gebhart/patrepeval huggingface dataset:
EXPLORING CONDITIONS FOR THE OPTIMALITY OF NAÏVE BAYES (2005)

Naïve Bayes is one of the most efficient and effective inductive learning algorithms for machine learning and data mining. Its competitive performance in classification is surprising, because the conditional independence assumption on which it is based is rarely true in real-world applications. An open question is: what is the true reason for the surprisingly good performance of Naïve Bayes in classification? In this paper, we propose a novel explanation for the good classification performance of Naïve Bayes. We show that, essentially, dependence distribution plays a crucial role. Here dependence distribution means how the local dependence of an attribute distributes in each class, evenly or unevenly, and how the local dependences of all attributes work together, consistently (supporting a certain classification) or inconsistently (canceling each other out). Specifically, we show that no matter how strong the dependences among attributes are, Naïve Bayes can still be optimal if the dependences distribute evenly in classes, or if the dependences cancel each other out. We propose and prove a sufficient and necessary condition for the optimality of Naïve Bayes. Further, we investigate the optimality of Naïve Bayes under the Gaussian distribution. We present and prove a sufficient condition for the optimality of Naïve Bayes, in which the dependences among attributes exist. This provides evidence that dependences may cancel each other out. Our theoretic analysis can be used in designing learning algorithms. In fact, a major class of learning algorithms for Bayesian networks are conditional independence-based (or CI-based), which are essentially based on dependence. We design a dependence distribution-based algorithm by extending the ChowLiu algorithm, a widely used CI based algorithm. Our experiments show that the new algorithm outperforms the ChowLiu algorithm, which also provides empirical evidence to support our new explanation.
Comparison of Targeted-Gene Replacement Frequencies in Drosophila melanogaster at the forked and white Loci (1996)

P element-induced gene conversion has been previously used to modify the white gene of Drosophila melanogaster in a directed fashion. The applicability of this approach of gene targeting in Drosophila melanogaster, however, has not been analyzed quantitatively for other genes. We took advantage of the P element-induced forked allele, f(hd), which was used as a target, and we constructed a vector containing a modified forked fragment for converting f(hd). Conversion frequencies were analyzed for this locus as well as for an alternative white allele, w(eh812). Combination of both P element-induced mutant genes allowed the simultaneous analysis of conversion frequencies under identical genetic, developmental, and environmental conditions. This paper demonstrates that gene conversion through P element-induced gap repair can be applied with similar success rates at the forked locus and in the white gene. The average conversion frequency at forked was 0.29%, and that at white was 0.17%. These frequencies indicate that in vivo gene targeting in Drosophila melanogaster should be applicable for other genes in this species at manageable rates. We also confirmed the homolog dependence of reversions at the forked locus, indicating that P elements transpose via a cut-and-paste mechanism. In a different experiment, we attempted conversion with a modified forked allele containing the su(Hw) binding site. Despite an increased sample size, there were no conversion events with this template. One interpretation (under investigation) is that the binding of the su(Hw) product prevents double-strand break repair.
Soft-Output Trellis/Tree Iterative Decoder for high-order BICM on MIMO Frequency Selective Rayleigh Fading Channels (2006)

This paper presents a reduced-complexity soft-output trellis/tree equalizer for a high-order modulated MIMO system undergoing equal-power, Rayleigh frequency-selective fading. The algorithm reduces the complexity of trellis decoding by applying the M-algorithm twice, once to reduce the number of states in the trellis, and the other to reduce the number of tree branches emanating from each state. For soft-information, the algorithm utilizes not only those fully-extended paths reaching the end of the trellis, but also paths that are traversed and discarded in the pruned trellis. Our results demonstrated that the proposed algorithm is capable of achieving near-optimal performance with a much reduced complexity.
Genetically modified v natural food... round two (1999)

Who would want to be a dietician at a time like this? Or a politician even?
A performance comparison study of ad hoc wireless multicast protocols (2002)

In this paper we investigate the performance of multicast routing protocols in wireless mobile ad hoc networks. An ad hoc network is composed of mobile nodes without the presence of a wired support infrastructure. In this environment, routing/multicasting protocols are faced with the challenge of producing multihop routes under host mobility and bandwidth constraints. In recent years, a number of new multicast protocols of different styles have been proposed for ad hoc networks. However, systematic performance evaluations and comparative analysis of these protocols in a common realistic environment has not yet been performed. In this study, we simulate a set of representative wireless ad hoc multicast protocols and evaluate them in various network scenarios. The relative strengths, weaknesses, and applicability of each multicast protocol to diverse situations are studied and discussed.
A transcriptionally active DNA-binding site for human p53 protein complexes. (1992)

Recent studies have demonstrated transcriptional activation domains within the tumor suppressor protein p53, while others have described specific DNA-binding sites for p53, implying that the protein may act as a transcriptional regulatory factor. We have used a reiterative selection procedure (CASTing: cyclic amplification and selection of targets) to identify new specific binding sites for p53, using nuclear extracts from normal human fibroblasts as the source of p53 protein. The preferred consensus is the palindrome GGACATGCCCGGGCATGTCC. In vitro-translated p53 binds to this sequence only when mixed with nuclear extracts, suggesting that p53 may bind DNA after posttranslational modification or as a complex with other protein partners. When placed upstream of a reporter construct, this sequence promotes p53-dependent transcription in transient transfection assays.
Inside Cover: Encoding Molecular‐Wire Formation within Nanoscale Sockets (Angew. Chem. Int. Ed. 21/2007) (2007)

Coordination chemistry provides a versatile method to form molecular-scale wires between nanoscale electrodes, as S. J. Wind, C. Nuckolls, and co-workers describe in their Communication on page 3892 ff. First, a bifunctional molecule is assembled into a monolayer on the electrode surface such that only one end of the molecule reacts with the electrode, and then a second molecule (e.g. a metal ion, as shown in the picture) is introduced to span the gap between the termini of the closely spaced nanoscale films.
Ultrafast optical probes of excited states in poly(1,4-phenylene vinylene) and poly(2-fluoro-1,4-phenylene vinylene) (1997)

We have investigated the photoexcitation dynamics of poly(1,4-phenylene vinylene) (PPV) and poly(2-fluoro-1,4-phenylene vinylene) (PFPV) by using the femtosecond transient absorption spectroscopic technique. It was demonstrated that photoinduced absorption originates from nonemissive indirect polaron pairs which are more efficiently produced in PFPV than in PPV. The decay processes of polaron pairs are mainly contributed by collisional annihilation and internal conversion by phonon emission in PFPV and PPV, respectively. The differences in photoexcitation dynamics between PPV and PFPV are believed to be caused by the strong electronegativity of substituted fluorine atom.
An Ink-Jet-Deposited Passive Component Process for RFID (2004)

An all ink-jet-deposited process capable of creating high-quality passive devices suitable for an RFID front-end is described. Gold nanocrystals are printed to create conductive lines with sheet resistance as low as 23 m/spl Omega/ per square. Optimal printing conditions are found for polyimide dielectric layers and films as thin as 340 nm are produced. These results are used to create spiral inductors, interconnect, and parallel plate capacitors.
ChemInform Abstract: Copper‐Catalyzed C—Se Coupling of Diphenyl Diselenide with Arylboronic Acids at Room Temperature. (2013)

Abstract The novel protocol allows a practical synthesis of diaryl selenides under mild conditions.
Size Comparisons among Integral Membrane Transport Protein Homologues in Bacteria , Archaea , and Eucarya (2001)

Integral membrane proteins from over 20 ubiquitous families of channels, secondary carriers, and primary active transporters were analyzed for average size differences between homologues from the three domains of life: Bacteria, Archaea, and Eucarya. The results showed that while eucaryotic homologues are consistently larger than their bacterial counterparts, archaeal homologues are significantly smaller. These size differences proved to be due primarily to variations in the sizes of hydrophilic domains localized to the N termini, the C termini, or specific loops between transmembrane alpha-helical spanners, depending on the family. Within the Eucarya domain, plant homologues proved to be substantially smaller than their animal and fungal counterparts. By contrast, extracytoplasmic receptors of ABC-type uptake systems in Archaea proved to be larger on average than those of their bacterial homologues, while cytoplasmic enzymes from different organisms exhibited little or no significant size differences. These observations presumably reflect evolutionary pressure and molecular mechanisms that must have been operative since these groups of organisms diverged from each other.
Androgen receptor variants with short glutamine or glycine repeats may identify unique subpopulations of men with prostate cancer. (1997)

The androgen receptor (AR) contains glutamine (CAG) and glycine (GGC) repeats that are each polymorphic in length. We screened clinically localized prostate cancers for somatic mutations in the length of the CAG and GGC repeats in the AR gene and characterized the length of these repeats in the germ-line AR gene. Somatic mutations were rare, and the range of germ-line repeat lengths in men with prostate cancer was within the range of normal in the general population. Most allele frequencies in Caucasian men with clinical prostate cancer were remarkably comparable to those in the general Caucasian population. However, a subpopulation of the men with clinical prostate cancer had a substantially higher frequency of AR alleles with 16 or 17 CAGs (6 of 59 men, 10%) than did the general population (6 of 370 alleles, 1.6%), and a different subpopulation of the men with prostate cancer had a higher frequency of AR alleles with 12 or 13 GGCs (7 of 54 men, 13%) than did the general population (1 of 110 alleles, 0.9%). Of the men with prostate cancer who had an AR gene with 16 or 17 CAGs, 83% had lymph node-positive disease, despite the lack of clinical evidence of metastatic spread. This suggests that a short AR CAG allele may be a risk factor for the development of clinically unsuspected lymph node-positive prostate cancer among men undergoing radical prostatectomy and raises the question of whether this short repeat length played an active role in the development of aggressive prostate cancer. The odds of having a germ-line AR gene with a short CAG repeat (</=17 CAGs) were substantially higher in Caucasian men with lymph node-positive prostate cancer than in Caucasian men with lymph node-negative disease or in the general Caucasian population. The odds of having a short germ-line AR CAG were the same for men with lymph node-negative prostate cancer as for the general Caucasian population. The odds of having a germ-line AR gene with a short glycine repeat (</=14 GGCs) were substantially higher in men with prostate cancer than in the general population, but the frequency of alleles with a short GGC repeat was the same in men with lymph node-positive versus lymph node-negative disease. This suggests that a short GGC repeat may be a risk factor for the development of clinical prostate cancer, a hypothesis that needs to be tested in cohort and case-control studies.
Multiple promoters and induction by heat shock of the gene encoding the alternative sigma factor AlgU (sigma E) which controls mucoidy in cystic fibrosis isolates of Pseudomonas aeruginosa (1995)

Overproduction of the exopolysaccharide alginate causes mucoid colony morphology in Pseudomonas aeruginosa and is considered a major virulence determinant expressed by this organism during chronic respiratory infections in cystic fibrosis. One of the principal regulatory elements governing conversion to mucoidy in P. aeruginosa is AlgU, an alternative sigma factor which is 66% identical to and functionally interchangeable with sigma E from Escherichia coli and Salmonella typhimurium. sigma E has been implicated in the expression of systems enhancing bacterial resistance to environmental stress. In this study, we report that the gene encoding AlgU is transcribed in wild-type nonmucoid P. aeruginosa from multiple promoters (P1 through P5) that fall into three categories: (i) the P1 and P3 promoters, which display strong similarity to the -35 and -10 canonical sequences of sigma E promoters and were found to be absolutely dependent on AlgU; (ii) the P2 promoter, which was less active in algU mutants, but transcription of which was not completely abrogated in algU::Tcr cells; and (iii) the transcripts corresponding to P4 and P5, which were not affected by inactivation of algU. Introduction of E. coli rpoE (encoding sigma E) or algU into P. aeruginosa algU::Tcr strains restored P1 and P3 transcription and brought the P2 signal back to the wild-type level. The AlgU-dependent promoters P1 and P3 were inducible by heat shock in wild-type nonmucoid P. aeruginosa PAO1. At the protein level, induction of AlgU synthesis under conditions of extreme heat shock was detected by metabolic labeling of newly synthesized proteins, two-dimensional gel analysis, and reaction with polyclonal antibodies raised against an AlgU peptide. Another AlgU-dependent promoter, the proximal promoter of algR, was also found to be induced by heat shock. Under conditions of high osmolarity, growth at elevated temperature induced alginate synthesis in the wild-type nonmucoid P. aeruginosa PAO1. Cumulatively, these results suggest that algU itself is subject to complex regulation and is inducible by extreme heat shock, that the alginate system is a subset of the stress-responsive elements controlled by AlgU, and that AlgU and, by extension, its homologs in other organisms (e.g., sigma E in S. typhimurium) may play a role in bacterial virulence and adjustments to adverse growth conditions.
Find the coaching in criticism (2014)

Feedback is crucial-but almost everyone, from new hires to C-suite executives, struggles with receiving it. The authors, who have spent 20 years working with managers on difficult conversations, outline six steps that can help you turn feedback into an important, and unthreatening, tool. Know your tendencies. Look for patterns in how you respond. (Do you defend yourself? Do you lash out?) Once you understand your standard operating procedure, you can make better choices about where to go from there. Separate the from the who. Your feelings about the messenger might be shortcircuiting your ability to learn from the message. Sort toward coaching. Work to hear feedback as well-meant advice, not as an indictment. Unpack the feedback. Resist snap judgments; explore where suggestions are coming from and where they're going. Request and direct feedback. Don't wait for a formal review; ask for bite-size pieces of coaching. Experiment. Try following a piece of advice and seeing what happens. Criticism is never easy to take-but learning to pull value from it is essential to your development and success
Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphingidae) and Its Natural Host Nicotiana attenuata . I. Large-Scale Changes in the Accumulation of Growth- and Defense-Related Plant mRNAs (2001)

Plants respond to herbivore attack with a dramatic functional reorganization that involves the activation of direct and indirect defenses and tolerance, which in turn make large demands on primary metabolism. Here we provide the first characterization of the transcriptional reorganization that occurs after insect attack in a model plant-herbivore system: Nicotiana attenuata Torr. ex Wats.-Manduca sexta. We used mRNA differential display to characterize one-twentieth of the insect-responsive transcriptome of N. attenuata and verified differential expression for 27 cDNAs. Northern analyses were used to study the effects of folivory and exposure to airborne methyl jasmonate and for kinetic analyses throughout a 16-h- light/8-h-dark cycle. Sequence similarity searches allowed putative functions to be assigned to 15 transcripts. Genes were related to photosynthesis, electron transport, cytoskeleton, carbon and nitrogen metabolism, signaling, and a group responding to stress, wounding, or invasion of pathogens. Overall, transcripts involved in photosynthesis were strongly down-regulated, whereas those responding to stress, wounding, and pathogens and involved in shifting carbon and nitrogen to defense were strongly up-regulated. The majority of transcripts responded similarly to airborne methyl jasmonate and folivory, and had tissue- and diurnal-specific patterns of expression. Transcripts encoding Thr deaminase (TD) and a putative retrotransposon were absent in control plants, but were strongly induced after herbivory. Full-length sequences were obtained for TD and the pathogen-inducible alpha-dioxygenase, PIOX. Effects of abiotic and biotic stimuli were investigated for transcripts encoding TD, importin alpha, PIOX, and a GAL83-like kinase cofactor.
CMOS micromachined capacitive cantilevers for mass sensing (2006)

In this paper, we present the design, fabrication and characterization of the CMOS micromachined cantilevers for mass sensing in the femtogram range. The cantilevers consisting of multiple metal and dielectric layers are fabricated after completion of a conventional CMOS process by dry etching steps. The cantilevers are electrostatically actuated to resonance by in-plane electrodes. The mechanical resonant frequency is detected capacitively with on-chip circuitry, where the modulation technique is applied to eliminate capacitive feedthrough from the driving port and to lessen the effect of flicker noise. The highest resonant frequency of the cantilevers is measured at 396.46 kHz with a quality factor of 2600 at 10 mTorr. The resonant frequency shift after deposition of a 0.1 µm SiO2 layer is 140 Hz, averaging 353 fg Hz−1.
Facial aging simulation based on super-resolution in tensor space (2008)

The facial change caused by aging progression might significantly degrade the performance of a face recognition system. One major way to deal with this problem is to predict the aging process. The work presented in this paper proposed a framework to simulate the face aging process by means of super-resolution. Considered the nature of multi- modalities in face image set, multi-linear algebra is introduced into the super-resolution method to represent and process the whole image set in tensor space. The simulating results represented in the paper are compared with the ground truth face image of the same people.
MAD2: A scalable high-throughput exact deduplication approach for network backup services (2010)

Deduplication has been widely used in disk-based secondary storage systems to improve space efficiency. However, there are two challenges facing scalable high-throughput deduplication storage. The first is the duplicate-lookup disk bottleneck due to the large size of data index that usually exceeds the available RAM space, which limits the deduplication throughput. The second is the storage node island effect resulting from duplicate data among multiple storage nodes that are difficult to eliminate. Existing approaches fail to completely eliminate the duplicates while simultaneously addressing the challenges. This paper proposes MAD2, a scalable high-throughput exact deduplication approach for network backup services. MAD2 eliminates duplicate data both at the file level and at the chunk level by employing four techniques to accelerate the deduplication process and evenly distribute data. First, MAD2 organizes fingerprints into a Hash Bucket Matrix (HBM), whose rows can be used to preserve the data locality in backups. Second, MAD2 uses Bloom Filter Array (BFA) as a quick index to quickly identify non-duplicate incoming data objects or indicate where to find a possible duplicate. Third, Dual Cache is integrated in MAD2 to effectively capture and exploit data locality. Finally, MAD2 employs a DHT-based Load-Balance technique to evenly distribute data objects among multiple storage nodes in their backup sequences to further enhance performance with a well-balanced load. We evaluate our MAD2 approach on the backend storage of B-Cloud, a research-oriented distributed system that provides network backup services. Experimental results show that MAD2 significantly outperforms the state-of-the-art approximate deduplication approaches in terms of deduplication efficiency, supporting a deduplication throughput of at least 100MB/s for each storage component.
Three-Dimensional Optical Sensing and Visualization Using Integral Imaging (2010)

Three-dimensional (3-D) optical image sensing and visualization technologies have been researched extensively for different applications in fields as diverse as entertainment, medical sciences, robotics, manufacturing, and defense. In many instances, the capabilities of 3-D imaging and display systems have revolutionized the progress of these disciplines, enabling new detection/display abilities that would not have been otherwise possible. As one of the promising methods in the area of 3-D sensing and display, integral imaging offers passive and relatively inexpensive way to capture 3-D information and to visualize it optically or computationally. The integral imaging technique belongs to the broader class of multiview imaging techniques and is based on a century old principle which has only been resurrected in the past decade owing to advancement of optoelectronic image sensors as well as the exponential increase in computing power. In this paper, historic and physical foundations of integral imaging are overviewed; different optical pickup and display schemes are discussed and system parameters and performance metrics are described. In addition, computational methods for reconstruction and range estimation are presented and several applications including 3-D underwater imaging, near infra red passive sensing, imaging in photon-starved environments, and 3-D optical microscopy are discussed among others.