gebhart/patrepeval huggingface dataset:
Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages (2015)

Gastric infections caused by the environmentally transmitted pathogen, Vibrio parahaemolyticus, have increased over the last two decades, including in many parts of the United States (US). However, until recently, infections linked to shellfish from the cool northeastern US waters were rare. Cases have risen in the Northeast, consistent with changes in local V. parahaemolyticus populations toward greater abundance or a shift in constituent pathogens. We examined 94 clinical isolates from a period of increasing disease in the region and compared them to 200 environmental counterparts to identify resident and non-indigenous lineages and to gain insight into the emergence of pathogenic types. Genotyping and multi-locus sequence analysis (MLSA) of clinical isolates collected from 2010 to 2013 in Massachusetts, New Hampshire, and Maine revealed their polyphyletic nature. Although 80% of the clinical isolates harbored the trh hemolysin either alone or with tdh, and were urease positive, 14% harbored neither hemolysin exposing a limitation for these traits in pathogen detection. Resident sequence type (ST) 631 strains caused seven infections, and show a relatively recent history of recombination with other clinical and environmental lineages present in the region. ST34 and ST674 strains were each linked to a single infection and these strain types were also identified from the environment as isolates harboring hemolysin genes. Forty-two ST36 isolates were identified from the clinical collection, consistent with reports that this strain type caused a rise in regional infections starting in 2012. Whole-genome phylogenies that included three ST36 outbreak isolates traced to at least two local sources demonstrated that the US Atlantic coastal population of this strain type was indeed derived from the Pacific population. This study lays the foundation for understanding dynamics within natural populations associated with emergence and invasion of pathogenic strain types in the region.
Stat5a Is Epigenetically Silenced by Oncogenic Tyrosine Kinase NPM/ALK and Acts as Tumor Suppressor by Reciprocally Inhibiting Expression of NPM/ALK. (2007)

Abstract Although Stat5a and Stat5b exhibit some non-redundant functional properties, their distinct contributions to carcinogenesis are not clearly defined. Here we report that Stat5a expression is selectively inhibited by DNA methylation of the Stat5a gene promoter region in cells expressing an oncogenic tyrosine kinase NPM/ALK. The DNA methylation is induced by NPM/ALK itself by employing its key effector Stat3, and is associated with binding to the promoter of MeCP2 capping protein and lack of binding of the Stat5a transcription activator Sp-1. Reversal of the methylation by DNA methyltransferase inhibitor, 5′-aza-2-deoxycytidine, restores the Sp-1 binding and Stat5a expression. Strikingly, the induced or exogenously expressed Stat5a binds to enhancer and exon 14 of the NPM/ALK gene and triggers selective suppression of NPM/ALK expression. These results demonstrate that NPM/ALK induces epigenetic silencing of Stat5a and that Stat5a can act as key tumor suppressor by reciprocally inhibiting expression of NPM/ALK.
Controlled self-assembly of α-helix-decorated peptide nanostructures (2011)

This study describes a strategy to control the degree of α-helix stabilization and the shape of α-helix-decorated nanostructures. Coassembly of a macrocyclic peptide and a β-sheet peptide diminished steric clashes between helical peptide segments, further stabilizing α-helices.
Non‐Invasive Assessment of the Embryo Viability via the Analysis of the Culture Media (2017)

Infertility in recent years is a growing public health issue throughout the developed world. Assisted reproductive techniques, especially in vitro fertilization, have the potential to partially overcome the low natural reproductive ratio. Nowadays, single embryo transfer gains grounds in clinical practice, urging the development of more reliable methods for selecting the best embryo. In the traditional clinical practice, embryos are selected for transfer based on morphological evaluation. In vitro culturing of embryos also provides a very important material for further non‐invasive evaluation by means of examining a biomarker in the spent culture medium (SEC). Current measure methods concentrate on the metabolomic activity of the developing embryos none compounds. These studies are mainly utilizing the tools of modern analytics and proteomics. In a paper published by Montskó et al. in 2015, the alpha‐1 chain of the human haptoglobin molecule was described as a quantitative biomarker of embryo viability. In a series of retrospective, blind experiments achieved more than 50% success rate. This chapter summarizes the currently available metabolomic and proteomic approaches as the non‐invasive molecular assessment of embryo viability.
Progress In Signal And Texture Discrimination In Medical Imaging (1985)

We begin with a review of the concepts of first, second, and higher order statistics and the ability of human observers to extract textural information of these orders from images. This ability has been found to be very high for first order statistics and very low for third and higher order statistics. We next explore some classes of second order statistics where the human observer is greatly outperformed by machine analysis and explain this within the "texton" theory of Julesz. Example images from phase-sensitive detection systems such as medical ultrasound are then presented. The signal detection theory used previously to study the detectability of first order changes in images is generalized to analyze the detectability and classification of textural changes within an image. We conclude that second order statistical properties contain a wealth of unused information that can be easily extracted both for system performance evaluation and for classification of tissue textural changes.
Correlation of Selective Modifications to a 2‘,5‘-Oligoadenylate−3‘,5‘-Deoxyribonucleotide Antisense Chimera with Affinity for the Target Nucleic Acid and with Ability To Activate RNase L (1997)

The use of an antisense oligonucleotide to address a specific targeted RNA sequence and subsequent localized activation of the 2-5A-dependent RNase (RNase L) to effect selective RNA degradation is a new approach to the control of gene expression called 2-5A-antisense. The previously reported biological activity of the 2-5A:AS chimeric oligonucleotide [p5'(A2'p)3A-antiPKR1], directed against nucleotides 55-73 of the coding sequence of the PKR mRNA, has been used as a point of reference to examine the effect of introducing mismatches into the chimeric oligonucleotide, altering the chain length of the antisense domain of the chimeras, removal of the 5'-monophosphate moiety, shortening the 2',5'-oligoadenylate domain, and substitution of 3',5'-linked 2'-deoxyadenosine nucleotides for the 2-5A domain. The general formula for the novel chimeric oligonucleotides is p5'(A2'p)3A2'p(CH2)4p(CH2)4p(5'N3'p)mN, where N is any nucleoside and m is any integer. When the biological activity of these new chimeric oligonucleotides was compared to that of the parent chimera, 2-5A-aPKR, for their ability to effect target PKR RNA cleavage in a cell-free and in an intact cell assay, it was determined that there was a close correlation between the activity of 2-5A-antisense chimeras and their affinity (Tm) for a targeted nucleic acid. In addition, there was also a close correlation between activity of the 2-5A-antisense chimeras and their ability to activate the 2-5A-dependent RNase L.
In-line fiber étalon for strain measurement (1993)

A description and demonstration of a fiber interferometer that uses a short segment of silica hollow-core fiber spliced between two sections of single-mode fiber to form a mechanically robust in-line cavity are presented. The hollow-core fiber is specifically manufactured to have an outer diameter that is equal to the outer diameter of the single-mode lead fibers, thereby combining the best qualities of existing intrinsic and extrinsic Fabry-Perot sensors. A dynamic strain resolution of ~22 nepsilon/ radicalHz at frequencies of >5 Hz with a sensor gauge length of 137 microm is demonstrated.
Production of Ethanol from Cellulosic Biomass Hydrolysates Using Genetically Engineered Saccharomyces Yeast Capable of Cofermenting Glucose and Xylose (2004)

Abstract Recent studies have proven ethanol to be the ideal liquid fuel for transportation, and renewable lignocellulosic materials to be the attractive feedstocks for ethanol fuel production by fermentation. The major fermentable sugars from hydrolysis of most cellulosic biomass are D-glucose and D-xylose. The naturally occurring Saccharomyces yeasts that are used by industry to produce ethanol from starches and cane sugar cannot metabolize xylose. Our group at Purdue University succeeded in developing genetically engineered Saccharomyces yeasts capable of effectively cofermenting glucose and xylose to ethanol, which was accomplished by cloning three xylose-metabolizing genes into the yeast. In this study, we demonstrated that our stable recombinant Saccharomyces yeast, 424A(LNH-ST), which contains the cloned xylose-metabolizing genes stably integrated into the yeast chromosome in high copy numbers, can efficiently ferment glucose and xylose present in hydrolysates from different cellulosic biomass to ethanol.
Swifter (2013)

Online streaming video systems have become extremely popular, yet navigating to target scenes of interest can be a challenge. While recent techniques have been introduced to enable real-time seeking, they break down for large videos, where scrubbing the timeline causes video frames to skip and flash too quickly to be comprehendible. We present Swifter, a new video scrubbing technique that displays a grid of pre-cached thumbnails during scrubbing actions. In a series of studies, we first investigate possible design variations of the Swifter technique, and the impact of those variations on its performance. Guided by these results we compare an implementation of Swifter to the previously published Swift technique, in addition to the approaches utilized by YouTube and Netfilx. Our results show that Swifter significantly outperforms each of these techniques in a scene locating task, by a factor of up to 48%.
Intelligent and Ultrasensitive Analysis of Mercury Trace Contaminants via Plasmonic Metamaterial‐Based Surface‐Enhanced Raman Spectroscopy (2014)

Label-free molecular logic gates (AND, INHIBIT, and OR) are constructed based on specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy. The DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2 × 10(-4) ppb.
Template-Synthesized DNA Nanotubes (2005)

There is considerable interest in DNA-functionalized nanotubes with proposed applications that include use as gene delivery vehicles, in DNA-assisted separation and assembly of carbon nanotubes, and in nanotube-based DNA sensing and separations. In all of these previous cases, the DNA molecules were attached to a nanotube composed of a second material, typically carbon; however, it might also be advantageous to have nanotubes composed entirely, or predominately, of DNA itself. We describe here a template synthesis method for preparing such DNA nanotubes. The synthetic strategy builds on prior work, where we used Mallouk's layer-by-layer alpha,omega-diorganophosphonate (alpha,omega-DOP) Zr(IV) chemistry to deposit layered alpha,omega-DOP/Zr(IV) nanotubes along the pore walls of an alumina template membrane. The DNA nanotubes described here have an outer skin of one or more of these alpha,omega-DOP/Zr(IV) layers, to provide structural integrity, surrounding an inner core of multiple double-stranded DNA layers held together by hybridization between the layers. The DNA molecules comprising these nanotubes can be varied at will, and the DNA can be released from the nanotube by melting of the DNA duplexes comprising the nanotubes.
Early detection and real-time reporting of deep-ocean tsunamis (2001)

An improved method of gas-liquid chromatography (GLC) for routine estimation of adrenal steroids in urine is presented. It was applied to the exploration of steroid output in 120 normal prepuberal children to both sexes aged 3 months-12 years. Urinary data were compared to plasmatic values of adrenal hormones estimated by radio-immuno-assays (RIA). Analysis of the relationships between steroids outputs and bone age revealed that the excretion of cortisol catabolites was expressed by a saturation curve whereas that of delta 4-3 keto androgens catabolites were expressed by geometrical pregression curves; urine dehydroepiandrosterone (DHEA) and plasma DHEA-sulfate showed outbreaks of high values beyond 6 years of age which ruled out all curve fitting attempts. The computation of these relationships allowed to determine the confidence belts of the various regressions which appear as a useful tool to estimate the delayed or accelerated character of adrenal activity in prepuberal childhood. Comparison of the various urinary (GLC) and plasmatic (RIA) parameters enabled us to comment on adrenal puberty.
Tumor Budding Detection in H&E-Stained Images Using Deep Semantic Learning (2020)

Tumor buddings (TB), a special formation of cancerous cells that bud from the tumor front, are fast becoming the key indicator in modern clinical applications where they play a significant role in prognostic and evaluation of colorectal cancers in histopathological images. Recently, computational methods have been rapidly evolving in the domain of digital pathology, yet the literature lacks computerized approaches to automate the localization and segmentation of TBs in hematoxylin and eosin (H&E)-stained images. This research addresses this very challenging task of tumor budding detection in H&E images by presenting different deep learning architectures designed for semantic segmentation. The proposed design for a new Convolutional Neural Network (CNN) incorporates convolution filters with different factors of dilations. Multiple experiments based on a newly constructed colorectal cancer histopathological image collection provided promising performances. The best average intersection over union (IOU) for TB of 0.11, IOU for non-TB of 0.86, mean IOU of 0.49 and weighted IOU of 0.83 were observed.
Designing Transmitter Ligands That Mediate Energy Transfer between Semiconductor Nanocrystals and Molecules (2017)

Molecular control of energy transfer is an attractive proposition because it allows chemists to synthetically tweak various kinetic and thermodynamic factors. In this Perspective, we examine energy transfer between semiconductor nanocrystals (NCs) and π-conjugated molecules, focusing on the transmitter ligand at the organic-inorganic interface. Efficient transfer of triplet excitons across this interface allows photons to be directed for effective use of the entire solar spectrum. For example, a photon upconversion system composed of semiconductor NCs as sensitizers, bound organic ligands as transmitters, and molecular annihilators has the advantage of large, tunable absorption cross sections across the visible and near-infrared wavelengths. This may allow the near-infrared photons to be harnessed for photovoltaics and photocatalysis. Here we summarize the progress in this recently reported hybrid upconversion platform and point out the challenges. Since triplet energy transfer (TET) from NC donors to molecular transmitters is one of the bottlenecks, emphasis is on the design of transmitters in terms of molecular energetics, photophysics, binding affinity, stability, and energy offsets with respect to the NC donor. Increasing the efficiency of TET in this hybrid platform will increase both the up- and down-conversion quantum yields, potentially exceeding the Shockley-Queisser limit for photovoltaics and photocatalysis.
Unobtrusive breath alcohol sensing system (2015)

Although the vast majority of vehicle drivers are sober, drunk driving remains to be a major contributor to fatal accidents. Massive deployment of unobtrusive breath alcohol sensing systems could potentially save tens of thousands of lives worldwide every year by preventing drunk driving [1]. The work reported here is ultimately aiming at such a system. The technical performance of the present sensing system with respect to automotive requirements is summarized, and new results towards unobtrusive breath alcohol determination within vehicle compartments are presented. Breath alcohol concentration (BrAC) can be determined unobtrusively if (i) the sensing system provides real-time signals with adequate accuracy corresponding to the local concentrations of both alcohol and a tracer gas, e g CO2, (ii) the dilution of the breath is not excessive in relation to background concentrations, (iii) the sensor location can be seamlessly integrated into the interior of a vehicle cabin. All three of these aspects are addressed in the present paper. More than a hundred prototypes based on infrared spectroscopy were fabricated and subjected to automotive qualification tests in the full temperature range -40 … +85⁰C. In the majority of tests, adequate performance was noted. Measures are now being taken to fill remaining performance gaps. Test results with human subjects were positive and in accordance with expectations with respect to physiological variations. In-vehicle tests showed that for the best sensor position, passive breath samples allowed BrAC to be determined at a resolution of 2-4% of the US legal limit, providing proof-of-principle for unobtrusive testing. Nevertheless, vehicle integration remains to be the major technological challenge to the objective of deployment on a large scale of unobtrusive driver breath alcohol determination. The feasibility of unobtrusive breath alcohol determination in vehicles, and adequate performance of a sensor system based on infrared spectroscopy have been experimentally demonstrated. The alcohol sensing system may advantageously be integrated into vehicles, and may also be combined with other technologies to monitor driver impairment.
ChemInform Abstract: 2‐ACETYLPYRIDINE THIOSEMICARBAZONES. 1. A NEW CLASS OF POTENTIAL ANTIMALARIAL L AGENTS (1979)

Abstract Insgesamt 85 Semicarbazone der Struktur (I) und 76 der Struktur (II) werden dargestellt, von denen erstere wirksam sind gegen Plasmodium berghei in Mäusen.
<i>In vivo</i> Therapeutic Synergism of Anti–Epidermal Growth Factor Receptor and Anti-HER2 Monoclonal Antibodies against Pancreatic Carcinomas (2007)

Anti-HER2 mAb has a synergistic therapeutic effect when combined with an anti-EGFR mAb on pancreatic carcinomas with low HER2 expression. These observations may open the way to the use of these two mAbs in a large panel of carcinomas expressing different levels of the two HER receptors.
Surface acoustic wave and piezoelectric properties of (Pb, Ln) (Ti, Mn)O3 ceramics (Ln = rare earths) (1981)

The surface acoustic wave (SAW) and piezoelectric properties of PbTi03 ceramics modified by the partial substitution of rare earths for Pb, particularly (Pb, Ln) (Ti, Mn)03 (Ln = La, Ce, Pr, Nd, Sm, or Gd) ceramics, are examined. The effects of the rare earths introduced on these properties are noted. Properties, such as velocities and electromechanical coupling factors, for bulk wave and SAW vary monotonically with the ionic sizes of the rare earths. On the other hand, the temperature coefficient of SAW delay time takes a minimum value when the Ln is Nd. It is shown that the variation of the temperature coefficient with rare earths corresponds well with those of the temperature coefficients of elastic constants CE33 and CE44.
Generation, Purification and Transplantation of Photoreceptors Derived from Human Induced Pluripotent Stem Cells (2010)

This report provides evidence that enriched populations of human photoreceptors can be derived from iPS cells.
Cross-borehole resistivity tomography (1991)

Abstract Electrical resistivity tomography (ERT) is a method for determining the electrical resistivity distribution in a volume from discrete measurements of current and voltage made within the volume or on its surface. We have developed an ERT algorithm that is an iterative, modified least squares inversion, based on a finite element forward solution of Laplace's equation. We report the results of tests on this algorithm designed to determine how resistance measurements made from two boreholes may be used to image the resistivity distribution between them. A number of simple but geophysically significant structures are modeled. These include a single isolated block anomaly, two layers, a thin isolated continuous layer, and a vertical band. The main features of most resistivity models were identifiable in the reconstructions. Limited data accuracy and noise were simulated and found to cause a deterioration of the image. However, even with measurements of only one significant figure accuracy, the algorithm converged toward the desired solution for at least the first iteration and the targets were identifiable in the reconstructions. Imprecision in the data influences convergence as well as image quality; more iterations eventually lead to divergence. Spatial resolution depends on such factors as data errors and the specific target geometry.
SciFinance: A Program Synthesis Tool for Financial Modeling (2000)

www.scicomp.com The SciFinanceTM software synthesis system automates the programming task for financial risk management activities ranging from algorithms research to production pricing to risk control. Introduced commercially in late 1998, the system is currently licensed to a number of major investment banks. SciFinance’s high-level, extensible specification language, ASPEN, enables quantitative analysts to generate code from concise model descriptions that are written in application-specific and mathematical terminology. From these spec-ifications, typically one page or less, the system will pro-duce a C program thousands of lines long. The specification language’s abstractions help analysts focus on their primary tasks—model description, validation, and analysis—rather
Real-time GHz-rate counting of infrared photons using nanostructured NbN superconducting detectors (2003)

We demonstrate that our ultrathin, nanometer-width NbN superconducting single-photon detectors are capable of above 1-GHz-frequency, real-time counting of near-infrared photons. The measured system jitter of the detector is below 15 ps.