gebhart/patrepeval huggingface dataset:
Bacteriophages from ExPEC Reservoirs Kill Pandemic Multidrug-Resistant Strains of Clonal Group ST131 in Animal Models of Bacteremia (2017)

Multi-drug resistant (MDR) enteric bacteria are of increasing global concern. A clonal group, Escherichia coli sequence type (ST) 131, harbors both MDR and a deadly complement of virulence factors. Patients with an immunocompromised system are at high risk of infections with these E. coli and there is strong epidemiologic evidence that the human intestinal tract, as well as household pets, may be a reservoir. Here, we examine if phages are an effective treatment strategy against this clonal group in murine models of bacteremia that recapitulate clinical infections. Bacteriophages isolated from known E. coli reservoirs lyse a diverse array of MDR ST131 clinical isolates. Phage HP3 reduced E. coli levels and improved health scores for mice infected with two distinct ST131 strains. Efficacy was correlated to in vitro lysis ability by the infecting phage and the level of virulence of the E. coli strain. Importantly, it is also demonstrated that E. coli bacteremia initiated from translocation across the intestinal tract in an immunocompromised host is substantially reduced after phage treatment. This study demonstrates that phage, isolated from the environment and with little experimental manipulation, can be effective in combating even the most serious of infections by E. coli "superbugs".
Superconducting Electronics: A New Frontier for Failure Analysis and Reliability (2019)

Abstract This column assesses the current state and outlook for superconducting device technology and its application in exascale computing.
Anti-oxLDL antibody isotype levels, as potential markers for progressive atherosclerosis in APOE−/− and APOE−/−CD40L−/− mice (2008)

In humans and animal models of atherosclerosis, antibodies against oxidized LDL have been associated with atherosclerotic lesion development. It has been suggested that IgM anti-oxLDL antibodies are anti-atherogenic, whereas IgG anti-oxLDL antibodies are pro-atherogenic. In this study, we examined the relation between IgM and IgG antibody levels and atherosclerosis severity in APOE(-/-)CD40L(-/-) mice, which are deficient for IgG and develop moderate advanced atherosclerosis, and compared results with mice developing severe (APOE(-/-)) or no atherosclerosis (C57Bl/6). Mice were followed in time for anti-oxLDL antibodies while on high-fat diet or normal chow. Anti-oxLDL antibody levels were determined by ELISA. Results revealed that 24-week-old APOE(-/-)CD40L(-/-) mice had enhanced IgM anti-oxLDL antibody levels when compared with wild-type mice, but similar levels to those of APOE(-/-) mice. As expected, IgG anti-oxLDL antibody levels were almost absent in APOE(-/-)CD40L(-/-) mice. The transition from early to advanced lesions in APOE(-/-) mice was reflected by elevated IgM anti-oxLDL antibody levels. IgM anti-oxLDL levels did not further increase during progression to more advanced lesions. No relation was found between IgG anti-oxLDL levels and atherosclerosis severity. In conclusion, the severity of advanced atherosclerosis in mice is not reflected by IgM and/or IgG anti-oxLDL antibody levels. Furthermore, less advanced atherosclerotic lesion development in APOE(-/-)CD40L(-/-) mice does not seem to be the result of higher levels of protective IgM anti-oxLDL antibodies. Therefore, our study does not support the idea that the previously observed inconsistency in the relation between anti-oxLDL and atherosclerosis severity is due to differences in antibody isotypes.
Deep neural networks and distant supervision for geographic location mention extraction (2018)

Our NER achieves an F1-score of 0.910 and significantly outperforms the previous state-of-the-art system. Using the additional data generated through distant supervision further boosts the performance of the NER achieving an F1-score of 0.927. The NER presented in this research improves over previous systems significantly. Our experiments also demonstrate the NER's capability to embed external features to further boost the system's performance. We believe that the same methodology can be applied for recognizing similar biomedical entities in scientific literature.
Experimental Design for Overparameterized Learning with Application to Single Shot Deep Active Learning (2020)

The impressive performance exhibited by modern machine learning models hinges on the ability to train such models on a very large amounts of labeled data. However, since access to large volumes of labeled data is often limited or expensive, it is desirable to alleviate this bottleneck by carefully curating the training set. Optimal experimental design is a well-established paradigm for selecting data point to be labeled so to maximally inform the learning process. Unfortunately, classical theory on optimal experimental design focuses on selecting examples in order to learn underparameterized (and thus, non-interpolative) models, while modern machine learning models such as deep neural networks are overparameterized, and oftentimes are trained to be interpolative. As such, classical experimental design methods are not applicable in many modern learning setups. Indeed, the predictive performance of underparameterized models tends to be variance dominated, so classical experimental design focuses on variance reduction, while the predictive performance of overparameterized models can also be, as is shown in this paper, bias dominated or of mixed nature. In this paper we propose a design strategy that is well suited for overparameterized regression and interpolation, and we demonstrate the applicability of our method in the context of deep learning by proposing a new algorithm for single shot deep active learning.
Location-Based Services: Back to the Future (2008)

What was wrong with first-generation location-based services? A brief historical overview identifies five factors that collectively laid the foundation for a new generation of LBSs.
Efficacité de la sclérothérapie dans le contrôle de I’hemorragie active sur varices cesophagiennes (1990)

Les auteurs rapportent les résultats d’une étude prospective de ’efficacité de la sclérose dans le traitement d’hémorragie active sur varices cesophagiennes (VO). L’étude porte sur 93 épisodes hémorragiques survenus chez 74 patients cirrhotiques. Dans tous les cas, une hémorragie active sur VO a été démontrée au cours de l’endoscopie d’urgence et fut traitée, au cours de la même exploration, par sclérose intravariqueuse avec éthanolamine, sans aucun traitement adjuvant. Une hémostase initiate a été obtenue dans 94,6 % des épisodes hémorragiques avec un taux d’hémorragie persistante limité (5,4 %). L’hémostase permanente, endéans les 72 premieres heures, a été obtenue dans 81,7 % des cas. La mortalité hospitaliére est de 20,2 %, et dans 8,1 % des cas seulement, elle fut attribuable á l’hémorragie. Aucune différence significative entre les résultats n’a été notée selon les classes de Pugh, ou encore en fonction de la sévérité de l’épisode hémorragique. Les complications prédominantes furent des pneumopathies par aspiration dans 7 cas. Ces résultats permettent d’affirmer que la sclérothérapie réalisée au cours de l’endoscopie diagnostique initiale, chez des malades atteints d’hémorragie active sur VO, est hautement efficace, et fournit des résultats indépendants du degré d’insuffisance hépatique ainsi que de la sévérité de l’hémorragie initiale.
International Standards For Neurological Classification Of Spinal Cord Injury (2003)

(2003). International Standards For Neurological Classification Of Spinal Cord Injury. The Journal of Spinal Cord Medicine: Vol. 26, No. sup1, pp. S50-S56.
Developmental differences in masked form priming are not driven by vocabulary growth (2014)

As children develop into skilled readers, they are able to more quickly and accurately distinguish between words with similar visual forms (i.e., they develop precise lexical representations). The masked form priming lexical decision task is used to test the precision of lexical representations. In this paradigm, a prime (which differs by one letter from the target) is briefly flashed before the target is presented. Participants make a lexical decision to the target. Primes can facilitate reaction time by partially activating the lexical entry for the target. If a prime is unable to facilitate reaction time, it is assumed that participants have a precise orthographic representation of the target and thus the prime is not a close enough match to activate its lexical entry. Previous developmental work has shown that children and adults' lexical decision times are facilitated by form primes preceding words from small neighborhoods (i.e., very few words can be formed by changing one letter in the original word; low N words), but only children are facilitated by form primes preceding words from large neighborhoods (high N words). It has been hypothesized that written vocabulary growth drives the increase in the precision of the orthographic representations; children may not know all of the neighbors of the high N words, making the words effectively low N for them. We tested this hypothesis by (1) equating the effective orthographic neighborhood size of the targets for children and adults and (2) testing whether age or vocabulary size was a better predictor of the extent of form priming. We found priming differences even when controlling for effective neighborhood size. Furthermore, age was a better predictor of form priming effects than was vocabulary size. Our findings provide no support for the hypothesis that growth in written vocabulary size gives rise to more precise lexical representations. We propose that the development of spelling ability may be a more important factor.
Two Rumex Species from Contrasting Hydrological Niches Regulate Flooding Tolerance through Distinct Mechanisms (2013)

Global climate change has increased flooding events, which affect both natural vegetation dynamics and crop productivity. The flooded environment is lethal for most plant species because it restricts gas exchange and induces an energy and carbon crisis. Flooding survival strategies have been studied in Oryza sativa, a cultivated monocot. However, our understanding of plant adaptation to natural flood-prone environments remains scant, even though wild plants represent a valuable resource of tolerance mechanisms that could be used to generate stress-tolerant crops. Here we identify mechanisms that mediate the distinct flooding survival strategies of two related wild dicot species: Rumex palustris and Rumex acetosa. Whole transcriptome sequencing and metabolite profiling reveal flooding-induced metabolic reprogramming specific to R. acetosa. By contrast, R. palustris uses the early flooding signal ethylene to increase survival by regulating shade avoidance and photomorphogenesis genes to outgrow submergence and by priming submerged plants for future low oxygen stress. These results provide molecular resolution of flooding survival strategies of two species occupying distinct hydrological niches. Learning how these contrasting flood adaptive strategies evolved in nature will be instrumental for the development of stress-tolerant crop varieties that deliver enhanced yields in a changing climate.
Differences in white matter integrity and hippocampal volumetrics across APOE genotype mice: A blinded preliminary study (2021)

Abstract Background Genome‐wide association studies have identified Apolipoprotein (APOE) as one of the strongest risk factors associated with Late‐Onset Alzheimer’s disease (LOAD) with females exhibiting a two‐fold higher incidence as compared to males. MRI studies of patients with LOAD link APOE‐ e 4 gene load with increased hippocampal volume loss as well as reduction in white matter integrity (WMI) in the limbic and medial temporal regions (Bagepally, 2012). However, there are few translational LOAD mouse model studies utilizing imaging. We hypothesized that hippocampal volume and WMI would be reduced in females and APOE e 4 carriers in our humanized APOE (hAPOE) LOAD mouse model. Method Six cohorts of APOE e 3 and e 4 genotype (M/F; N=53; mean age = 17.95 month) skull‐extracted ex‐vivo mouse brains were imaged (7T Bruker Biospec MRI scanner). Imaging included structural and diffusion weighted imaging. Bilateral hippocampal volumes, as well as total brain volume (TBV), were extracted using a well‐validated mouse brain atlas (Dorr, 2008). Fractional anisotropy (FA) was used to quantify WMI and between‐group comparisons were made using a groupwise connectometry approach (Yeh, 2013; Yeh, 2016). Result MRI image analysis indicated genotypic differences in white matter FA where APOE‐e4 carriers exhibited lower FA values (mean tractography FA = 0.263 ± 0.043) compared to APOE‐e3/3 (mean tractography FA = 0.311 ± 0.067) in a total of 10657 tracts (FDR corrected p &lt; 0.003; Figure 1). No statistically significant differences were identified across genotypes for left or right hippocampal volumes. However, right hippocampal volume was significantly greater in males as compared to females (p = 0.007) whereas no effect was observed between sexes for left hippocampus. Conclusion Outcomes of MRI analyses indicate a significant reduction in FA values and reduced white matter integrity across the brain in APOE e4 carriers, irrespective of sex. Contrary to human literature, no significant volumetric differences between genotypes were found in this mouse sample. Consistent with sex‐dependent literature, males exhibited greater total brain volume and additionally greater right hippocampal volume compared to females, irrespective of genotype. These findings may provide evidence of deficits in cholesterol or lipid transport manifest in decreased white matter integrity in this hAPOE mouse model.
Effects of PQQ on Protective System in Cucumber Cotyledons under Low Temperature Stress (1998)

作者学习了同时， superoxide dismutase (草皮)上的 quinone ( PQQ )， Ascorbid 酸( AsA ) peroxidase ( AsAPOD )， glutathion ( GSH )和在在低温度下面的黄瓜幼苗的子叶的电解的漏强调的 Pyrroioguinloine 的效果8对苯二酚( 8-HQ )和 AsA ( activeoxiygen scavengers )与 PQQ 比较被使用了。结果显示 GSH 的草皮， AsAPOD 和内容的活动能被 PQQ 增加。在黄瓜幼苗的子叶的相对传导性被减少因为 PQQ 拥有清理氧的免费 redical 的能力。我们来到了 PQQ 能作为一种活跃的氧 scavenger 扮演并且在氧的自由的基上调整新陈代谢在植物平衡并且在植物最后提高抵抗的结论。
ChemInform Abstract: Selective Direct N‐Alkylation of Amines with Alcohols Using Iron(III) Phthalocyanine Chloride under Solvent‐Free Conditions. (2016)

Abstract N‐alkyl amines are prepared with excellent selectivity by mono‐alkylation of various primary aromatic amines with benzyl alcohols using microwave irradiation.
ChemInform Abstract: A Photocurrent Spectroscopic Investigation of Passive Films on Ferritic Stainless Steels. (1988)

Abstract The three different ferritic stainless steels investigated show detectable photoeffects only after long polarization in Cl‐ containing solution.
Prospects of diamond devices (2001)

The prospects of two classes of diamond devices are reviewed, namely electronic devices on single-crystal substrates and microsystems devices on Si substrate. The transistor structures on single-crystal diamond represent still proof-of-concept experiments; however, they already allow us to extract their potential. The microsystems actuator and sensor devices already reflect the materials properties in their characteristics. Two of the most complex structures and future trends are discussed.
Pile Behavior Established from Model Tests (1990)

Eleven one‐tenth scale tubular steel pile tests are conducted to establish the behavior of pinned‐head friction piles in loose sand, fixed‐head friction piles in both loose and compacted sand, and a fixed‐head bearing pile in loose sand. The piles are instrumented with electrical resistance strain gauges and the vertical and horizontal pile movements at grade were measured with displacement transducers. By differentiation and integration of pile strain functions, obtained by curve‐fitting the measured strain data, the soil resistance and displacement relationships are developed in the form of modified Ramberg‐Osgood expressions. The characteristic soil parameters, describing the skin friction and vertical displacement f‐z curves, end‐bearing and settlement p‐z curve, and lateral resistance and displacement p‐y curves, are used in finite element studies that idealized the nonlinear soil behavior by isolated Winkler springs. The analytical results for the pile strains along the embedment length and displacements at the soil surface of a particular pile test correlate reasonably well with the measured values, considering the sensitivity of techniques used to establish the soil responses.
Design of an Assistive Communication Glove Using Combined Sensory Channels (2012)

This paper presents a new design of a wireless sensor glove developed for American Sign Language finger spelling gesture recognition. Five contact sensors are installed on the glove, in addition to five flex sensors on the fingers and a 3D accelerometer on the back of the hand. Each pair of flex and contact sensors are combined into the same input channel on the BSN node in order to save the number of channels and the installation area. After which, the signal is analyzed and separated back into flex and contact features by software. With electrical contacts and wirings made of conductive fabric and threads, the glove design has become thinner and more flexible. For validation, ASL finger spelling gesture recognition experiments have been performed on signals collected from six speech-impaired subjects and a normal subject. With the new sensor glove design, the experimental results have shown a significant increase in classification accuracy.
Reduction of epoxides to olefins with low valent titanium (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of epoxides to olefins with low valent titaniumJohn E. McMurry and Michael P. FlemingCite this: J. Org. Chem. 1975, 40, 17, 2555–2556Publication Date (Print):August 1, 1975Publication History Published online1 May 2002Published inissue 1 August 1975https://pubs.acs.org/doi/10.1021/jo00905a040https://doi.org/10.1021/jo00905a040research-articleACS PublicationsRequest reuse permissionsArticle Views413Altmetric-Citations64LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
VLSI for multimedia U-NII WLANs (2002)

This paper summarizes aspects of the VLSI development of a high-speed wireless local area network (WLAN). The implications for system-on-a-chip designs are summarized.
Numerical simulations in virtual anatomical models: The devil is in the details (2015)

Virtual anatomical models are increasingly used for a number of applications, ranging from (non)-ionizing radiation assessment to medical treatment and implant development. Accordingly, the number of available models has been increasing rapidly during recent years, and dosimetric studies for engineering and medical purposes are blooming. Here, we discuss an example of passive implant safety assessment to demonstrate how numerical simulations results can vary with the quality and detail of particular anatomical models.
Variation and change in the nominal pitch-accent system of South Kyungsang Korean (2016)

This paper considers whether the phonology of the lexical pitch accent of Kyungsang Korean is being maintained by younger innovative speakers. We examine the pitch-accent patterns of nouns with various suffixes by comparing the speech of innovative Kyungsang speakers to that of older conservative speakers. It will be shown that while innovative speakers maintain the underlying distinction in the lexical pitch accent found with conservative speakers, the acoustic difference across the contrastive accent classes is substantially weaker in the speech of innovative speakers, for both noun stems and suffixes. Observation of individual differences in the phonetic realisation of the pitch accent and comparison with tonal patterns of Seoul Korean provide an insight into this sound change, offering evidence for how and why the acoustic distinction has weakened. This study thus documents a process of diachronic change in the prosody of Kyungsang Korean.
Integrating Immunology into a Clinical Presentation-Based Medical School Curriculum (37.4) (2009)

Abstract Immunology can be a difficult discipline for first and second year medical students. As a teacher or learning facilitator it is sometimes hard to decide where to start. Even different text books adopt a variety of approaches. Clearly there is no one best way to begin to study the complex adaptive system that comprises our ability to respond to a wide variety of microorganisms, many of which have developed medically relevant means to evade the immune system. A further problem unique to the educational process of medical students is how to provide a relevant framework to enhance their retention of the concepts of basic immunology and their ability to apply these concepts later as they begin to practice medicine. Paul L. Foster School of Medicine is an emerging medical school that has adopted a clinical presentation-based curriculum. In this curriculum, students learn the basic science that is relevant to clinical science in the context of 120 specific common patient presentations. Novel approaches and the pros and cons of the integration of the basic science of immunology into a clinical-presentation based curriculum will be illustrated.
The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2 (2021)

COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We characterize CpG content by a CpG force that accounts for statistical constraints acting on the genome at the nucleotidic and amino acid levels. The CpG force, as the CpG content, is overall low compared with other pathogenic betacoronaviruses; however, it widely fluctuates along the genome, with a particularly low value, comparable with the circulating seasonal HKU1, in the spike coding region and a greater value, comparable with SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3'UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the zinc finger antiviral protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias, and the pressure to lower CpG content.