gebhart/patrepeval huggingface dataset:
Microarray-Based Identification of Bacteria in Clinical Samples by Solid-Phase PCR Amplification of 23S Ribosomal DNA Sequences (2004)

The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory.
Probiotics, fibre and herbal medicinal products for functional and inflammatory bowel disorders (2016)

This article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc.
Fluency and use of segmental dialect features in the acquisition of a second language (French) by English speakers (2002)

The study investigates the use of two parameters, fluency and use of segmental dialect features (accent) to rate the overall ability of speakers of French as a second language. A group of ten native English Canadians read a short text of 139 words in French (their second language). Their degree of fluency was established by a combination of the following measures: speech rate (words/min, syll/min, syll/s), number and duration of pauses, and hesitations. We also investigated their use of various segmental dialect features such as diphthonguization of long vowels, affrication of /t d/, and high vowel deletion. These results were then compared to those of a group of ten native French speakers of the same region (Montreal).
Surface Engineered Nanoparticles: Considerations for Biomedical Applications (2017)

The development of reproducible methods for the fabrication of nanoparticles in the 21st century is a major scientific achievement. Currently, there are many well‐established methods for the production of nanoparticles of different shapes, sizes, and compositions. Along with these advancements in nanotechnology, nanoparticles have emerged as excellent tools for a diverse range of applications and have become a focus of research globally. With fundamental research being established, efforts are now being directed toward intelligently designed nanoparticles in which the properties of the nanomaterial are finely tuned depending on the application of interest. Usually, this involves the functionalization of the nanoparticle surface with a ligand. In this review, the impact of nanoparticle surface chemistry is discussed as it applies to biological systems.
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current (2018)

Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order <i>Caudovirales</i> across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.
Simulation of Gas and Resin Transport Mechanisms in Manufacturing Process of Composite Structures and Their Effect on Porosity (2017)

Porosity, as a manufacturing process-induced defect, highly affects the mechanical properties of cured composites. There are several contributing factors to the formation of porosity in composite structures, most notably entrapped air, bag leaks, and volatiles or off gassing. These sources highlight the multi-scale and multi-physics nature of the formation of porosity which make it such a challenging problem to solve. Understanding how these mechanisms contribute to the formation of porosity becomes a key tool in minimizing their negative effect. Experimental evidences show that local resin pressure history plays a major role in void growth during a cure cycle. Local reductions in resin pressure due to factors such as geometric features or cure shrinkage can lead to growth of existing voids and increase the likelihood of porosity becoming locked into the final part structure. Prediction of local resin pressure has been the focus of this approach to modeling the cure of composite structures. This study is focused on developing an efficient FE modeling framework to simulate the resin pressure and porosity (bubble) formation in a composite part. The case study presented here features a laminate with ply drop-off subjected to compaction pressure via a caul plate.
<title>Laser induced reorientation process in dye-doped nematic systems: role of the azo-dye structure</title> (2007)

Photoinduced molecular reorientation in dye-doped liquid crystal cells has been studied for a set of azodyes with a "pump-probe" optical device. The rotating angle of the nematic director as a function of irradiation time has been calculated. The lateral chemical groups of the azo-dye molecules have not an important influence on the orientation effect; this aspect supports the idea that the trans-cis photoisomerization of the dye molecules is the predominant mechanism responsible for the molecular reorientation in azo-dye-doped liquid crystal systems.
Longitudinal studies of blood lymphocyte capacity in Hodgkin's disease (1981)

Blood lymphocyte functional capacity and serum immunoglobulins were studied in 40 patients with Hodgkin's disease (HD) admitted to Radiumhemmet, Stockholm, before treatment and in complete remission 2-56 months following termination of radiotherapy (total nodal irradiation [TNI]; n = 29) or chemotherapy (MOPP; n = 11). Lymphocyte studies included determination of total lymphocyte and T-cell counts and evaluation of spontaneous DNA synthesis during the first day of culture and mitogen-(concanavalin A, pokeweed mitogen) and antigen (purified protein derivative, PPD)-induced activation on the third day. Blood lymphocyte and T-cell counts decreased dramatically following TNI. A slow restitution was seen, but pretreatment levels were not reached even four years following therapy. The responses to ConA and PPD but not PWM were significantly reduced shortly after TNI. The mitogen response did not increase with time as did the PPD response. Lymphocyte counts and lymphocyte stimulation, which were severely depressed before treatment of patients in the chemotherapy group, remained unchanged 2-36 months after termination of therapy. A significant reduction of IgM levels was observed regardless of the mode of treatment. Splenectomy prevented the profound reduction of blood lymphocyte and T-cell counts following therapy but did not influence the other immunologic variables under study.
A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response (2021)

Targeted therapies have demonstrated efficacy against specific subsets of molecularly defined cancers1–4. Although most patients with lung cancer are stratified according to a single oncogenic driver, cancers harbouring identical activating genetic mutations show large variations in their responses to the same targeted therapy1,3. The biology underlying this heterogeneity is not well understood, and the impact of co-existing genetic mutations, especially the loss of tumour suppressors5–9, has not been fully explored. Here we use genetically engineered mouse models to conduct a ‘co-clinical’ trial that mirrors an ongoing human clinical trial in patients with KRAS-mutant lung cancers. This trial aims to determine if the MEK inhibitor selumetinib (AZD6244)10 increases the efficacy of docetaxel, a standard of care chemotherapy. Our studies demonstrate that concomitant loss of either p53 (also known as Tp53) or Lkb1 (also known as Stk11), two clinically relevant tumour suppressors6,9,11,12, markedly impaired the response of Kras-mutant cancers to docetaxel monotherapy. We observed that the addition of selumetinib provided substantial benefit for mice with lung cancer caused by Kras and Kras and p53 mutations, but mice with Kras and Lkb1 mutations had primary resistance to this combination therapy. Pharmacodynamic studies, including positron-emission tomography (PET) and computed tomography (CT), identified biological markers in mice and patients that provide a rationale for the differential efficacy of these therapies in the different genotypes. These co-clinical results identify predictive genetic biomarkers that should be validated by interrogating samples from patients enrolled on the concurrent clinical trial. These studies also highlight the rationale for synchronous co-clinical trials, not only to anticipate the results of ongoing human clinical trials, but also to generate clinically relevant hypotheses that can inform the analysis and design of human studies.
Glucose-Derived 3‘-(Carboxymethyl)-3‘-deoxyribonucleosides and 2‘,3‘-Lactones as Synthetic Precursors for Amide-Linked Oligonucleotide Analogues1 (2000)

Treatment of a 1,2-O-isopropylidene-3-ketopentofuranose derivative (obtained from D-glucose) with [(ethoxycarbonyl)methylene]triphenylphosphorane and catalytic hydrogenation of the resulting alkene gave stereodefined access to 3-(carboxymethyl)-3-deoxy-D-ribofuranose derivatives. Esters of 5-O-acetyl- or 5-azido-5-deoxy-3-(carboxymethyl)-D-ribofuranose were coupled with nucleobases to give branched-chain nucleoside derivatives. Ester saponification and protecting group manipulation provided 2'-O-(tert-butyldimethylsilyl) ethers of 5'-azido-5'-deoxy- or 5'-O-(dimethoxytrityl) derivatives of 3'-(carboxymethyl)-3'-deoxyribonucleosides that are effective precursors for synthesis of amide-linked oligoribonucleosides.
REAL-TIME FEEDBACK CONTROL OF DROPLET GENERATION FOR EWOD DIGITIAL MICROFLUIDICS (2016)

We report the successful implementation of real-time feedback control of the droplet generation process on the electrowetting-on-dielectric (EWOD) digital microfluidics. Demonstrated in the air environment in this paper, the feedback allows precise (&amp;lt; ±1%) droplet generation and also empowers users to prescribe the volume through software.
CAD vs. Sketching: An Exploratory Case Study (2012)

This paper presents a preliminary comparison between the role of computer-aided design (CAD) and sketching in engineering through a case study of a senior design project and interviews with industry and academia. The design team consisted of four senior level mechanical engineering students each with less than 1 year of professional experience are observed while completing an industry sponsored mechanical engineering capstone design project across a 17 week semester. Factors investigated include what CAD tools are used, when in the design process they are implemented, the justification for their use from the students' perspectives, the actual knowledge gained from their use, the impact on the final designed artifact, and the contributions of any sketches generated. At each design step, comparisons are made between CAD and sketching. The students implemented CAD tools at the onset of the project, generally failing to realize gains in design efficiency or effectiveness in the early conceptual phases of the design process. As the design became more concrete, the team was able to recognize clear gains in both efficiency and effectiveness through the use of computer assisted design programs. This study is augmented by interviews with novice and experienced industry users and academic instructors to align the trends observed in the case study with industry practice and educational emphasis. A disconnect in the perceived capability of CAD tools was found between novice and experienced user groups. Opinions on the importance of sketching skills differed between novice educators and novice industry professionals, suggesting that there is a change of opinion as to the importance of sketching formed when recent graduates transition from academia to industry. The results suggest that there is a need to emphasize the importance of sketching and a deeper understanding as to the true utility of CAD tools at each stage of the design process.
Natural language processing-optimized case selection for real-world evidence studies. (2022)

1556 Background: Much information describing a patient’s cancer treatment remains in unstructured text in electronic health records and is not recorded in discrete data fields. Accurate data completeness is essential for quality care improvement and research studies on de-identified patient records. Accessing this high-value content often requires manual and extensive curation review. Methods: AstraZeneca, CancerLinQ, ConcertAI, and Tempus have developed a natural language processing (NLP)-assisted process to improve clinical cohort selection for targeted curation efforts. Hybrid, machine-learning model development included text classification, named entity recognition, relation extraction and false positive removal. A subset of nearly 60,000 lung cancer cases were included from the CancerLinQ database, comprised of multiple source EHR systems. NLP models extracted EGFR status, stage, histology, radiation therapy, surgical resection and oral medications. Based on the results, cases were selected for additional manual curation, where curators confirmed findings of the NLP-processed data. Results: NLP methods improved cohort identification. Successfully returned cases using the NLP method ranged from 75.2% to 96.5% over more general case selection criteria based on limited structured data. For all cohorts combined, 84.2% of the cases sent out for NLP curation were returned with curated content (Table). Each cohort contained a range of NLP-derived elements for curators to further review. In comparison, more general case selection criteria yielded a total of 3,878 cases returned out of 41,186 lung cancer cases sent for curation, for a success rate of only 9.6%. Conclusions: NLP-driven case selection of six distinct, complex lung cohorts resulted in an order of magnitude improvement in eligibility over candidate selection using structured EHR data alone. This study demonstrates NLP-assisted approaches can significantly improve efficiency in curating unstructured health data. [Table: see text]
Rapid, electronically controllable transverse mode selection in a multimode fiber laser (2013)

A novel technique for the electronically-controllable generation and switching of transverse modes within a multi-mode fiber laser oscillator is presented. Preliminary results demonstrate individual transverse mode lasing and fast switching between modes with watt-level output powers. When applied to a core-pumped Tm-doped silica fiber laser with a multimode core the fundamental mode (LP₀₁), the next higher order mode (LP₁₁), or a donut-shaped LP₁₁ superposition were selectively excited with power levels in excess of 5 W. Fast switching between LP₀₁ and LP₁₁ modes at up to 20 kHz was also realized.
Reliable Millimeter Wave Communication for IoT Devices (2021)

In this paper, we propose a nearest line-of-sight relay (NLR) selection technique for internet of things (IoT) devices in millimeter wave (mmWave) relaying systems. We present a tractable analytical framework to characterize the network connectivity for the proposed technique using tools from stochastic geometry. Moreover, we investigate the impact of the relay-selected region and the distance between the base station and IoT device on the network connectivity of mmWave relaying systems. The analytical results unveil a high degree of accuracy which is confirmed by extensive simulations at different relay densities, blockage densities, and signal-to-noise ratio (SNR) thresholds. Results obtained via both simulations and analyses reveal the trade-off between the network connectivity and the energy consumption of IoT devices. Results also reveal a significant impact of blockage density and controlling the relay-selected region on the network connectivity and energy consumption.
Applications of CpG Motifs from Bacterial DNA in Cancer Immunotherapy (2002)

This chapter contains sections titled: History of Cancer Immunotherapy with Bacterial Extracts and Nucleic Acids CpG Motifs in bDNA Explain its Immune Stimulatory Activity Identification of a Specific Receptor for CpG motifs, Toll-like Receptor (TLR)-9 Backbone-dependent Immune Effects of CpG Motifs and Delineation of CpG-A versus CpG-B Classes of ODN Applications of CpG DNA in Immunotherapy of Cancer CpG-A or CpG-B DNA as a Monotherapy CpG DNA as an Adjuvant for Cancer Vaccines Application of CpG DNA to Enhance ADCC for Treating Cancer Conclusion
Isolation and Genetic Characterization of Bacteria That Degrade Chloroaromatic Compounds (1981)

Bacteria were isolated from a landfill site previously used for disposal of chlorinated organic wastes. These soil isolates were capable of utilizing various chloroaromatic compounds. One such bacterial strain, designated Pseudomonas cepacia HCV (2,6-DCT) and growing on 2,6-dichlorotoluene, transferred this trait to a catechol-1,2-oxygenase mutant of Pseudomonas aeruginosa.
Natural Language Object Retrieval (2015)

In this paper, we address the task of natural language object retrieval, to localize a target object within a given image based on a natural language query of the object. Natural language object retrieval differs from text-based image retrieval task as it involves spatial information about objects within the scene and global scene context. To address this issue, we propose a novel Spatial Context Recurrent ConvNet (SCRC) model as scoring function on candidate boxes for object retrieval, integrating spatial configurations and global scene-level contextual information into the network. Our model processes query text, local image descriptors, spatial configurations and global context features through a recurrent network, outputs the probability of the query text conditioned on each candidate box as a score for the box, and can transfer visual-linguistic knowledge from image captioning domain to our task. Experimental results demonstrate that our method effectively utilizes both local and global information, outperforming previous baseline methods significantly on different datasets and scenarios, and can exploit large scale vision and language datasets for knowledge transfer.
Suppression of cytotoxic and proliferative xenogeneic T‐cell responses by transgenic expression of indoleamine 2,3‐dioxygenase (2008)

Tryptophan catabolism initiated by the enzyme indoleamine 2,3-dioxygenase (IDO) has been postulated to be a natural regulatory mechanism for T cells. In this study, we generated a pig endothelial cell line expressing full-length human IDO (P-HuIDO) to serve as a simple model of a cellular xenogeneic graft. Splenocytes from mice primed to P-HuIDO cells were found to be as responsive to secondary stimulation as splenocytes from mice primed to parental cells. However, in T-cell proliferation assays using P-HuIDO cells as stimulators, a significant inhibition of both naive and memory xenogeneic proliferative responses was noted. Furthermore, the production of interferon-gamma and cytotoxic T lymphocyte function were also affected. When severe combined immunodeficiency mice were grafted with P-HuIDO cells, then challenged with primed splenocytes from BALB/c mice, cellular infiltration to the graft was delayed. Our findings suggest that transgenic expression of IDO in xenografts contributes to prolonged graft survival.
The Response of Maize Seedlings of Different Ages to Hypoxic and Anoxic Stress (Changes in Induction of Adh1 mRNA, ADH Activity, and Survival of Anoxia) (1994)

Previously we showed that there is only a transient induction of alcohol dehydrogenase 1 (Adh1) transcripts and only a small induction of alcohol dehydrogenase (ADH) enzyme activity in root tips of maize (Zea mays L.) seedlings subjected to strict anaerobiosis without prior acclimation by exposure to low O2 (D.L. Andrews, B.G. Cobb, J.R. Johnson, M.C. Drew [1993] Plant Physiol 101: 403-414). Acclimation of root tips of seedlings by low O2 before anoxia appeared to be necessary for full induction of ADH. Here we have examined the effect of seedling age on changes in the protein content, induction of Adh1 transcripts, and ADH enzyme activity in 5-mm root tips, root axes, and shoots of maize (cv TX5855). Their ability to survive anoxia was also recorded. Some seedlings were sparged with 4% O2 for 6 or 18 h (a hypoxic pretreatment) followed by anoxia (sparged with N2) for up to 48 h. Other seedlings were not acclimated before anoxia. In general, younger seedlings had higher initial (aerobic) levels of total protein, Adh1 transcripts, and ADH activity than did seedlings that were 2 d older. For younger seedlings, anoxia alone induced Adh1 transcripts, which reached a peak within 6 to 12 h, whereas ADH activity increased throughout the 48-h treatment. For older seedlings, anoxia caused only a small, transient induction of Adh1 transcripts or ADH activity. For seedlings of either age, hypoxia induced Adh1 transcripts and ADH activity, both of which were increased further by subsequent anoxia in the younger seedlings but to a lesser extent in the older seedlings. Despite differences in ADH activity, roots of seedlings of either age showed a similar resistance to anoxia. Thus, acclimation of maize seedlings to survive anoxia does not appear to be related to induction of high levels of ADH activity.
All-plasma PEMFC: new polymer membrane and high performance of ultra low Pt loaded electrodes, (2009)

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