorax are the most seriously injured body regions in rollovers.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper also describes a research program aimed at defining rollover sensing requirements to activate belt pretensioners, roof-rail airbags and convertible pop-up rollbars. The work required an understanding of the most relevant conditions for field rollovers, vehicle responses and occupant kinematics in the vehicle. The most common rollovers involve a soil trip, fall-over and curb trip. These conditions were simulated in laboratory tests where measurements were made with rate gyros, accelerometers and instrumented dummies. Cross-plots of vehicle roll rate and angle were used to consider triggering requirements for safety systems and to determine the timing of occupant motion in the vehicle. Some rollovers require triggering of safety systems when the vehicle has only a 10°-20° roll angle because roll angular velocities exceed 100°/s.&lt;/div&gt;
An accurate and reproducible discrimination tool for inflammatory bowel disease subtype using genetics, serologies, and smoking status (2011)

Distinguishing Crohn's disease (CD) from ulcerative colitis (UC) can be difficult in up to 10% of inflammatory bowel disease (IBD) patients. Predicting highly morbid inflammatory bowel disease outcomes in this group of patients is a major clinical challenge and current risk stratification strategies are suboptimal. We hypothesized that genotype data, serologic assays, and smoking status—all objective data-points that discriminate CD from UC—could be used simultaneously to produce a highly accurate and reproducible tool for IBD diagnosis and risk stratification. Employing a reference population of 2509 non-IBD controls, a training cohort of 3171 IBD patients, and two validation cohorts totaling 1767 IBD patients, we fit genotype data from 100 confirmed IBD loci, tobacco smoking status, and serologic-based biomarkers into models designed to discriminate CD from UC. Using a physician diagnosis of CD or UC as the gold standard, we generated receiver-operator-characteristic curves and compared the area under the curve (AUC) as a measure of model performance. We then assessed the ability of the model to predict CD in 20 “class switchers” (SW) who initially received a diagnosis of UC but were subsequently found to have CD, mostly post-colectomy. Wilcoxon rank sum tests were used to detect differences in raw results between the SW group and the UC group. The AUC's for a genetics-only model and for a serology-only model was 0.74 and 0.84 respectively in the validation cohort. A discrimination model trained on genetics, serologic markers, and smoking status in unison had an AUC of 0.95 in the training dataset and 0.92 in the independent validation cohort. The model correctly identified “CD” in 16/20 SW patients (80%, p=5.8×10-9) who were found to have CD with small bowel involvement. In a subset of these patients, it correctly identified “CD” in 13/14 (93%, p=2.2×10-16) of SW patients who subsequently developed internal-penetrating and/or stricturing CD. We have developed an accurate and reproducible model for the discrimination of CD from UC built exclusively from objective molecular inputs with the addition of smoking status. Further, we have preliminarily shown that this model performs well in precisely the types of patients for which a risk stratification test would most directly benefit—those who may have poor surgical outcomes. Taken together, we believe that prospective validation of this discrimination model in larger numbers of high-risk IBD patients is warranted.
Performance of XIPS Electric Propulsion in On-orbit Station Keeping of the Boeing 702 Spacecraft (2002)

Five years after its initial launch and with over 70 units in use on 18 satellites, Xenon Ion Propulsion (XIPS) has become the premier technology for on-orbit station keeping of commercial communications satellites. The latest in XIPS technology, the 25 cm thruster, is used on the Boeing 702 satellites, which were first launched in December 1999. The Boeing 702 25 cm XIPS system uses nominally 4.5 kW of power for “high power” orbit raising and 2.2 kW of power for “low power” station keeping. The 25 cm XIPS system provides 100% of the in-orbit propulsion requirements for the 702 spacecraft, including drift, eccentricity and inclination control in addition to momentum dumping. The 25 cm XIPS systems have accumulated to date over 7000 hours of operation on five spacecraft with daily reproducible, reliable inorbit performance.
Characterization of phenotypic and genotypic diversity in subclones derived from a clonal cell line (2018)

Regulatory guidelines require the sponsors to provide assurance of clonality of the production cell line, and when such evidence is not available, additional studies are typically required to further ensure consistent long-term manufacturing of the product. One potential approach to provide such assurance of clonal derivation of a production cell line is to characterize subclones generated from the original cell line and assess their phenotypic and genotypic similarity with the hypothesis that cell lines derived from a clonal bank will share performance, productivity and product quality characteristics. In this study, a production cell line that was cloned by a validated FACS approach coupled with day 0 imaging for verification of single-cell deposition was subcloned using validated FACS and imaging methods. A total of 46 subclones were analyzed for growth, productivity, product quality, copy number, and integration site analysis. Significant diversity in cell growth, protein productivity, product quality attributes, and copy number was observed between the subclones, despite stability of the parent clone over time. The diversity in protein productivity and quality of the subclones were reproduced across time and production scales, suggesting that the resulting population post sub-cloning originating from a single cell is stable but with unique properties. Overall, this work demonstrates that the characteristics of isolated subclones are not predictive of a clonally derived parental clone. Consequently, the analysis of subclones may not be an effective approach to demonstrate clonal origin of a cell bank. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:613-623, 2018.
Plasmonic-chip Enhanced Fluorescence Biosensor in the Back Illumination System (2020)

The plasmonic chip which has wavelength-size grating pattern coated with a thin silver or gold film is applied to a sensitive biosensor because it can provide the enhanced fluorescence excited by the surface plasmon field. We have already reported on the sensitive immunodetection with the plasmonic sensor chip under the illumination system from top panel of a plasmonic chip. In this study, the structure of a biosensor chip was optimized for the illumination system from rear panel and the detection sensitivity of the system under the back illumination was compared with that for the other conditions including the top illumination system.
MIMO iterative decoding of serial concatenation using space-time trellis codes (2002)

A multiple input, multiple output (MIMO) iterative decoding structure of serial concatenated codes with space-time trellis code (STTC) as outer coder and rate-1 recursive convolutional encoders as inner code is proposed. To both preserve the full diversity gain of space-time code and achieve additional coding gain, the proposed MIMO iterative decoder decodes jointly the received symbol streams from all the transmit antennas. The bit error rate simulation of four-state STTC employing the proposed scheme shows additional 3 dB coding gain without reducing code rate compared to that achievable by STTC alone.