gebhart/patrepeval huggingface dataset:
Differential Pathogenesis of Lung Adenocarcinoma Subtypes Involving Sequence Mutations, Copy Number, Chromosomal Instability, and Methylation (2012)

The lung adenocarcinoma intrinsic molecular subtypes co-occur with grossly distinct genomic alterations and with patient therapy response. These results advance the understanding of lung adenocarcinoma etiology and nominate patient subgroups for future evaluation of treatment response.
The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review (2010)

Abstract Recent developments in methods and instrumentation have contributed to major advances in our understanding of the fine structure of amylose and amylopectin. The structure of the starch granule slowly unravels with new insight into key structural features. Following a brief presentation of the structural features common to all starches, the most recent findings for the structure of amylose and amylopectin are reported. The organization of different types of chains in amylopectin is discussed with a critical review of the ‘cluster’ model leading to the presentation of alternative models. The locations of molecular components in the starch granule are described according to a progress structural order. The description of the crystalline components is followed by a presentation of their supramolecular arrangements. The crystalline components comprise platelet nanocrystals which have already been identified and characterized, and other less well characterized ‘blocklet components’. The location and state of amylose within the granule is also presented. This comprehensive review aims at distinguishing between those structural features that have received widespread acceptance and those that are still under debate, with the ambition of being educational and to provide stimulation for further fundamental investigation into the starch granule as a macromolecular assembly.
The HB-6, CDw75, and CD76 differentiation antigens are unique cell-surface carbohydrate determinants generated by the beta-galactoside alpha 2,6-sialyltransferase. (1992)

Expression of the beta-galactoside alpha 2,6-sialyltransferase (alpha 2,6-ST) was shown to regulate the generation of multiple cell-surface differentiation antigens (Ags) that may be necessary for lymphocyte function. A new mAb was produced, termed HB-6, that was shown to identify a novel neuraminidase-sensitive cell-surface Ag expressed by subpopulations of human lymphocytes and erythrocytes. In attempting to isolate a cDNA encoding the HB-6 antigen by expression cloning, a cDNA encoding the alpha 2,6-ST (EC 2.4.99.1) was obtained. Since expression of the alpha 2,6-ST protein was shown to be limited to the Golgi apparatus, the cell-surface HB-6 Ag was demonstrated to be the product of alpha 2,6-ST activity. Interestingly, alpha 2,6-ST expression also generated two other neuraminidase-sensitive lymphocyte cell-surface differentiation Ags, CDw75, and CD76. The HB-6, CDw75, and CD76 mAb identified distinct Ags that were differentially expressed by different B cell lines and exhibited different patterns of expression in tissue sections. These results indicate that alpha 2,6-ST expression is a critical regulatory step in the formation of the Ags that are recognized by these mAb, and that an alpha 2,6-linked sialic acid residue is an essential component of each Ag. Thus, expression of a single ST can result in the generation of multiple distinct antigenic determinants on the cell surface which can be distinguished by mAb and may have regulatory roles in lymphocyte function.
[mRNA expression of transforming growth factor-beta 1 in the cornea after photorefractive keratectomy in rabbits]. (2002)

TGF-beta 1 may involve in corneal wound healing after PRK and may increase haze by promoting the synthesis of the extracellular matrix and the proliferation of keratocytes.
GridLAB-D: An open-source power systems modeling and simulation environment (2008)

GridLAB-D is a new power system modeling and simulation environment developed by the US Department of Energy. This paper describes its basic design concept, method of solution, and the initial suite of models that it supports.
Localized Treatment with a Novel FDA-Approved Proteasome Inhibitor Blocks the Degradation of Dystrophin and Dystrophin-Associated Proteins in mdx Mice (2007)

Duchenne Muscular Dystrophy (DMD) is an incurable inherited disease of childhood, characterized by progressive muscle degeneration and weakness. Our previous findings supported the idea that dystrophin and associated proteins, absent or greatly reduced in DMD, are degraded in dystrophin-deficient muscle by the proteasomal-dependent pathway. Indeed, treatment with the proteasome inhibitor MG-132 of skeletal muscles from mdx mice--a spontaneous mouse model of DMD--as well as from DMD patients, effectively rescued the expression and correct cellular localization of dystrophin and associated proteins. These promising results led us to further explore the use of proteasome inhibitors as a therapy for DMD. Therefore, we directed our attention towards two new dipeptide boronic acid inhibitors blocking the proteasomal-dependent degradation pathway: Velcade (bortezomib or PS-341) and MLN273 (PS-273). The exciting aspect of this development is that these drugs have already progressed to preclinical and clinical trials, in different fields than muscular dystrophy. Indeed, Velcade has been already FDA-approved for treatment of multiple myeloma and its side effects had been already explored and managed. Promisingly, MLN273 is currently in the preclinical trial phase. Here, we test the effectiveness of Velcade and MLN273 by local injection into the gastrocnemius muscle of mdx mice. We show the rescue of expression and membrane localization of alpha-dystroglycan, beta-dystroglycan, alpha-sarcoglycan, and dystrophin after Velcade and MLN273 localized treatment, versus untreated (PBS only) mdx mice. Intriguingly, we also show that localized treatment with Velcade and MLN273 reduces the activation of Nuclear Factor-kappaB (NFkB). Because the NFkB pathway has been shown to be involved in inflammation responses in myopathies and DMD, our current results may have important clinical implications. Clearly, more investigations are needed, but our results emphasize the effectiveness of the pharmacological approach as a potential treatment for Duchenne muscular dystrophy.
The Ethics of Placebo-Controlled Trials — A Middle Ground (2001)

The first placebo-controlled trial was probably conducted in 1931, when sanocrysin was compared with distilled water for the treatment of tuberculosis.1 Ever since then, placebo-controlled trials have been controversial, especially when patients randomly assigned to receive placebo have forgone effective treatments.25 Recently, the debate has become polarized. One view, dubbed “placebo orthodoxy” by its opponents, is that methodologic considerations make placebo-controlled trials necessary.611 The other view, which might be called “active-control orthodoxy,” is that placebo orthodoxy sacrifices ethics and the rights and welfare of patients to presumed scientific rigor.1014 The latest revision of the Declaration of Helsinki, . . .
Context Aware Voice User Interfaces for Workflow Support (2007)

Audio is a significant factor in the design of the human computer interface in ubiquitous computing. The characteristics of the medium allow for a hands-free interaction without the need to switch the focus to a display (eyes-free).Moreover, determining the graphical capabilities of the wearable device to adapt the output to the device is not needed. But audio based interfaces are also challenging, since humans are visually oriented. The ubiquitous computing community recognized the advantages of the audio channel, but the restrictions inherent to the medium are mostly ignored. Authors of such systems who know about these challenges often look for a solution by using additional modalities, preferably visually oriented. This thesis analyses these challenges with respect to the human’s cognitive capabilities and shows a possible solution using audio design patterns. Users on the move face additional challenges, since wearable devices do not have the computational power and storage capacity of desktop PCs which are required to use speech recognizers and speech synthesizers off the shelf. Thus recognition and synthesis software running on such a device does not have the capabilities of their desktop size counterparts. Streaming technologies can use high-end voice technology on a server at the cost of network dependency. This thesis introduces a new approach combining both worlds. In order to aid the user best, context information is used, location at first place. The context information is obtained from the current environment and from the task that she wants to accomplish. workflow engines are a standard for storing and controlling tasks as processes. Additionally, workflow engines consider the data flow which is a fundamental aspect of each process. Initial approaches to using context information in workflow engines exist but they lack a reusable concept.This thesis introduces such a concept. The process descriptions in workflow engines are modality independent in order to have reusable business logic. Modality dependant specifications of the current activity reside outside the workflow engine and are stored in a meta format that can be used to address multiple modalities. The user interfaces are generated by code generators at run-time. Current concepts consider neither a separation of modality independent business logic nor do they regard data flow. If a user is working on multiple processes in parallel, she needs support in returning into the context of an interrupted process. The challenges inherent to audio are not well suited to aid her resuming the task efficiently. In this thesis, we introduce a first concept of an audio-only support for task resumption.
High Levels of Miticides and Agrochemicals in North American Apiaries: Implications for Honey Bee Health (2010)

Background: Recent declines in honey bees for crop pollination threaten fruit, nut, vegetable and seed production in the United States. A broad survey of pesticide residues was conducted on samples from migratory and other beekeepers across 23 states, one Canadian province and several agricultural cropping systems during the 2007-08 growing seasons.
Significant reduction in systolic blood pressure following renal artery stenting in patients with uncontrolled hypertension: Results from the HERCULES trial (2012)

HERCULES demonstrates clinically and statistically significant SBP reduction in patients with uncontrolled HTN, low in-stent restenosis, and complication rates. This study highlights that when appropriate patients are selected for renal artery stenting, impressive reductions in blood pressure may be anticipated. Although the magnitude of absolute reduction in SBP was related to baseline SBP, elevated baseline BNP levels were not predictive of reduction in SBP. Further studies for predictors of clinical response following percutaneous renal revascularization are needed.
Interkingdom metabolic transformations captured by microbial imaging mass spectrometry (2012)

In polymicrobial infections, microbes can interact with both the host immune system and one another through direct contact or the secretion of metabolites, affecting disease progression and treatment options. The thick mucus in the lungs of patients with cystic fibrosis is highly susceptible to polymicrobial infections by opportunistic pathogens, including the bacterium Pseudomonas aeruginosa and the fungus Aspergillus fumigatus. Unravelling the hidden molecular interactions within such polymicrobial communities and their metabolic exchange processes will require effective enabling technologies applied to model systems. In the present study, MALDI-TOF and MALDI-FT-ICR imaging mass spectrometry (MALDI-IMS) combined with MS/MS networking were used to provide insight into the interkingdom interaction between P. aeruginosa and A. fumigatus at the molecular level. The combination of these technologies enabled the visualization and identification of metabolites secreted by these microorganisms grown on agar. A complex molecular interplay was revealed involving suppression, increased production, and biotransformation of a range of metabolites. Of particular interest is the observation that P. aeruginosa phenazine metabolites were converted by A. fumigatus into other chemical entities with alternative properties, including enhanced toxicities and the ability to induce fungal siderophores. This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations.
Renewable polymeric materials from vegetable oils: a perspective (2013)

The utilization of vegetable oils is currently in the spotlight of the chemical industry, as they are one of the most important renewable platform chemicals due to their universal availability, inherent biodegradability, low price, and superb environmental credentials (i.e., low ecotoxicity and low toxicity toward humans). These natural properties are now being taken advantage of in research and development, with vegetable oil derived polymers/composites being used in numerous applications including paints and coatings, adhesives, and biomedicine.
Peptide Nucleic Acid Containing a Meta-Substituted Phenylpyrrolocytosine Exhibits a Fluorescence Response and Increased Binding Affinity toward RNA (2009)

Peptide nucleic acids (PNA) containing meta-substituted 6-phenylpyrrolocytosine (PhpC), [mono-m-(aminoethoxy)phenyl]pyrrolocytosine (mmePhpC), [mono-m-(aminopropoxy)phenyl]pyrrolocytosine (mmpPhpC), and [mono-m-(guanidinoethoxy)phenyl]pyrrolocytosine (mmguaPhpC), have been synthesized. Meta-substituted PhpCs have been hybridized with overall higher binding affinity toward DNA and RNA than previously synthesized moePhpC or newly synthesized mopPhpC. The guanidinium-containing nucleobase, mmguaPhpC, exhibited the highest increase in binding affinity toward RNA while fluorometrically responding on the state of hybridization.
Mer receptor tyrosine kinase is a therapeutic target in pre–B-cell acute lymphoblastic leukemia (2013)

Acute lymphoblastic leukemia (ALL) is currently treated with an intense regimen of chemotherapy yielding cure rates near 85%. However, alterations to treatment strategies using available drugs are unlikely to provide significant improvement in survival or decrease therapy-associated toxicities. Here, we report ectopic expression of the Mer receptor tyrosine kinase in pre-B-cell ALL (B-ALL) cell lines and pediatric patient samples. Inhibition of Mer in B-ALL cell lines decreased activation of AKT and MAPKs and led to transcriptional changes, including decreased expression of antiapoptotic PRKCB gene and increase in proapoptotic BAX and BBC3 genes. Further, Mer inhibition promoted chemosensitization, decreased colony-forming potential in clonogenic assays, and delayed disease onset in a mouse xenograft model of leukemia. Our results identify Mer as a potential therapeutic target in B-ALL and suggest that inhibitors of Mer may potentiate lymphoblast killing when used in combination with chemotherapy. This strategy could reduce minimal residual disease and/or allow for chemotherapy dose reduction, thereby leading to improved event-free survival and reduced therapy-associated toxicity for patients with B-ALL. Additionally, Mer is aberrantly expressed in numerous other malignancies suggesting that this approach may have broad applications.
Mechanistic studies of silicon oxidation (1999)

The microscopic mechanism of the formation of ultrathin oxides on Si(100) has been investigated using a combination of infrared spectroscopy and ab initio quantum chemical cluster calculations. The 0→2 monolayer oxide films are grown sequentially from the “bottom-up” using repeated water exposures and annealing cycles, with the partial pressure of water ranging from 10−10 to 10 Torr. The resultant films were then compared to the equivalent thicknesses of thermal and native oxide films. In this way, we obtain unprecedented insight into the essential chemical structures formed during the initial oxidation and subsequent layer growth of these technologically relevant films.
Multiple description source coding using forward error correction codes (2003)

We present an efficient multiple description (MD) source coding scheme to achieve robust communication over unreliable channels. In contrast to the popular signal processing based methods, we propose channel coding principles to correlate the descriptions, and then use this correlation for combating channel impairments. We propose a fast, nearly optimal algorithm that aims to maximize the expected quality at the receiver given the channel state and the side channel rates. Our scheme can be used in conjunction with any source coder that is scalable, and is most easily matched to coders outputting a progressive bitstream. It has applications to the transmission of audio, images, as well as delay-constrained video signals, and can also be used to achieve reliable multicast transmission over the existing Internet with the use of simple protocols. Comparisons of our scheme on standard test images to some of the existing state-of-the-art signal processing based MD methods suggest that our simple scheme outperforms them by significant margins.
Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 (1998)

The product specificity and pH optimum of the thermostable cyclodextrin glycosyltransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes EM1 was engineered using a combination of x-ray crystallography and site-directed mutagenesis. Previously, a crystal soaking experiment with the Bacillus circulans strain 251 beta-CGTase had revealed a maltononaose inhibitor bound to the enzyme in an extended conformation. An identical experiment with the CGTase from T. thermosulfurigenes EM1 resulted in a 2.6-A resolution x-ray structure of a complex with a maltohexaose inhibitor, bound in a different conformation. We hypothesize that the new maltohexaose conformation is related to the enhanced alpha-cyclodextrin production of the CGTase. The detailed structural information subsequently allowed engineering of the cyclodextrin product specificity of the CGTase from T. thermosulfurigenes EM1 by site-directed mutagenesis. Mutation D371R was aimed at hindering the maltohexaose conformation and resulted in enhanced production of larger size cyclodextrins (beta- and gamma-CD). Mutation D197H was aimed at stabilization of the new maltohexaose conformation and resulted in increased production of alpha-CD. Glu258 is involved in catalysis in CGTases as well as alpha-amylases, and is the proton donor in the first step of the cyclization reaction. Amino acids close to Glu258 in the CGTase from T. thermosulfurigenes EM1 were changed. Phe284 was replaced by Lys and Asn327 by Asp. The mutants showed changes in both the high and low pH slopes of the optimum curve for cyclization and hydrolysis when compared with the wild-type enzyme. This suggests that the pH optimum curve of CGTase is determined only by residue Glu258.
The chalcone synthase superfamily of type III polyketide synthases (2002)

This review covers the functionally diverse type III polyketide synthase (PKS) superfamily of plant and bacterial biosynthetic enzymes. from the discovery of chalcone synthase (CHS) in the 1970s through the end of 2001. A broader perspective is achieved by a comparison of these CHS-like enzymes to mechanistically and evolutionarily related families of enzymes, including the type I and type II PKSs, as well as the thiolases and beta-ketoacyl synthases of fatty acid metabolism. As CHS is both the most frequently occurring and best studied type III PKS, this enzyme's structure and mechanism is examined in detail. The in vivo functions and biological activities of several classes of plant natural products derived from chalcones are also discussed. Evolutionary mechanisms of type III PKS divergence are considered, as are the biological functions and activities of each of the known and functionally divergent type III PKS enzymc families (currently twelve in plants and three in bacteria). A major focus of this review is the integration of information from genetic and biochemical studies with the unique insights gained from protein X-ray crystallography and homology modeling. This structural approach has generated a number of new predictions regarding both the importance and mechanistic role of various amino acid substitutions observed among functionally diverse type III PKS enzymes.
Application of the Solid Dispersion Method to Controlled Release of Medicine. II. Sustained Release Tablet Using Solid Dispersion Granule and the Medicine Release Mechanism. (1992)

In our previous paper, the utility of the solid dispersion for the control of medicine release was studied and the solid dispersion was prepared by the evaporation of ethanol after dissolving a water soluble medicine (oxprenolol hydrochloride), soluble hydroxypropyl cellulose and insoluble ethylcellulose into ethanol. In this paper, the tableting of the above mentioned solid dispersion granule and mechanism of medicine release from this solid dispersion granule were studied. Microcrystalline cellulose was used as the excipient in this tableting. The disintegration time, crushing strength and porosity were measured for the obtained tablets. The pore size distribution in the solid dispersion granules was measured before and after the dissolution test with a mercury porosimeter to clarify the mechanism of medicine release from the granules. The state of medicine in the granules was analyzed by infrared spectrometry, thermal analysis and X-ray diffractometry.As a result, it was clarified that oxprenolol hydrochloride in ethylcellulose was released from the granules by diffusing and dissolving into the medium in the channels formed by the dissolving of hydroxypropyl cellulose and oxprenolol hydrochloride, as inferred in the previous paper. Furthermore, the compression pressure and pH scarcely affected the dissolution behavior of oxprenolol hydrochloride from the granules. It was thought that the homogeneity of the content of oxprenolol hydrochloride in the granules was very high, and the dissolution rate from the granules could be controlled by the particle size of the granules and the composition ratio of ethylcellulose and hydroxypropyl cellulose in the granules. These results suggest the solid dispersion granule and the tablet prepared with this granule are useful for the sustained release granule and tablet.