gebhart/patrepeval huggingface dataset:
Rupture of the Pectoralis Major (1975)

Two cases of rupture of the pectoralis major are reported, one caused by excessive tension and direct violence, while the other was a result of direct violence alone. The site of the rupture was at the lateral third portion of the pectoralis major in one and at the musculotendinous junction in the other. Both patients were treated surgically, and regained full function of their shoulders. Review of the literature suggests that surgical repair is generally advisable and more gratifying than conservative management.
Contrastive Example-Based Control (2023)

While many real-world problems that might benefit from reinforcement learning, these problems rarely fit into the MDP mold: interacting with the environment is often expensive and specifying reward functions is challenging. Motivated by these challenges, prior work has developed data-driven approaches that learn entirely from samples from the transition dynamics and examples of high-return states. These methods typically learn a reward function from high-return states, use that reward function to label the transitions, and then apply an offline RL algorithm to these transitions. While these methods can achieve good results on many tasks, they can be complex, often requiring regularization and temporal difference updates. In this paper, we propose a method for offline, example-based control that learns an implicit model of multi-step transitions, rather than a reward function. We show that this implicit model can represent the Q-values for the example-based control problem. Across a range of state-based and image-based offline control tasks, our method outperforms baselines that use learned reward functions; additional experiments demonstrate improved robustness and scaling with dataset size.
ARLTS1 Trp149Stop Mutation and the Risk of Ovarian Cancer (2007)

In Response:We completely agree with Masojc et al. that “Trp149Stop is a mutation” yielding a dysfunctional product with a role in tumorigenesis. Moreover, their data reporting comparable frequency of ARLTS1 Trp149Stop variant in unselected ovarian cancers and controls agrees with our initial observations that the frequency of this variant is similar in patients with sporadic cancer and control cases (1).We also proposed that down-regulation of ARLTS1 by deletion and/or hypermethylation is a frequent event in sporadic cancers, including ovarian cancers, and that this mechanism may represent the counterpart of ARLTS1 mutations observed with increased frequency in familial cancers (1, 2). In support of ARLTS1 involvement in familial cancer predisposition, a second variant (Cys148Arg) has been shown to confer increased risk for familial breast cancer (3).In the light of two studies by Frank et al. linking Trp149Stop variant to increased risk of familial breast cancer in BRCA1-negative and BRCA2-negative families (4) and bilateral breast cancer (3), it would be interesting to determine the difference in Trp149Stop frequency between sporadic and familial ovarian tumors in various human populations.
Dual-Mode Infrared Absorption by Segregating Dopants within Plasmonic Semiconductor Nanocrystals (2020)

When aliovalent dopants are sufficiently segregated to the core or near the surface of semiconductor nanocrystals, charge carriers donated by the dopants are also segregated to the core or near the surface, respectively. In Sn-doped indium oxide nanocrystals, we find that this contrast in free charge carrier concentration creates a core and shell with differing dielectric properties and results in two distinctly observable plasmonic extinction peaks. The trends in this dual-mode optical response with shell growth differ from core/shell nanoparticles composed of traditional plasmonic metals such as Au and Ag. We developed a model employing a core/shell effective medium approximation that can fit the dual-mode spectra and explain the trends in the extinction response. Lastly, we show that dopant segregation can improve sensitivity of plasmon spectra to changes in refractive index of the surrounding environment.
Computational Investigation of the Reaction Mechanisms of Nitroxyl and Thiols (2010)

Nitroxyl, or nitrosyl hydride, (HNO) is a pharmacologically relevant molecule whose physiological responses have been thought to result from modification of intracellular thiols. The reaction of HNO with thiols has been shown to lead to disulfides and sulfinamides. The free energies of reaction (DeltaG) and activation (DeltaG(++)) were determined for the reaction pathways of HNO and five different thiols using computational methods. The methods employed included B3LYP, MP2, and CBS-QB3, as well as IEF-PCM to approximate implicit water solvation. The five examined thiols were hydrogen sulfide, methanethiol, trifluoromethanethiol, thiophenol, and cysteine. A putative N-hydroxysulfenamide intermediate was the initial product for the reaction of HNO with a thiol. Analysis of the Wiberg bond indices indicated that the formation of the S-N bond was concerted with the proton transfers that led to the intermediate. The calculated pK(a) of protonated N-hydroxysulfenamide was approximately 13, and from the protonated N-hydroxysulfenamide intermediate, two irreversible reactions that lead to either the disulfide or sulfinamide were found. The calculated values of DeltaG(++) indicated the preferred reaction pathway would be dependent upon the hydrophobicity of the environment, the availability of a local base, and the identity of the thiol substituent. In a hydrophobic environment, the formation of the disulfide was kinetically favored. Formation of the sulfinamide product was expected to occur upon the protonation of the hydroxy group of the N-hydroxysulfenamide intermediate.
Utility of Scalp Hair Follicles as a Novel Source of Biomarker Genes for Psychiatric Illnesses (2014)

Scalp hair follicles could be a beneficial genetic biomarker resource for brain diseases, and further studies of FABP4 are merited in schizophrenia pathogenesis.
Acoustic modal analysis and control in w-shaped triple-layer optical fibers with highly-germanium-doped core and F-doped inner cladding (2008)

The numerical study of acoustic modal properties in w-shaped optical fibers with high-delta germanium-doped core and F-doped inner cladding (F-HDF) is demonstrated. The cutoff conditions of acoustic modes in the F-HDF show opposite behaviors in contrast with those of optical ones because F-doped inner cladding contributes differently to acoustic and optical waveguides. The acoustic dispersion characteristics vary to a great extent with respect to the location of the acoustic modes in the fiber's core or in the fiber's inner cladding. The resonance frequency spacing between neighboring acoustic modes is theoretically and experimentally found to have a quadratic relation to the core's germanium concentration. We also investigate the critical conditions to move high-order acoustic modes into the F-doped inner cladding and validate the optimal feasibility of employing L(01) and L(03) acoustic modes to fiber-optic Brillouin-based discriminative sensing of strain and temperature.
The Wide Field/Planetary Camera 2 (WFPC-2) molecular adsorber (1995)

A device has been developed at the Jet Propulsion Laboratory, California Institute of Technology, for the adsorption of contaminants inside a space instrument during flight. The molecular adsorber was developed for use on the Wide Field Planetary Camera 2, and it has been shown to perform at its design specifications in the WFPC-2. The basic principle of the molecular adsorber is a zeolite-coated ceramic honeycomb. The arrangement is efficient for adsorption and also provides the needed rigidity to retain the special zeolite coating during the launch vibrational environment. The adsorber, on other forms, is expected to be useful for all flight instruments sensitive to internal sources of contamination. Typically, some internal contamination is unavoidable. A common design solution is to increase the venting to the exterior. However, for truly sensitive instruments, the external contamination environment is more severe. The molecular adsorber acts as a one-way vent to solve this problem. Continued development is planned for this device.
Collaborative Sampling Using Heterogeneous Marine Robots Driven by Visual Cues (2017)

This paper addresses distributed data sampling in marine environments using robotic devices. We present a method to strategically sample locally observable features using two classes of sensor platforms. Our system consists of a sophisticated autonomous surface vehicle (ASV) which strategically samples based on information provided by a team of inexpensive sensor nodes. The sensor nodes effectively extend the observational capabilities of the vehicle by capturing georeferenced samples from disparate and moving points across the region. The ASV uses this information, along with its own observations, to plan a path so as to sample points which it expects to be particularly informative. We compare our approach to a traditional exhaustive survey approach and show that we are able to effectively represent a region with less energy expenditure. We validate our approach through simulations and test the system on real robots in field.
The metabolic syndrome: in need of a global mission statement (2009)

Through appreciation of its purpose, and recognition of both its limitations and those attributes that make it unique and valuable, we believe we have demonstrated here that the metabolic syndrome deserves its place in the global toolbox of diabetes and CVD prevention.
ChemInform Abstract: Ligand‐Based Virtual Screening by Novelty Detection with Self‐Organizing Maps. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Data from hTERT Is Expressed in Cancer Cell Lines Despite Promoter DNA Methylation by Preservation of Unmethylated DNA and Active Chromatin around the Transcription Start Site (2023)

&lt;div&gt;Abstract&lt;p&gt;hTERT, which encodes the catalytic subunit of telomerase and is expressed in most immortalized and cancer cells, has been reported to have increased DNA methylation in its promoter region in many cancers. This pattern is inconsistent with observations that DNA methylation of promoter CpG islands is typically associated with gene silencing. Here, we provide a comprehensive analysis of promoter DNA methylation, chromatin patterns, and expression of &lt;i&gt;hTERT&lt;/i&gt; in cancer and immortalized cells. Methylation-specific PCR and bisulfite sequencing of the &lt;i&gt;hTERT&lt;/i&gt; promoter in breast, lung, and colon cancer cells show that all cancer cell lines retain alleles with little or no methylation around the transcription start site despite being densely methylated in a region 600 bp upstream of the transcription start site. By real-time reverse transcription-PCR, all cancer cell lines express &lt;i&gt;hTERT&lt;/i&gt;. Chromatin immunoprecipitation (ChIP) analysis reveals that both active (acetyl-H3K9 and dimethyl-H3K4) and inactive (trimethyl-H3K9 and trimethyl-H3K27) chromatin marks are present across the &lt;i&gt;hTERT&lt;/i&gt; promoter. However, using a novel approach combining methylation analysis of ChIP DNA, we show that active chromatin marks are associated with unmethylated DNA, whereas inactive marks of chromatin are associated with methylated DNA in the region around the transcription start site. These results show that DNA methylation patterns of the &lt;i&gt;hTERT&lt;/i&gt; promoter (−150 to +150 around the transcription start) are consistent with the usual dynamics of gene expression in that the absence of methylation in this region and the association with active chromatin marks allow for the continued expression of &lt;i&gt;hTERT&lt;/i&gt;. [Cancer Res 2007;67(1):194–201]&lt;/p&gt;&lt;/div&gt;
Unusual ground states via monotonic convex pair potentials (2011)

We have previously shown that inverse statistical-mechanical techniques allow the determination of optimized isotropic pair interactions that self-assemble into low-coordinated crystal configurations in the d-dimensional Euclidean space R(d). In some of these studies, pair interactions with multiple extrema were optimized. In the present work, we attempt to find pair potentials that might be easier to realize experimentally by requiring them to be monotonic and convex. Encoding information in monotonic convex potentials to yield low-coordinated ground-state configurations in Euclidean spaces is highly nontrivial. We adapt a linear programming method and apply it to optimize two repulsive monotonic convex pair potentials, whose classical ground states are counterintuitively the square and honeycomb crystals in R(2). We demonstrate that our optimized pair potentials belong to two wide classes of monotonic convex potentials whose ground states are also the square and honeycomb crystal. We show that these unexpected ground states are stable over a nonzero number density range by checking their (i) phonon spectra, (ii) defect energies and (iii) self assembly by numerically annealing liquid-state configurations to their zero-temperature ground states.
COPA: Certifying Robust Policies for Offline Reinforcement Learning\n against Poisoning Attacks (2022)

As reinforcement learning (RL) has achieved near human-level performance in a\nvariety of tasks, its robustness has raised great attention. While a vast body\nof research has explored test-time (evasion) attacks in RL and corresponding\ndefenses, its robustness against training-time (poisoning) attacks remains\nlargely unanswered. In this work, we focus on certifying the robustness of\noffline RL in the presence of poisoning attacks, where a subset of training\ntrajectories could be arbitrarily manipulated. We propose the first\ncertification framework, COPA, to certify the number of poisoning trajectories\nthat can be tolerated regarding different certification criteria. Given the\ncomplex structure of RL, we propose two certification criteria: per-state\naction stability and cumulative reward bound. To further improve the\ncertification, we propose new partition and aggregation protocols to train\nrobust policies. We further prove that some of the proposed certification\nmethods are theoretically tight and some are NP-Complete problems. We leverage\nCOPA to certify three RL environments trained with different algorithms and\nconclude: (1) The proposed robust aggregation protocols such as temporal\naggregation can significantly improve the certifications; (2) Our certification\nfor both per-state action stability and cumulative reward bound are efficient\nand tight; (3) The certification for different training algorithms and\nenvironments are different, implying their intrinsic robustness properties. All\nexperimental results are available at https://copa-leaderboard.github.io.\n
The Polyphenols Resveratrol and S17834 Prevent the Structural and Functional Sequelae of Diet-Induced Metabolic Heart Disease in Mice (2012)

Resveratrol and S17834 administered concurrently with a HFHS diet prevent the development of left ventricular hypertrophy, interstitial fibrosis, and diastolic dysfunction. Multiple mechanisms may contribute to the beneficial effects of the polyphenols, including a reduction in myocardial oxidative stress and related protein modifications, amelioration of insulin resistance, and increased plasma adiponectin. The polyphenols resveratrol and S17834 may be of value in the prevention of diet-induced metabolic heart disease.
Costimulatory Pathways in Lymphocyte Proliferation Induced by the Simian Immunodeficiency Virus SIVsmmPBj14 (1998)

The PBj14 isolate of the simian immunodeficiency virus SIVsmmPBj14 is unique among primate lentiviruses in its ability to induce lymphocyte proliferation and acutely lethal disease. The studies reported here show that viral induction of T-cell proliferation requires accessory cells, such as primary monocytes or Raji B-lymphoma cells, as well as the presence of a putative immunoreceptor tyrosine-based activation motif within the viral Nef protein. Addition of CTLA4-immunoglobulin fusion protein or anti-B7 antibodies to virally infected T cells led to substantial, but not complete, inhibition of monocyte-costimulated T-cell proliferation-suggesting that both CD28/B7-dependent and non-CD28-dependent pathways may contribute to the costimulation of virally induced lymphoproliferation. Finally, cyclosporin A, a specific inhibitor of the calcium-calmodulin-regulated phosphatase activity of calcineurin, which influences activation of the transcription factor nuclear factor of activated T cells, was shown to block virally mediated T-cell proliferation. Taken together, these findings suggest that the effect of SIVsmmPBj14 on T-cell activation may be functionally analogous, at least in part, to the effect of engagement of the T-cell receptor.
Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates (2018)

Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals.
Calcareous sponges from the French Polynesia (Porifera: Calcarea) (2020)

Although the French Polynesian reefs are among the most well studied reefs of the world, sponges are still poorly known, with only 199 species or OTUs of sponges having been described from French Polynesia, 167 at an OTU level and 32 at a species level. From those 199 species, just five are calcareous sponges. As it is possible that this number is underestimated, the aim of the present work was to study the diversity of calcareous sponges from French Polynesia. Hence, different French Polynesian archipelagos were surveyed by SCUBA from 3 to 60 m of depth. Identifications were performed using morphological and molecular (ITS and C-LSU) tools. We found a total of nine species of Calcarea, comprising five different genera. Five species are new to science: Clathrina fakaravae sp. nov., Clathrina huahineae sp. nov., Ernstia variabilis sp. nov., Leucascus digitiformis sp. nov., and Leucandra tahuatae sp. nov. With the present work, the number of identified sponges from French Polynesia at a species level increased from 32 to 41. The only calcareous sponge previously known from French Polynesia that was recollected by our group was Leucetta chagosensis. Our results suggest that the Eastern Indo-Pacific Realm shows more affinity with the Central and the Western Indo-Pacific Realms. Four species supported these affinities: Ascandra cf. crewsi, previously known only from Papua New Guinea, Leucascus simplex from South Australia, and Leucetta chagosensis and L. microraphis, both widespread species in the Indo-Pacific. These two Leucetta species, however, most likely represent species complexes. Once again the molecular markers ITS and C-LSU helped in the identification of calcareous sponges, showing how important is an integrative taxonomy. Although our work has increased in 250% (6 spp to 15 spp) the diversity of calcareous sponges in French Polynesia, it is most possible that this number is still underestimated.
ChemInform Abstract: Reversal of P‐Glycoprotein Mediated Multidrug Resistance by Novel Anthranilamide Derivatives. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Linear Coherent Optical Receivers (2010)

The development of linear coherent receivers at UCSB is reviewed. The progression of the feedback receiver architecture toward closer integration, lower feedback delay and higher performance is outlined. The alternative XOR receiver approach is summarized.
Impurity incorporation in InGaN grown by rf plasma-assisted molecular beam epitaxy (2002)

Impurity incorporation into InGaN films grown by rf-plasma assisted molecular beam epitaxy was investigated using secondary ion mass spectroscopy. A factor of 3 increase in both oxygen and boron incorporation into InGaN films relative to GaN films at 600 °C was demonstrated, and a factor of 10 increase in oxygen relative to the detectable base line in GaN grown under optimal conditions. Oxygen incorporation is related specifically to the different structures of the gallium and indium wetting layers on the growth surface. It is also shown using secondary ion mass spectroscopy that the formation of the gallium wetting layer during GaN growth is disrupted by the presence of excess indium; increased oxygen incorporation was observed during growth with an incomplete gallium wetting layer and indium on the growth surface. This study demonstrates the profound impact of surface atomic structure on impurity incorporation and reveals the protective nature of the gallium wetting layer as compared to the indium wetting layer during growth by rf-plasma assisted molecular beam epitaxy.
Measurements of Anisotropy in the Cosmic Microwave Background Radiation at Degree Angular Scales Near the Stars Sigma Hercules and Iota Draconis (1994)

We present results from two four-frequency observations centered near the stars Sigma Hercules and Iota Draconis during the fourth flight of the Millimeter-wave Anisotropy eXperiment (MAX). The observations were made of 6 x 0.6-degree strips of the sky with 1.4-degree peak to peak sinusoidal chop in all bands. The FWHM beam sizes were 0.55+/-0.05 degrees at 3.5 cm-1 and a 0.75+/-0.05 degrees at 6, 9, and 14 cm-1. Significant correlated structures were observed at 3.5, 6 and 9 cm-1. The spectra of these signals are inconsistent with thermal emission from known interstellar dust populations. The extrapolated amplitudes of synchrotron and free-free emission are too small to account for the amplitude of the observed structures. If the observed structures are attributed to CMB anisotropy with a Gaussian autocorrelation function and a coherence angle of 25', then the most probable values are DT/TCMB = (3.1 +1.7-1.3) x 10^-5 for the Sigma Hercules scan, and DT/TCMB = (3.3 +/- 1.1) x 10^-5 for the Iota Draconis scan (95% confidence upper and lower limits). Finally a comparison of all six MAX scans is presented.