gebhart/patrepeval huggingface dataset:
Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity (1985)

Full-length double-stranded cDNA was prepared from purified circular RNA of two new Australian field isolates of citrus exocortis viroid (CEV) using two synthetic oligodeoxynucleotide primers. The cDNA was then cloned into the phage vector M13mp9 for sequence analysis. Sequencing of nine cDNA clones of isolate CEV-DE30 and eleven cDNA clones of isolate CEV-J indicated that both isolates consisted of a mixture of viroid species and led to the discovery of eleven new sequence variants of CEV. These new variants, together with the six reported previously, form two classes of sequence which differ by a minimum of 26 nucleotides in a total of 370 to 375 residues. These two classes correlate with two biologically distinct groups when propagated on tomato plants where one produces severe symptoms and the other gives rise to mild symptoms. Two regions of the native structure of CEV, comprising 18% of the total residues, differ between the sequence variants of mild and severe isolates. Whether or not both of these regions are essential for the variation in pathogenicity has yet to be determined.
Automatic Information Extraction in Semi-structured Official Journals (2008)

Information extraction systems are used to extract only relevant text information in digital repositories. The current work proposes an automatic system to extract information in semi-structured official journals. In our approach, given an input document, a Machine Learning (ML) algorithm classifies the document’s fragments into class labels which correspond to the data fields to be extracted. The implemented system deployed different features sets and algorithms used in the classification of the fragments. The system was evaluated through experiments on a sample containing 22770 lines of the Pernambuco’s Official Journal. The experiments performed revealed, in general, good results in terms of precision, which ranged from 70.14% to 98.63% depending on the feature set and algorithm used in the classification of the fragments.
A Method of Breast Tumour MRI Segmentation and 3D Reconstruction (2015)

Proposed a method of 3D reconstruction on the segmentation of breast and tumor. Firstly, the contour of the breast is extracted by use of the combination method of Otsu and region growing. Secondly, the level set based on energy and gradient is made to segment the tumor exactly from breast. Finally, volume rendering is selected to deal with the segmentation results and ray casting method based on the bounding box with a combination of VTK library is adopted to realize the reconstruction. Experiments show that the proposed method has a good segmentation result and provides a more vivid 3D visual effect for doctors.
Silver-catalyzed TEMPO oxidative homocoupling of indoles for the synthesis of 3,3′-biindolin-2-ones (2015)

A silver-catalyzed TEMPO oxidative homo dimerization of indoles was first successful demonstrated. This new methodology is both atom and step efficient, allowing the synthesis of substituted C3–C3′ bisindolin-2-ones in moderate to excellent yields.
Status and trends in bioremediation treatment technology (1991)

Abstract This article is a critical analysis of the treatment potential of bioremediation technology to degrade eight major environmental pollutants, polycyclic aromatic hydrocarbons, phenols, pentachlorophenols, creosote, polychlorinated biphenyls, trichloroethylene, chlorobenzoates, and chlorophenols. The discussion includes information on transformation mechanisms, identification of intermediate metabolites, elucidation of partial or complete pathways, effects of environmental parameters, as well as current and future industrial application. Results indicate that bioremediation used in conjunction with other physical and chemical treatment methodologies can effectively transform most prevalent nonchlorinated organic contaminants and some chlorinated contaminants, such as creosote and pentachlorophenol, into innocuous materials. Successful biodegradation of several other chlorinated organic compounds, notably polychlorinated biphenyls and trichloroethylene, is currently possible only under controlled laboratory conditions. Future successful field applications, however, appear promising.
An Assessment of the Screening Method to Evaluate Vaccine Effectiveness: The Case of 7-Valent Pneumococcal Conjugate Vaccine in the United States (2012)

The screening method, which employs readily available data, is an inexpensive and quick means of estimating vaccine effectiveness (VE). We compared estimates of effectiveness of heptavalent pneumococcal conjugate vaccine (PCV7) against invasive pneumococcal disease (IPD) using the screening and case-control methods. Cases were children aged 19-35 months with pneumococcus isolated from normally sterile sites residing in Active Bacterial Core surveillance areas in the United States. Case-control VE was estimated for 2001-2004 by comparing the odds of vaccination among cases and community controls. Screening-method VE for 2001-2009 was estimated by comparing the proportion of cases vaccinated to National Immunization Survey-derived coverage among the general population. To evaluate the plausibility of screening-method VE findings, we estimated attack rates among vaccinated and unvaccinated persons. We identified 1,154 children with IPD. Annual population PCV7 coverage with ≥1 dose increased from 38% to 97%. Case-control VE for ≥1 dose was estimated as 75% against all-serotype IPD (annual range: 35-83%) and 91% for PCV7-type IPD (annual range: 65-100%). By the screening method, the overall VE was 86% for ≥1 dose (annual range: -240-70%) against all-serotype IPD and 94% (annual range: 62-97%) against PCV7-type IPD. As cases of PCV7-type IPD declined during 2001-2005, estimated attack rates for all-serotype IPD among vaccinated and unvaccinated individuals became less consistent than what would be expected with the estimated effectiveness of PCV7. The screening method yields estimates of VE that are highly dependent on the time period during which it is used and the choice of outcome. The method should be used cautiously to evaluate VE of PCVs.
The effect of glucocorticoids on bone and muscle (2015)

This article examines the current knowledge of the effects of both exogenous and endogenous glucocorticoids on bone and muscle. It demonstrates the similarity of effects of supraphysiologic loads of glucocorticoids regardless of whether they enter the body in the form of medication or are manufactured by the body in response to stimuli such as inflammation. The effects of endogenous glucocorticoids and the systemic inflammatory response resulting from pediatric burn injury are compared and the difficulty in sorting out which of the two factors is responsible for the ultimate effects on bone and muscle is pointed out. The focus then switches to the body's response to the influence of both glucocorticoids and inflammatory cytokines and evidence supporting a common pathway of response to oxidative damage caused by both is discussed. Current recommended medical management of glucocorticoid-induced bone and muscle loss is discussed and the failure to reconcile current management with known mechanisms is highlighted.
Cyclin E gene ( <i>CCNE</i> ) amplification and <i>hCDC4</i> mutations in endometrial carcinoma (2003)

Cyclin E overexpression occurs in a subset of endometrial carcinomas (ECs), but the molecular mechanisms underlying this alteration remain to be established. The present study has analysed amplification of the cyclin E gene (CCNE) and mutation in hCDC4, the gene coding for the F-box protein, which tags phosphorylated cyclin E for proteosomal degradation, to ascertain whether these alterations might be responsible for cyclin E overexpression in ECs. Cyclin E and p53 expression was studied by immunohistochemistry in eight atypical endometrial hyperplasias (AEHs), 51 endometrioid endometrial carcinomas (EECs), and 22 non-endometrioid endometrial carcinomas (NEECs). CCNE amplification was analysed by fluorescence in situ hybridization (FISH). Mutations in exons 2-11 of the hCDC4 gene were screened by PCR-SSCP-sequencing. Finally, the polymorphic marker D4S1610 was used to assess loss of heterozygosity (LOH) in the hCDC4 gene. Cyclin E overexpression was found in 26/81 (32%) cases and was associated with the histological type of the lesion, since it was not found in any AEHs but was present in 27% of EECs and 54.5% of NEECs (p=0.035). Cyclin E overexpression was associated with histological grade (p=0.011) and p53 immunostaining in EECs (p=0.033). CCNE amplification was found in 6 of 37 (16%) ECs examined. There was a significant association between CCNE amplification and the histological type of the lesion, since five (83%) of the six cases with amplification were NEECs (p=0.008). One EEC harboured an hCDC4 mutation: a CGA to CAA (Arg/Gln) change at codon 479. In addition, D4S1610 LOH was found in 7 of 23 (30%) informative cases analysed, but no correlation with cyclin E overexpression was found. However, the tumour with hCDC4 mutation also showed LOH. This is the first study demonstrating that cyclin E overexpression is associated with gene amplification in ECs, these alterations being more frequent in NEECs. Although hCDC4 exhibits a low mutation frequency in ECs overexpressing cyclin E, it seems to function as a tumour suppressor gene that is involved in endometrial carcinogenesis.
Methodologies for evaluating post-etching damage in ultra-low-k dielectrics and new chemistry for damage reduction (2017)

In this study, we demonstrated an approach to evaluate the post-etching damage in SiOCH organosilica ultra-low-k dielectric films. Upon plasma dry etching, the ultra-low-k materials were etched by using hydrofluorocarbons and fluorocarbon (HFCs) molecules. Methodologies to determine the post-etching damage on both ultra-low-k blanket and pattern wafers were used for fundamental investigation by using conventional HFCs. Based on the understanding, a new etching chemistry is proposed and its benefits are presented.
A new high isolation dual-antennas with miniature decoupling network design (2007)

This study proposes a compact high isolation dual-antennas structure designed for Taiwan UHF RFID. The decoupling and matching networks just with reactive element, are used in order to avoid power loss. The function of the decoupling and the matching networks like a circulator provide high isolation in the transceiver, and an antenna 1 and an antenna 2 have the same radiation pattern at 915 MHz.
High-speed imaging and tracking of very small single nanoparticles by contrast enhanced microscopy (2018)

Nanoparticles have been used extensively in biology-related research and many applications require direct visualization of individual nanoparticles by optical microscopy. For long-term and high-speed measurements, scattering-based microscopy is a unique technique because of the stable and indefinite scattering signals. In scattering-based single-particle measurements, large nanoparticles are usually needed in order to generate sufficient signals for detection. However, larger nanoparticles introduce greater mass loading, experience stronger steric hindrance, and are more prone to crosslinking. In this work, we demonstrate coherent brightfield (COBRI) microscopy with enhanced contrast and show its capability of direct visualization of very small nanoparticles in scattering at a high speed. COBRI microscopy allows us to visualize and track single metallic and dielectric nanoparticles, as small as 10 nm, at 1000 frames per second. A quantitative relationship between the linear scattering cross section of the nanoparticle and its COBRI contrast is reported. Using COBRI microscopy, we further demonstrate the tracking of 10 nm gold nanoparticles labeled to lipid molecules in supported bilayer membranes, showing that the small nanoparticles may facilitate single-molecule measurements with reduced perturbation. Furthermore, the identical imaging sensitivities of COBRI and interferometric scattering (iSCAT) microscopy, the reflection counterpart of COBRI, is demonstrated at an equal illumination intensity. Finally, future improvements in the speed and sensitivity of scattering-based interference microscopy are discussed.
DORIOS: Demonstration of an All-Optical Distributed CPU, Memory, Storage Intra DCN Interconnect (2015)

We show an all-optical ultra-low latency server-to-remote memory/storage data center interconnection, exploiting programmable, flexible, bi-directional and data-rate transparent 4x16 Spectrum Selective Switches and supporting elastic WDM/TDM services using fast nanosecond tunable lasers.
Automatic detection and segmentation of pronunciation variants in German speech corpora (2002)

In this paper we present a hybrid statistical and rule-based segmentation system which takes into account phonetic variation of German. Input to the system is the orthographic representation and the speech signal of an utterance to be segmented. The output is the transcription (SAM-PA) with the highest overall likelihood and the corresponding segmentation of the speech signal. The system consists of three main parts: In a first stage the orthographic representation is converted into a linear string of phonetic units by lexicon lookup. Phonetic rules are applied yielding a graph that contains the canonic form and presumed variations. In a second HMM-based stage the speech signal of the concerning utterance is time-aligned by a Viterbi search which is constrained by the graph of the first stage. The outcome of this stage is a string of phonetic labels and the corresponding segment boundaries. A rule-based refinement of the segment boundaries using phonetic knowledge takes place in a third stage.
Adenofibroma and adenosarcoma of the uterus: A clinicopathologic study of 35 cases (1981)

The clinical and histopathologic features of ten adenofibromas and 25 adenosarcomas of the uterus were studied. The most useful criterion for distinguishing adenofibroma from adenosarcoma was the frequency of mitotic figures found in the stroma. Adenofibromas had fewer than four mitotic figures per 100 HPF in the most active areas; adenosarcomas had four or more. Myometrial invasion, histologically malignant heterologous mesenchymal elements, and marked atypia of stromal cells were histologic features detected only in adenosarcoma. Of the women with adenosarcoma, ten (40%) had recurrences, with a median interval to recurrence of five years. The only morphologic feature that correlated with aggressive behavior of adenosarcoma was deep myometrial invasion. Adenofibroma and adenosarcoma are in the family of mixed mesodermal tumors, but are distinct clinical and pathologic entities.
The Curious Case of Neural Text Degeneration (2020)

Despite considerable advances in neural language modeling, it remains an open question what the best decoding strategy is for text generation from a language model (e.g. to generate a story). The counter-intuitive empirical observation is that even though the use of likelihood as training objective leads to high quality models for a broad range of language understanding tasks, maximization-based decoding methods such as beam search lead to degeneration — output text that is bland, incoherent, or gets stuck in repetitive loops. To address this we propose Nucleus Sampling, a simple but effective method to draw considerably higher quality text out of neural language models. Our approach avoids text degeneration by truncating the unreliable tail of the probability distribution, sampling from the dynamic nucleus of tokens containing the vast majority of the probability mass. To properly examine current maximization-based and stochastic decoding methods, we compare generations from each of these methods to the distribution of human text along several axes such as likelihood, diversity, and repetition. Our results show that (1) maximization is an inappropriate decoding objective for open-ended text generation, (2) the probability distributions of the best current language models have an unreliable tail which needs to be truncated during generation and (3) Nucleus Sampling is the best decoding strategy for generating long-form text that is both high-quality — as measured by human evaluation — and as diverse as human-written text.
Reducing Driving Voltages for Liquid Crystal Lens Using Weakly Conductive Thin Film (2008)

A low-voltage driving liquid crystal (LC) lens of large aperture is realized using a newly developed water-borne thermosetting paint with weak conductivity. The conductive film turns the spatially abruptly varying electric field into a smoothly varying electric field to produce the lenslike distribution of refractive index in the LC layer. An LC lens of 15 mm aperture is fabricated. The lens can work either as a positive lens or a negative lens at driving voltages as low as only around 20 Vrms.
Patterning of sub-10-nm Ge islands on Si(100) by directed self-assembly (2005)

A process is reported for creating arbitrary patterns of sub-10-nm Ge islands on a Si(100) substrate by directed self-assembly. Carbon-based templates are created on Si substrates by electron-beam-induced deposition using high-resolution electron beam lithography. Ozone etching, followed by annealing in ultra-high vacuum, yields small (&lt;4nm) SiC nucleation sites for subsequently deposited Ge. Quantitative analysis of atomic force microscope images reveals templated Ge islands with mean diameter d∼8nm, averaging 2000±500 atoms per island, with controlled spacings as small as 35 nm, and 2 nm absolute positional accuracy. The Ge∕Si nanostructures reported here may find use in end-of-scaling classical computing and single-electron devices and spin-based quantum computing architectures.
Lessons for working with WEB designers (2002)

La bibliotheque de l'Universite de Yale a choisi de faire appel a des designers graphiques pour reconcevoir les pages d'accueil de son site web. Bien que fructueuse, cette experience de sous-traitance a presente diverses difficultes, dont l'A. tire ici les lecons. Une premiere phase a consiste a determiner la repartition des tâches et a elaborer des principes de conception et des specifications techniques. Le processus impliquait notamment la fusion avec un autre site destine a la recherche, et le rattachement avec l'identite web au sens large de l'universite. Une grande attention a ete portee aux tests d'utilisabilite, a l'encodage, a la conformite aux normes d'accessibilite et a la facilite d'utilisation pour les auteurs et developpeurs de l'universite. La communication et l'acceptation de compromis de part et d'autre ont joue un role essentiel dans la reussite de cette reconception.
Adherence to a Smartphone Application for Weight Loss Compared to Website and Paper Diary: Pilot Randomized Controlled Trial (2013)

ClinicalTrials.gov NCT01744535; http://clinicaltrials.gov/ct2/show/NCT01744535 (Archived by WebCite at http://www.webcitation.org/6FEtc3PVB).
A foldable CFTRΔF508 biogenic intermediate accumulates upon inhibition of the Hsc70–CHIP E3 ubiquitin ligase (2004)

CFTRDeltaF508 exhibits a correctable protein-folding defect that leads to its misfolding and premature degradation, which is the cause of cystic fibrosis (CF). Herein we report on the characterization of the CFTRDeltaF508 biogenic intermediate that is selected for proteasomal degradation and identification of cellular components that polyubiquitinate CFTRDeltaF508. Nonubiquitinated CFTRDeltaF508 accumulates in a kinetically trapped, but folding competent conformation, that is maintained in a soluble state by cytosolic Hsc70. Ubiquitination of Hsc70-bound CFTRDeltaF508 requires CHIP, a U box containing cytosolic cochaperone. CHIP is demonstrated to function as a scaffold that nucleates the formation of a multisubunit E3 ubiquitin ligase whose reconstituted activity toward CFTR is dependent upon Hdj2, Hsc70, and the E2 UbcH5a. Inactivation of the Hsc70-CHIP E3 leads CFTRDeltaF508 to accumulate in a nonaggregated state, which upon lowering of cell growth temperatures, can fold and reach the cell surface. Inhibition of CFTRDeltaF508 ubiquitination can increase its cell surface expression and may provide an approach to treat CF.
Consumer information search behavior and the internet (2003)

Abstract There is no question that the Internet has, and will continue to have, a major impact on consumer information search behavior. However, under what conditions, and how, that impact will be felt is not clear. This article offers 14 propositions to stimulate and guide investigations of consumer information search behavior in the context of the Internet. A major conclusion is that broad generalizations regarding the impact of the Internet on consumer information search behavior are not warranted and that, if the propositions possess any truth value, the Internet is not likely to be an information panacea for consumers. Because of the complexities of the Internet and information search behavior (individually and even more so when considered conjunctively), investigations of consumer information search behavior in the context of the Internet should especially focus on moderators of that behavior and interactions among the various antecedents of the behavior. © 2003 Wiley Periodicals, Inc.
Optimal positive airway pressure predicts oral appliance response to sleep apnoea (2009)

Patients with less severe obstructive sleep apnoea (OSA) are usually prescribed oral appliances and/or smaller optimal nasal continuous positive airway pressure (P(nCPAP)) in nCPAP therapy. We hypothesised that OSA patients with greater P(nCPAP) would not respond favourably to oral appliances. Oral appliances were inserted in nCPAP users after washing-out the nCPAP effect. Follow-up polysomnography was undertaken with the adjusted oral appliance in place. The predictability of P(nCPAP) was evaluated with receiver-operating characteristic (ROC) curves. The median baseline apnoea/hypopnoea index (AHI) was reduced with the oral appliance from 36 to 12 events.h(-1) in 35 patients. When responders were defined as patients showing a follow-up AHI of <5 events.h(-1) with >50% reduction in baseline AHI, the area under the ROC curve for P(nCPAP) was 0.76. The best cut-off value of P(nCPAP) turned out to be 10.5 cmH(2)O with a high negative predictive value (0.93) and a low negative likelihood ratio (0.18). OSA patients with a P(nCPAP) of >10.5 cmH( 2)O are unlikely to respond to oral appliance therapy. This prediction is clinically helpful to both OSA patients and medical personnel in discussing oral appliances as a temporary substitute and/or alternative for nCPAP.