gebhart/patrepeval huggingface dataset:
The interaction of bubbles with solidification interfaces (1977)

The behavior of bubbles at a dendritic solidification interface was studied during the coasting phase of a sounding rocket flight. Sequential photographs of the gradient freeze experiment showed nucleation, growth and coalescence of bubbles at the moving interface during both the low-gravity and one-gravity tests. In the one-gravity test the bubbles were observed to detach from the interface and float to the top of the melt. However, in the low-gravity tests no bubble detachment from the interface or steady state bubble motion occurred and large voids were grown into the crystal. These observations are discussed in terms of the current theory of thermal migration of bubbles and in terms of their implications on the space processing of metals.
A Metalloproteinase Mirolysin of Tannerella forsythia Inhibits All Pathways of the Complement System (2015)

Recent reports focusing on virulence factors of periodontal pathogens implicated proteinases as major determinants of remarkable pathogenicity of these species, with special emphasis on their capacity to modulate complement activity. In particular, bacteria-mediated cleavage of C5 and subsequent release of C5a seems to be an important phenomenon in the manipulation of the local inflammatory response in periodontitis. In this study, we present mirolysin, a novel metalloproteinase secreted by Tannerella forsythia, a well-recognized pathogen strongly associated with periodontitis. Mirolysin exhibited a strong effect on all complement pathways. It inhibited the classical and lectin complement pathways due to efficient degradation of mannose-binding lectin, ficolin-2, ficolin-3, and C4, whereas inhibition of the alternative pathway was caused by degradation of C5. This specificity toward complement largely resembled the activity of a previously characterized metalloproteinase of T. forsythia, karilysin. Interestingly, mirolysin released the biologically active C5a peptide in human plasma and induced migration of neutrophils. Importantly, we demonstrated that combination of mirolysin with karilysin, as well as a cysteine proteinase of another periodontal pathogen, Prevotella intermedia, resulted in a strong synergistic effect on complement. Furthermore, mutant strains of T. forsythia, devoid of either mirolysin or karilysin, showed diminished survival in human serum, providing further evidence for the synergistic inactivation of complement by these metalloproteinases. Taken together, our findings on interactions of mirolysin with complement significantly add to the understanding of immune evasion strategies of T. forsythia and expand the knowledge on molecular mechanisms driving pathogenic events in the infected periodontium.
Heat Induced Structural Rearrangement and Crystallite Formation in Thin Films of Room Temperature Plasma-Polymerized Titanium (IV) Isopropoxide (2010)

Analysis of plasma polymerized TiOxCyNz films annealed in the temperature range of 300-700°C, revealed different mechanisms responsible for film densification below 300°C and the formation of TiO2 crystalline phases at temperatures over 500°C.
THE OIL PALM AND ITS SUSTAINABILITY (2004)

As the palm oil industry progresses, its many aspects, such as economic, environmental and social benefits, from its production are reviewed. More recently, sustainability has received great attention with efforts to integrate it into the palm oil business strategy. In the sustainability framework, the economic (financial), environmental and social aspects are reviewed for their impacts in both the short- and long-terms. The threepronged strategy of high income, value addition and zero waste is scrutinized as part of the journey towards corporate sustainability. Doing so has once again demonstrated the benefits of the crop in supplying oil to the world. The paper also puts together the evidence, firstly, that the oil palm can be used as a vehicle for rural poverty eradication in Malaysia and perhaps be used as a model for other countries with similar soils, climate and labour availability. Secondly, that it is a steady supplier of affordable food, non-food, biocomposites, nutritional and pharmaceutical products. And thirdly, that it is a showcase for environmental improvement. For the latter, palm oil mills are fast becoming generators of renewable energy from their biomass and biogas. R&D in these areas have provided new angles for increasing its economic sustainability, moving the industry beyond the current business of just producing palm oil. Further, new business ventures based on new R&D findings are being set up to look at product sustainability. They include businesses such as in bioplastics, greenness of energy production, savings in fossil fuels, reduction in greenhouse gas emissions and production from several new best developed practices, thereby helping the industry to slow down the process of climate change.
Supplementary Figure 6 from Reversal of NK-Cell Exhaustion in Advanced Melanoma by Tim-3 Blockade (2023)

&lt;p&gt;PDF file - 119K, Fig. S6. Tim-3 engagement by Galectin-9 on NK cells from healthy donors and melanoma patients inhibits their cytotoxicity.&lt;/p&gt;
Leptin secreted from testicular microenvironment modulates hedgehog signaling to augment the endogenous function of Leydig cells (2022)

Although testosterone deficiency (TD) may be present in one out of five men 40 years or older, the factors responsible for TD remain largely unknown. Leydig stem cells (LSCs) differentiate into adult Leydig cells (ALC) and produce testosterone in the testes under the pulsatile control of luteinizing hormone (LH) from the pituitary gland. However, recent studies have suggested that the testicular microenvironment (TME), which is comprised of Sertoli and peritubular myoid cells (PMC), plays an instrumental role in LSC differentiation and testosterone production under the regulation of the desert hedgehog signaling pathway (DHH). It was hypothesized that the TME releases paracrine factors to modulate LSC differentiation. For this purpose, cells (Sertoli, PMCs, LSCs, and ALCs) were extracted from men undergoing testis biopsies for sperm retrieval and were evaluated for the paracrine factors in the presence or absence of the TME (Sertoli and PMC). The results demonstrated that TME secretes leptin, which induces LSC differentiation and increases testosterone production. Leptin's effects on LSC differentiation and testosterone production, however, are inversely concentration-dependent: positive at low doses and negative at higher doses. Mechanistically, leptin binds to the leptin receptor on LSCs and induces DHH signaling to modulate LSC differentiation. Leptin-DHH regulation functions unidirectionally insofar as DHH gain or loss of function has no effect on leptin levels. Taken together, these findings identify leptin as a key paracrine factor released by cells within the TME that modulates LSC differentiation and testosterone release from mature Leydig cells, a finding with important clinical implications for TD.
Super-Learning of an Optimal Dynamic Treatment Rule (2016)

We consider the estimation of an optimal dynamic two time-point treatment rule defined as the rule that maximizes the mean outcome under the dynamic treatment, where the candidate rules are restricted to depend only on a user-supplied subset of the baseline and intermediate covariates. This estimation problem is addressed in a statistical model for the data distribution that is nonparametric, beyond possible knowledge about the treatment and censoring mechanisms. We propose data adaptive estimators of this optimal dynamic regime which are defined by sequential loss-based learning under both the blip function and weighted classification frameworks. Rather than a priori selecting an estimation framework and algorithm, we propose combining estimators from both frameworks using a super-learning based cross-validation selector that seeks to minimize an appropriate cross-validated risk. The resulting selector is guaranteed to asymptotically perform as well as the best convex combination of candidate algorithms in terms of loss-based dissimilarity under conditions. We offer simulation results to support our theoretical findings.
Scale‐dependent fiber kinematics of elastomeric electrospun scaffolds for soft tissue engineering (2009)

Electrospun poly(ester urethane)urea (PEUU) scaffolds contain complex multiscale hierarchical structures that work simultaneously to produce unique macrolevel mechanical behaviors. In this study, we focused on quantifying key multiscale scaffold structural features to elucidate the mechanisms by which these scaffolds function to emulate native tissue tensile behavior. Fiber alignment was modulated via increasing rotational velocity of the collecting mandrel, and the resultant specimens were imaged using SEM under controlled biaxial strain. From the SEM images, fiber splay, tortuosity, and diameter were quantified in the unstrained and deformed configurations. Results indicated that not only fiber alignment increased with mandrel velocity but also, paradoxically, tortuosity increased concurrently with mandrel velocity and was highly correlated with fiber orientation. At microlevel scales (1-10 mum), local scaffold deformation behavior was observed to be highly heterogeneous, while increasing the scale resulted in an increasingly homogenous strain field. From our comprehensive measurements, we determined that the transition scale from heterogenous to homogeneous-like behavior to be approximately 1 mm. Moreover, while electrospun PEUU scaffolds exhibit complex deformations at the microscale, the larger scale structural features of the fibrous network allow them to behave as long-fiber composites that deform in an affine-like manner. This study underscores the importance of understanding the structure-function relationships in elastomeric fibrous scaffolds, and in particular allowed us to link microscale deformations with mechanisms that allow them to successfully simulate soft tissue mechanical behavior.
Abstract 5132: Pooled shRNA screens conducted in vitro and in vivo identify genes that are essential for the growth and/or survival of human tumor cells (2012)

Abstract Identification of novel drug targets is a major challenge in cancer research. While numerous studies have identified genes that are mutated and/or amplified in cancers, the functional significance of most of these genetic alterations remains unknown. To directly identify genes that are required for the growth of human tumor cells, and that could potentially be targets for therapeutic monoclonal antibodies, we employed a custom shRNA library containing ∼13,000 shRNAs targeting 3,210 genes (∼4 shRNAs per gene) that encode cell surface or secreted proteins. Cultured tumor cells were infected with the virally-packaged shRNA library such that each shRNA (and an associated molecular barcode) was integrated into ∼200 cells. Cells that expressed shRNAs that target essential genes were progressively depleted from the population upon in vitro passage or following implantation into mice, resulting in decreased representation of those shRNAs/barcodes versus reference samples. In vitro screens were conducted in 3 colorectal cancer cell lines (HCT116, DLD1 and Colo320DM) and in NCI-H1975 lung cancer cells. About 1-3% of the genes in the library were identified as essential for tumor cell growth and/or survival in vitro. Importantly, these genes included positive controls such as PCNA that were included in the library to validate the screening procedure, as well as components of pathways that are known to control cell growth such as IGF-1R, Wnt9a, sonic hedgehog and RON. In vivo screens were performed with HCT116 and NCI-H1975 cells by implanting cells into mice immediately following shRNA integration. Representation of shRNAs versus the reference sample was assessed in small tumors (∼100 mm3) and in large tumors (1000 mm3). While we observed very few hits in small tumors, the number of hits in large tumors was greater than that observed in vitro (e.g., ∼3-fold higher for HCT116), suggesting that tumor growth in vivo is dependent on a larger set of genes than is cell growth in vitro. Interestingly, the genes that were uniquely essential in tumors versus in vitro included several that are involved in cell/cell adhesion (e.g., cadherin 24, claudin 3) and cell signaling (epidermal growth factor receptor). In summary, our shRNA screens focusing on secreted and cell surface targets have identified genes that may be essential for tumor growth, including many genes that have not previously been implicated in this process. Upon further validation, these genes could potentially serve as novel targets for therapeutic antibodies in cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5132. doi:1538-7445.AM2012-5132
Correlation of Nonproportionality and Scintillation Properties with Cerium Concentration in YAlO3:Ce (2018)

Cerium-doped YAlO3:Ce (YAP:Ce) is an interesting oxide scintillator that exhibits a wider range of light yield nonproportionality on a sample-to-sample basis than most other well-known oxide scintillators. In general, most oxide materials, such as Bi4Ge3O12 and Lu2SiO5:Ce, are thought to have an intrinsic proportional response that is nearly constant between samples and independent of growth conditions. Since light yield nonproportionality is responsible for degrading the achievable energy resolution of all known scintillators, it is important to understand what contributes to the behavior. In an attempt to understand if the phenomenon can be affected by growth parameters or by other means, seven samples of YAP:Ce were collected from various sources, and eight samples were grown in-house using the Czochralski method. Based on optical and scintillation measurement as well as direct measurement of the cerium concentration, it was determined that the light yield proportionality in YAP:Ce is strongly related to the cerium concentration. Samples that were found to have higher relative cerium concentration displayed a more proportional light yield response. In addition, it was determined that samples with higher cerium concentration also exhibit a faster decay time and an enhanced energy resolution when compared to samples with less cerium. It was also determined that growth in a reducing atmosphere can effectively suppress a parasitic optical absorption band.
Log-likelihood ratio based signal sensing strategy for cognitive radios (2009)

Cognitive radios require spectrum sensing. IEEE 802.22 defines constraints on conceivable spectrum sensing techniques. In order to fulfill theses constraints on the required detection probability and allowed false alarm probability, the signal sensing requires a certain sensing time period and an appropriately adjusted decision threshold. This manuscript presents a novel dynamic spectrum sensing scheme which is based on soft outputs. The novel scheme allows the reduction of the sensing time in order to save calculation and power effort.
Androgen receptor splice variant, AR-V7, and resistance to enzalutamide and abiraterone in men with metastatic castration-resistant prostate cancer (mCRPC). (2014)

5001 Background: Androgen receptor splice variant-7 (AR-V7) is a truncated form of the androgen receptor that lacks the ligand-binding domain, the target of enzalutamide and abiraterone, but remains constitutively active as a transcription factor. We hypothesized that detection of AR-V7 in circulating tumor cells (CTCs) from men with mCRPC may be associated with primary resistance to enzalutamide and abiraterone. Methods: We used quantitative reverse-transcription PCR (qRT-PCR) to interrogate CTCs for the presence or absence of AR-V7 from prospectively enrolled patients with mCRPC initiating treatment with enzalutamide or abiraterone. We examined associations between AR-V7 status and PSA response rates, PSA progression-free survival (PSA-PFS), and clinical/radiographic progression-free survival (PFS). Multivariable Cox regression analyses were performed to determine the independent effect of AR-V7 status on these clinical outcomes. 30 men (per cohort) were required to detect a difference in PSA response rates from 10% (in AR-V7–positive men) to 60% (in AR-V7–negative men), using a 2-sided α=0.10 and β=0.15. Results: 31 enzalutamide-treated patients and 31 abiraterone-treated patients were enrolled, of which 38.7% and 19.4% had detectable AR-V7 from CTCs, respectively. Among men receiving enzalutamide, AR-V7–positive patients had inferior PSA response rates (0% vs 52.6%, P=0.004), PSA-PFS (median 1.4 vs 5.9 months, P<0.001), and PFS (median 2.1 vs 6.1 months, P<0.001) compared to AR-V7–negative patients. Similarly, among men receiving abiraterone, AR-V7–positive patients had inferior PSA response rates (0% vs 68.0%, P=0.004), PSA-PFS (median 1.3 months vs not reached, P<0.001), and PFS (median 2.3 months vs not reached, P<0.001). The negative prognostic impact of AR-V7 was maintained after adjusting for full-length AR expression levels. Conclusions: Detection of AR-V7 in CTCs from men with mCRPC is associated with resistance to enzalutamide and abiraterone. AR-V7 status may be used as a biomarker to predict resistance to AR-targeting agents, facilitate treatment selection, and fuel the development AR N-terminal domain inhibitors.
Toward a theory of test data selection (1975)

Examines the theoretical and practical role of testing in software development. The authors prove a fundamental theorem showing that properly structured tests are capable of demonstrating the absence of errors in a program. The theorem's proof hinges on our definition of test reliability and validity, but its practical utility hinges on being able to show when a test is actually reliable. The authors explain what makes tests unreliable (for example, they show by example why testing all program statements, predicates, or paths is not usually sufficient to insure test reliability), and they outline a possible approach to developing reliable tests. They also show how the analysis required to define reliable tests can help in checking a program's design and specifications as well as in preventing and detecting implementation errors.
Soluble tumor necrosis factor receptors and interleukin-6 levels in patients with severe preeclampsia (1996)

The increased levels of soluble tumor necrosis factor receptors found in patients with severe preeclampsia may represent a protective response to increased tumor necrosis factor activity and be a marker for immune activation. Increased interleukin-6 concentrations in maternal plasma before labor suggest the involvement of this cytokine as well in the altered immune response and its contribution to endothelial cell dysfunction.
Chapter 8. NOx Storage and Reduction: Effects of Pt Dispersion, Reductant Type, and Cycle Timing (2018)

Studies of the lean NOx trap (LNT) using NOx storage and reduction (NSR) technology on several aspects are addressed. First, the effect of catalyst composition – precious metal loading and dispersion – on the performance of a LNT is examined. A model is described to predict the cycle-averaged NOx conversion and selectivity into N2 and NH3 as a function of Pt loading and dispersion. Second, the impact of cycle time and non-isothermal effects are examined by both experiments and modeling using H2 as the reductant. The mechanism of fast cycling features better utilization of NOx storage sites, resulting in a higher NOx conversion and lower NH3 selectivity. Significant exotherms are detected and modeled under traditional ∼1 min cycle, resulting in increased NOx slip, whereas reduced NOx slip is encountered during near-isothermal, sub-10 s cycle time operation (fast cycling). Third, the spatio-temporal concentration and temperature profiles are measured using C3H6 as the reductant, providing insight into NOx reduction pathways with hydrocarbons, including the water–gas shift reaction and steam reforming. Lastly, the effects of reductant type during fast cycling are experimentally studied. The stronger thermal effect with H2 compared to C3H6 may be due to its higher molecular diffusivity. Comparisons between C3H6 and H2 show that improved NOx storage site utilization is the main factor responsible for NOx conversion enhancement during fast cycling with the HC-intermediate pathway being a secondary factor.
Wavelet transforms for the analysis of microarray experiments (2004)

Array comparative genomic hybridization (cgh) is a microarray technology for measuring the relative copy number of thousands of genomic regions. Visual examination of cgh profiles shows that genomic changes occur on a variety of length scales. Such changes may be characteristic of phenotypic variables such as tumor type and gene mutational status. To aid in identifying such features and exploring their relationship with phenotypic outcomes, we are applying wavelet transforms to the analysis of such profiles. This allows us to decompose a cgh signal into components on different length scales, even when the genome is severely aberrated, providing a convenient basis for exploring their behavior. Wavelet transforms may also be useful in the realm of gene expression. The expression signal given by genes in clustered order can be wavelet transformed, which compresses the signal from many genes into a few components, possibly aiding in the development of new tumor classifiers.
On the Convergence of Bound Optimization Algorithms (2012)

Many practitioners who use the EM algorithm complain that it is sometimes slow. When does this happen, and what can be done about it? In this paper, we study the general class of bound optimization algorithms - including Expectation-Maximization, Iterative Scaling and CCCP - and their relationship to direct optimization algorithms such as gradient-based methods for parameter learning. We derive a general relationship between the updates performed by bound optimization methods and those of gradient and second-order methods and identify analytic conditions under which bound optimization algorithms exhibit quasi-Newton behavior, and conditions under which they possess poor, first-order convergence. Based on this analysis, we consider several specific algorithms, interpret and analyze their convergence properties and provide some recipes for preprocessing input to these algorithms to yield faster convergence behavior. We report empirical results supporting our analysis and showing that simple data preprocessing can result in dramatically improved performance of bound optimizers in practice.