gebhart/patrepeval huggingface dataset:
A New Approach for Algebraically Homomorphic Encryption. (2008)

The existence of an efficient and provably secure algebraically homomorphic scheme (AHS), i.e., one that supports both addition and multiplication operations, is a long stated open problem.All proposals so far are either insecure or not provable secure, inefficient, or allow only for one multiplication (and arbitrary additions).As only very limited progress has been made on the existing approaches in the recent years, the question arises whether new methods can lead to more satisfactory solutions.In this paper we show how to construct a provably secure AHS based on a coding theory problem.It allows for arbitrary many additions and for a fixed, but arbitrary number of multiplications and works over arbitrary finite fields.Besides, it possesses some useful properties: i) the plaintext space can be extended adaptively without the need for re-encryption, ii) it operates over arbitrary infinite fields as well, e.g., rational numbers, but the hardness of the underlying decoding problem in such cases is less studied, and iii) depending on the parameter choice, the scheme has inherent error-correcting up to a certain number of transmission errors in the ciphertext.However, since our scheme is symmetric and its ciphertext size grows exponentially with the expected total number of encryptions, its deployment is limited to specific client/server applications with few number of multiplications.Nevertheless, we believe room for improvement due to the huge number of alternative coding schemes that can serve as the underlying hardness problem.For these reasons and because of the interesting properties of our scheme, we believe that using coding theory to design AHS is a promising approach and hope to encourage further investigations.
Fast Spiral Coronary Artery Imaging (1992)

A flow-independent method for imaging the coronary arteries within a breath-hold on a standard whole-body MR imager was developed. The technique is based on interleaved spiral k-space scanning and forms a cardiac-gated image in 20 heartbeats. The spiral readouts have good flow properties and generate minimal flow artifacts. The oblique slices are positioned so that the arteries are in the plane and so that the chamber blood does not obscure the arteries. Fat suppression by a spectral-spatial pulse improves the visualization of the arteries.
Targeting Amino Acid Transport in Metastatic Castration-Resistant Prostate Cancer: Effects on Cell Cycle, Cell Growth, and Tumor Development (2013)

Inhibition of LAT transporters may provide a novel therapeutic target in metastatic castration-resistant prostate cancer, via suppression of mammalian target of rapamycin complex 1 activity and M-phase cell cycle genes.
Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells (2004)

We describe the generation of a complete set of orthogonal 21st synthetase-amber, ochre and opal suppressor tRNA pairs including the first report of a 21st synthetase-ochre suppressor tRNA pair. We show that amber, ochre and opal suppressor tRNAs, derived from Escherichia coli glutamine tRNA, suppress UAG, UAA and UGA termination codons, respectively, in a reporter mRNA in mammalian cells. Activity of each suppressor tRNA is dependent upon the expression of E.coli glutaminyl-tRNA synthetase, indicating that none of the suppressor tRNAs are aminoacylated by any of the twenty aminoacyl-tRNA synthetases in the mammalian cytoplasm. Amber, ochre and opal suppressor tRNAs with a wide range of activities in suppression (increases of up to 36, 156 and 200-fold, respectively) have been generated by introducing further mutations into the suppressor tRNA genes. The most active suppressor tRNAs have been used in combination to concomitantly suppress two or three termination codons in an mRNA. We discuss the potential use of these 21st synthetase-suppressor tRNA pairs for the site-specific incorporation of two or, possibly, even three different unnatural amino acids into proteins and for the regulated suppression of amber, ochre and opal termination codons in mammalian cells.
Synergy between Polyethylenimine and Different Families of Antibiotics against a Resistant Clinical Isolate of Pseudomonas aeruginosa (2008)

The in vitro activities of 10 families of antimicrobial agents alone and in combination with a synthetic polycationic polymer, polyethylenimine (PEI), against a resistant clinical isolate of Pseudomonas aeruginosa were investigated by MIC assays, checkerboard testing, and killing curve studies. At a concentration of 250 nM, PEI (10 kDa) was not directly bactericidal or bacteriostatic; but when it was used in combination with novobiocin, ceftazidime, ampicillin, ticarcillin, carbenicillin, piperacillin, cefotaxime, chloramphenicol, rifampin, or norfloxacin, it significantly reduced the MICs of these antibiotics by 1.5- to 56-fold. However, the MICs of aminoglycosides, polymyxins, and vancomycins were increased by 1.2- to 5-fold when these drugs were combined with PEI; and the MICs of tetracycline, erythromycin, ciprofloxacin, and ofloxacin were not affected when these drugs were combined with PEI. In the killing curve studies, combinations of PEI with novobiocin, ceftazidime, chloramphenicol, or rifampin resulted in 5- to 8-log(10) CFU/ml reductions in bacterial counts when 25% of the MIC of each antibiotic was used. These results indicate that infections due to resistant Pseudomonas strains could be treated by the use of a synergistic combination of PEI and antimicrobial drugs.
Assembly and Self-Organization of Silver Nanocrystal Superlattices:  Ordered “Soft Spheres” (1998)

Hydrophobic dodecanethiol-capped silver nanocrystals ranging from 50 to 80 Å in diameter were synthesized using arrested growth methods. Size-selective precipitation was employed to isolate nanocrystals homogeneous in size and shape which exhibited close-packed structural order after drying on a carbon or mica substrate. Elemental analysis, H1 NMR and FTIR spectroscopies were used to characterize the compositional features of the adsorbed thiolate ligands on nanocrystals suspended in solution and condensed in nanocrystal films. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) were used to probe the structure of both individual nanocrystals and superlattices, and to estimate the energetic interactions between these sterically stabilized particles. In terms of these measurements, the effects of the capping ligand coverage, particle faceting and shape, and interparticle attractions on superlattice formation are elucidated. In particular, the concept of nanocrystals as “soft spheres” which order with an effective hard sphere diameter is introduced. In addition, the ways in which nanocrystals deviate from such an ideal model are discussed.
Angle-and polarization-dependent collective excitation of plasmonic nanoarrays for surface enhanced infrared spectroscopy (2011)

Our recent work has showed that diffractively coupled nanoplasmonic arrays for Fourier transform infrared (FTIR) microspectroscopy can enhance the Amide I protein vibrational stretch by up to 10(5) times as compared to plain substrates. In this work we consider computationally the impact of a microscope objective illumination cone on array performance. We derive an approach for computing angular- and spatially-averaged reflectance for various numerical aperture (NA) objectives. We then use this approach to show that arrays that are perfectly optimized for normal incidence undergo significant response degradation even at modest NAs, whereas arrays that are slightly detuned from the perfect grating condition at normal incidence irradiation exhibit only a slight drop in performance when analyzed with a microscope objective. Our simulation results are in good agreement with microscope measurements of experimentally optimized periodic nanoplasmonic arrays.
Nanofluidic channels fabrication and manipulation of DNA molecules (2006)

Nanofluidic channel arrays, which have a width of about 40 nm, depth of 60 nm and length of 50 mum, were created using a focused-ion-beam milling instrument on a silicon nitride film swiftly and exactly, as is necessary. Stained -DNA molecules were put inside these sub-100 nm conduits by capillary force and they were stretched and transferred along these conduits, which were dealt with activating reagent Brij aqueous solution in advance. The movements of DNA molecules in these channels were discussed. These nano-structure channels may be useful in the study and analysis of the statics as well as the dynamics of single biomolecules.
Doing Immunology on a Chip (2000)

Using DNA microarrays to measure changes in gene expression patterns may reveal the mysteries of normal immune cells and also of diseases in which immune cells go astray, such as autoimmunity and cancer. Information gleaned by microarray analysis should also help to both diagnose disease and find new therapies. But like other chip users, immunologists are facing a looming data overload, as every single chip provides information on thousands of gene changes; distilling the few that actually matter for the biological activity under investigation will require the ability to present the data in a way the human mind can comprehend.
A retrospective investigation of the relationship between baseline covariates and rate of ALSFRS-R decline in ALS clinical trials (2017)

The revised ALS functional rating scale (ALSFRS-R) is a longitudinal measure of global function commonly used to assess progression of amyotrophic lateral sclerosis (ALS), and as an endpoint in ALS clinical trials. Understanding how baseline covariates affect the rate of functional decline in ALS offers valuable information to clinical trialists. We used a mixed modeling approach in a retrospective study of the pooled resource open-Access ALS clinical trials database to elucidate the associations between baseline covariates and the rate of ALSFRS-R decline over time. In a cohort of 3203 patients followed for an average of 337 days, older age at disease onset (p < 0.001), less time since disease onset (p < 0.001), and bulbar site of onset (p < 0.001) were associated with a significantly faster decline of the ALSFRS-R, while sex did not have a statistically significant effect (p = 0.82). Selective inclusion of 'age at disease onset' and 'time since disease onset' as covariates provided the best tradeoff between model fit and model precision. The effect of bulbar onset on rate of disease progression was primarily due to accelerated decline in the bulbar subscale of the ALSFRS-R. These findings, which are novel in the clinical trial time frame, contribute to the understanding of disease trajectory in ALS and can be used to guide future design and analysis of clinical trials.
Further biochemical characterization, including the detection of surface glycoproteins, of human, calf, and simian rotaviruses (1977)

Polyacrylamide gel electrophoretic analysis of purified preparation of the simian rotavirus SA-11 indicated eight polypeptide components that migrated in a manner remarkably similar to those of the previously characterized human and calf rotaviruses. Analyses of preparations of single-shelled and double-shelled particles of human, calf, and simian an rotaviruses have also permitted assignment of the polypeptides to the inner or outer shells. The major components of the outer shells of each virus have been identified as glycoproteins, and the importance of this in terms of host cell specificity is discussed. Sensitivities of the various rotaviruses to acid, proteases, and glycosidases were also investigated.
An Approach to Studying Lung Cancer-related Proteins in Human Blood (2005)

Early stage lung cancer detection is the first step toward successful clinical therapy and increased patient survival. Clinicians monitor cancer progression by profiling tumor cell proteins in the blood plasma of afflicted patients. Blood plasma, however, is a difficult cancer protein assessment medium because it is rich in albumins and heterogeneous protein species. We report herein a method to detect the proteins released into the circulatory system by tumor cells. Initially we analyzed the protein components in the conditioned medium (CM) of lung cancer primary cell or organ cultures and in the adjacent normal bronchus using one-dimensional PAGE and nano-ESI-MS/MS. We identified 299 proteins involved in key cellular process such as cell growth, organogenesis, and signal transduction. We selected 13 interesting proteins from this list and analyzed them in 628 blood plasma samples using ELISA. We detected 11 of these 13 proteins in the plasma of lung cancer patients and non-patient controls. Our results showed that plasma matrix metalloproteinase 1 levels were elevated significantly in late stage lung cancer patients and that the plasma levels of 14-3-3 sigma, beta, and eta in the lung cancer patients were significantly lower than those in the control subjects. To our knowledge, this is the first time that fascin, ezrin, CD98, annexin A4, 14-3-3 sigma, 14-3-3 beta, and 14-3-3 eta proteins have been detected in human plasma by ELISA. The preliminary results showed that a combination of CD98, fascin, polymeric immunoglobulin receptor/secretory component and 14-3-3 eta had a higher sensitivity and specificity than any single marker. In conclusion, we report a method to detect proteins released into blood by lung cancer. This pilot approach may lead to the identification of novel protein markers in blood and provide a new method of identifying tumor biomarker profiles for guiding both early detection and therapy of human cancer.
Prognosis of hepatocellular carcinoma expressing cytokeratin 19: Comparison with other liver cancers (2012)

Primary liver cancers with biliary components tended to show poorer surgical outcome. This suggested that immuno-phenotype of liver cancers was as important as their morphological classification.
Smart assistants for smart homes (2013)

The smarter homes of tomorrow promise to increase comfort, aid elderly and disabled people, and help inhabitants save energy. Unfortunately, smart homes today are far from this vision – people who already live in such a home struggle with complicated user interfaces, inflexible home configurations, and difficult installation procedures. Under these circumstances, smart homes are not ready for mass adoption. This dissertation addresses these issues by proposing two smart assistants for smart homes. The first assistant is a recommender system that suggests useful services (i.e actions that the home can perform for the user). The recommended services are fitted to the user’s current situation, habits, and preferences. With these recommendations it is possible to build much simpler user interfaces that highlight the most interesting choices currently available. Configuration becomes much more flexible: since the recommender system automatically learns user habits, user routines no longer have to be manually described. Evaluations with two smart home datasets show that the correct service is included in the top five recommendations in 90% of all cases. The second assistant addresses the difficult installation procedures. The unique feature of this assistant is that it removes the need for manually describing device functionalities (such descriptions are needed by the recommender system). Instead, users can simply plug in a new device, begin using it, and let the installation assistant identify what the device is doing. The installation assistant has minimal requirements for manufacturers of smart home devices and was successfully integrated with an existing smart home. Evaluations performed with this smart home show that the assistant can quickly and reliably learn device functionalities.
Circular permutation of a synthetic eukaryotic chromosome with the telomerator (2014)

Chromosome engineering is a major focus in the fields of systems biology, genetics, synthetic biology, and the functional analysis of genomes. Here, we describe the "telomerator," a new synthetic biology device for use in Saccharomyces cerevisiae. The telomerator is designed to inducibly convert circular DNA molecules into mitotically stable, linear chromosomes replete with functional telomeres in vivo. The telomerator cassette encodes convergent yeast telomere seed sequences flanking the I-SceI homing endonuclease recognition site in the center of an intron artificially transplanted into the URA3 selectable/counterselectable auxotrophic marker. We show that inducible expression of the homing endonuclease efficiently generates linear molecules, identified by using a simple plate-based screening method. To showcase its functionality and utility, we use the telomerator to circularly permute a synthetic yeast chromosome originally constructed as a circular molecule, synIXR, to generate 51 linear variants. Many of the derived linear chromosomes confer unexpected phenotypic properties. This finding indicates that the telomerator offers a new way to study the effects of gene placement on chromosomes (i.e., telomere proximity). However, that the majority of synIXR linear derivatives support viability highlights inherent tolerance of S. cerevisiae to changes in gene order and overall chromosome structure. The telomerator serves as an important tool to construct artificial linear chromosomes in yeast; the concept can be extended to other eukaryotes.
Expanded GGGGCC repeat RNA associated with amyotrophic lateral sclerosis and frontotemporal dementia causes neurodegeneration (2013)

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) share phenotypic and pathologic overlap. Recently, an expansion of GGGGCC repeats in the first intron of C9orf72 was found to be a common cause of both illnesses; however, the molecular pathogenesis of this expanded repeat is unknown. Here we developed both Drosophila and mammalian models of this expanded hexanucleotide repeat and showed that expression of the expanded GGGGCC repeat RNA (rGGGGCC) is sufficient to cause neurodegeneration. We further identified Pur α as the RNA-binding protein of rGGGGCC repeats and discovered that Pur α and rGGGGCC repeats interact in vitro and in vivo in a sequence-specific fashion that is conserved between mammals and Drosophila. Furthermore, overexpression of Pur α in mouse neuronal cells and Drosophila mitigates rGGGGCC repeat-mediated neurodegeneration, and Pur α forms inclusions in the fly eye expressing expanded rGGGGCC repeats, as well as in cerebellum of human carriers of expanded GGGGCC repeats. These data suggest that expanded rGGGGCC repeats could sequester specific RNA-binding protein from their normal functions, ultimately leading to cell death. Taken together, these findings suggest that the expanded rGGGGCC repeats could cause neurodegeneration, and that Pur α may play a role in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia.
Heat Shock Protein 47 and Renal Fibrogenesis (2005)

Recent research has greatly increased our knowledge regarding the molecular mechanisms of collagen synthesis and processing. Heat specific shock protein (HSP47) is a collagen-specific molecular chaperone, and helps in post-translational modifications of procollagens, during biosynthesis of collagen. Both in vivo and in vitro studies have convincingly demonstrated that HSP47 is localized in the endoplasmic reticulum of collagen-producing cells, and that its synthesis is closely associated with the rate of procollagen assembly. Recent studies are directed towards the pathological relevance of HSP47 in tissue scarring, a process that is characterized by excessive accumulation of collagens. It appears likely that increased levels of HSP47 in fibrotic diseases assist in increased assembly of procollagen, and thereby help in excessive accumulation of collagens in the fibrotic mass. Such profibrotic effects of HSP47 suggest that modulation of HSP47 expression in scarring diseases might alter the course of fibrotic diseases. In this brief article, we review the role of HSP47 in renal fibrotic diseases and its relevance to other scarring diseases.
Cloning and Expression of a Developmentally Regulated Protein That Induces Mitogenic and Neurite Outgrowth Activity (1990)

A heparin binding mitogenic protein isolated from bovine uterus shares NH2-terminal amino acid sequence with a protein isolated from newborn rat brain. The cDNA's of the bovine, human, and rat genes have been isolated and encode extraordinarily conserved proteins unrelated to known growth or neurotrophic factors, although identity of nearly 50 percent has been found with the predicted sequence of a retinoic acid induced transcript in differentiating mouse embryonal carcinoma cells. Lysates of COS-7 cells transiently expressing this protein were mitogenic for NRK cells and initiated neurite outgrowth from mixed cultures of embryonic rat brain cells. RNA transcripts encoding this protein were widely distributed in tissues and were developmentally regulated. This protein, previously designated as heparin binding growth factor (HBGF)-8, is now renamed pleiotrophin (PTN) to reflect its diverse activities. PTN may be the first member of a family of developmentally regulated cytokines.
Immunochemistry of groups A, B, and C meningococcal polysaccharide-tetanus toxoid conjugates. (1981)

The successful coupling of the meningococcal groups A, B, and C polysaccharides to tetanus toxoid to yield water soluble conjugates is described. Reactive aldehyde groups were strategically introduced into the terminal residues of the polysaccharides by the controlled periodate oxidation of the native groups B and C polysaccharides and of the group A polysaccharide previously modified by the reduction of its terminal reducing N-acetyl-mannosamine residue. This produced essentially monovalent polysaccharide molecules, which were subsequently covalently linked to tetanus toxoid by means of reductive amination. Although the groups A and C polysaccharides proved to be poor immunogens in rabbits and mice, their tetanus toxoid conjugates produced high levels of polysaccharide-specific antibodies in both animals. By contrast, even in the form of its tetanus toxoid conjugate, the group B polysaccharide failed to elicit homologous polysaccharide-specific antibodies in either animal; a major proportion of the antibodies actually produced had a specificity for the linkage area of the conjugate. This evidence is compatible with the hypothesis of the poor immunogenicity of the group B polysaccharide being structure related. Hyperimmunization of mice with the groups A and C polysaccharide-tetanus toxoid conjugates produced antisera with good bactericidal activity against their respective homologous organisms, and indicated the potential of these conjugates as potential human vaccines.