gebhart/patrepeval huggingface dataset:
Design of Artificial Short-Chained RNA Species That Are Replicated by Q.beta. Replicase (1995)

Different RNA species that are replicated by Q beta replicase have related secondary structures: for both plus and minus strands, "leader" stem structures were found at their 5' termini, while their 3' termini were unpaired. Parallel structures in complementary strands rather than antiparallel ones require the occurrence of wobble pairs and other imperfections in the stem regions. To test whether the leader structures are required for replication, artificial RNA sequences were synthesized by transcription from synthetic oligodeoxynucleotides with T7 RNA polymerase and assayed for their ability to be replicated by Q beta replicase. A synthetic short RNA species known to be replicated was amplified, forming a stable quasi-species; i.e., its sequence was conserved during hundreds of replication rounds. A synthetic mutant of this sequence that stabilized the leader in one strand but favored a 3'-terminal stem in the other one led to the complete loss of template activity. When new RNA sequences with the described structural requirements were designed and synthesized, their template activity was too low to be directly measurable; however, incubation with replicase produced replicating RNA whose sequence was closely related to the synthesized RNA species. The most likely interpretation is that the designed sequences were in a low montainous region in the replication fitness landscape and were optimized during amplification by Q beta replicase to a nearby fitness peak. The structural features postulated to be required for replication were not only conserved but even improved in the outgrowing mutants.(ABSTRACT TRUNCATED AT 250 WORDS)
DESIGN CONSIDERATIONS FOR RADIO FREQUENCY ENERGY HARVESTING DEVICES (2012)

Radio Frequency Energy harvesting is a research topic of increasing interest, related to sustainability, which could become a promising alternative to existing energy resources. The paper will show all the activities addressed to design a wideband system to recover wideband energy from electromagnetic sources present in the environment. The main idea is to develop battery-free wireless sensors able to capture the available energy into the mentioned bandwidth. The flnal goal is to realize self-powered Wireless Networks based on Ultra Lower Power | ULP sensors minimizing the need of dedicated batteries. This last feature is particularly attractive in difierent kind of applications, ranging from military to civil cases. A flrst system prototype is shown and discussed. Conclusion follows.
Stereoselective Total Synthesis of Iso‐Cladospolide B and the 12 Membered‐Macrolactone (6S,12R)‐6‐Hydroxy‐12‐methyloxacyclododecane‐2,5‐dione (2015)

Abstract Total syntheses of iso‐cladospolide B ( 1 ) and the 12‐membered macrolactone (6 S ,12 R )‐6‐hydroxy‐12‐methyloxacyclododecane‐2,5‐dione ( 2 ), a non‐natural product, were achieved from a common intermediate starting from commercially available 1,9‐nonane diol.
Preparation of Cellulose Acetate - Action of Sulfuric Acid (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of Cellulose Acetate - Action of Sulfuric AcidCarl J. Malm, Leo J. Tanghe, and Barbara C. LairdCite this: Ind. Eng. Chem. 1946, 38, 1, 77–82Publication Date (Print):January 1, 1946Publication History Published online1 May 2002Published inissue 1 January 1946https://pubs.acs.org/doi/10.1021/ie50433a033https://doi.org/10.1021/ie50433a033research-articleACS PublicationsRequest reuse permissionsArticle Views1363Altmetric-Citations44LEARN 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 options Get e-Alerts
MEMS-Based Nanospray-Ionization Mass Spectrometer (2010)

An electrospray-ionization mass spectrometer (ESI-MS) whose main components are all fabricated using silicon microelectromechanical systems (MEMS) techniques is demonstrated for the first time. The ion source consists of a microengineered alignment bench containing a V-groove mounting for a nanospray capillary, an ion-extraction electrode, and a pneumatic nebulizer. The vacuum interface consists of two plates, each carrying a 50-μm-diameter capillary, that are selectively etched and bonded together to provide a differentially pumped internal cavity. The quadrupole filter consists of a microfabricated frame that provides mountings for stainless-steel rods measuring 650 μm in diameter and 30 mm in length. Two different quadrupoles are compared: a first-generation bonded silicon device and a second-generation silicon-on-glass device with a Brubaker prefilter. Differential pumping of a MEMS component is demonstrated for the first time, atmospheric pressure ionization and ion transfer into vacuum are characterized, ESI-MS operation is demonstrated, and spectra are presented for a variety of compounds.
Identification of Serum Monocyte Chemoattractant Protein-1 and Prolactin as Potential Tumor Markers in Hepatocellular Carcinoma (2013)

Early diagnosis of hepatocellullar carcinoma (HCC) remains a challenge. The current practice of serum alpha-fetoprotein (AFP) measurement is inadequate. Here we utilized a proteomic approach to identify novel serum biomarkers for distinguishing HCC patients from non-cancer controls. We profiled the serum proteins in a group of 58 resectable HCC patients and 11 non-HCC chronic hepatitis B (HBV) carrier samples from the Singapore General Hospital (SGH) using the RayBio® L-Series 507 Antibody Array and found 113 serum markers that were significantly modulated between HCC and control groups. Selected potential biomarkers from this list were quantified using a multiplex sandwich enzyme-linked immunosorbent assay (ELISA) array in an expanded SGH cohort (126 resectable HCC patients and 115 non-HCC chronic HBV carriers (NC group)), confirming that serum prolactin and monocyte chemoattractant protein-1 (MCP-1) were significantly upregulated in HCC patients. This finding of serum MCP-1 elevation in HCC patients was validated in a separate cohort of serum samples from the Mochtar Riady Institute for Nanotechnology, Indonesia (98 resectable HCC, 101 chronic hepatitis B patients and 100 asymptomatic HBV/HCV carriers) by sandwich ELISA. MCP-1 and prolactin levels were found to correlate with AFP, while MCP-1 also correlated with disease stage. Subsequent receiver operating characteristic (ROC) analysis of AFP, prolactin and MCP-1 in the SGH cohort and comparing their area under the ROC curve (AUC) indicated that neither prolactin nor MCP-1 on their own performed better than AFP. However, the combination of AFP+MCP-1 (AUC, 0.974) had significantly superior discriminative ability than AFP alone (AUC, 0.942; p<0.001). In conclusion, prolactin and MCP-1 are overexpressed in HCC and are conveniently quantifiable in patients' sera by ELISA. MCP-1 appears to be a promising complementary biomarker for HCC diagnosis and this MCP-1+AFP model should be further evaluated as potential biomarker on a larger scale in patients at-risk of HCC.
Egocentric Hand Track and Object-Based Human Action Recognition (2019)

Egocentric vision is an emerging field of computer vision that is characterized by the acquisition of images and video from the first person perspective. In this paper we address the challenge of egocentric human action recognition by utilizing the presence and position of detected regions of interest in the scene explicitly, without further use of visual features. Initially, we recognize that human hands are essential in the execution of actions and focus on obtaining their movements as the principal cues that define actions. We employ object detection and region tracking techniques to locate hands and capture their movements. Prior knowledge about egocentric views facilitates hand identification between left and right. With regard to detection and tracking, we contribute a pipeline that successfully operates on unseen egocentric videos to find the camera wearer's hands and associate them through time. Moreover, we emphasize on the value of scene information for action recognition. We acknowledge that the presence of objects is significant for the execution of actions by humans and in general for the description of a scene. To acquire this information, we utilize object detection for specific classes that are relevant to the actions we want to recognize. Our experiments are targeted on videos of kitchen activities from the Epic-Kitchens dataset. We model action recognition as a sequence learning problem of the detected spatial positions in the frames. Our results show that explicit hand and object detections with no other visual information can be relied upon to classify hand-related human actions. Testing against methods fully dependent on visual features, signals that for actions where hand motions are conceptually important, a region-of-interest-based description of a video contains equally expressive information with comparable classification performance.
Fast nonconvex deconvolution of calcium imaging data (2018)

Calcium imaging data promises to transform the field of neuroscience by making it possible to record from large populations of neurons simultaneously. However, determining the exact moment in time at which a neuron spikes, from a calcium imaging data set, amounts to a non-trivial deconvolution problem which is of critical importance for downstream analyses. While a number of formulations have been proposed for this task in the recent literature, in this article, we focus on a formulation recently proposed in Jewell and Witten (2018. Exact spike train inference via $\ell_{0} $ optimization. The Annals of Applied Statistics12(4), 2457-2482) that can accurately estimate not just the spike rate, but also the specific times at which the neuron spikes. We develop a much faster algorithm that can be used to deconvolve a fluorescence trace of 100 000 timesteps in less than a second. Furthermore, we present a modification to this algorithm that precludes the possibility of a "negative spike". We demonstrate the performance of this algorithm for spike deconvolution on calcium imaging datasets that were recently released as part of the $\texttt{spikefinder}$ challenge (http://spikefinder.codeneuro.org/). The algorithm presented in this article was used in the Allen Institute for Brain Science's "platform paper" to decode neural activity from the Allen Brain Observatory; this is the main scientific paper in which their data resource is presented. Our $\texttt{C++}$ implementation, along with $\texttt{R}$ and $\texttt{python}$ wrappers, is publicly available. $\texttt{R}$ code is available on $\texttt{CRAN}$ and $\texttt{Github}$, and $\texttt{python}$ wrappers are available on $\texttt{Github}$; see https://github.com/jewellsean/FastLZeroSpikeInference.
<title>Automatically determining the orientation of chest images</title> (1997)

A review console displaying digital radiographs should automatically display the chest images in proper orientation to save radiologists' time. To accomplish this feat, the authors have developed a simple, rapid algorithm that can be implemented in hardware. Linear regression is used on two orthogonal profiles to determine the top of the image. The edge of the heart is found to make sure the image is not displayed as a mirror image. The algorithm was 90.4 percent successful on 115 chest images.
DNA-templated nanowires as sacrificial materials for creating nanocapillaries (2008)

DNA has shown great promise as a template for the controlled localization of various materials and the construction of wires with nanometer-dimension cross sections. We have recently developed a strategy for fabrication of nanocapillaries, using DNA-templated nanowires as a sacrificial material. We first form metal nanowires through the selective electrochemical deposition of nickel atop a surface-aligned DNA molecule. We then deposit a thin layer of silicon dioxide on top of the DNA nanostructures. Next, we photolithographically pattern openings over the ends of the wires and etch through the silicon dioxide layer to expose the metal nanowires. Finally, we etch out the DNA-templated nickel nanowires. This process results in the formation of nanocapillaries having the same dimensions as the originally formed DNA-templated nanowires. We have characterized these DNA-templated nanocapillaries using atomic force microscopy, optical microscopy and scanning electron microscopy. These constructs have potential for application in nanofluidics, power generation, sample preconcentration, and chemical sensing.
Integration of a structural features-based preclassifier and a man-machine interactive classifier for a fast multi-stroke character recognition (2003)

A transputer-based parallel machine for handwritten character recognition is proposed. An algorithm based on structural features and on a tree classifier was used to accomplish the pre-classification of the unknown sample in order to speed up the recognition process. The algorithm for the final classification is based on the description of the strokes through Fourier descriptors. The learning phase is accomplished through a man-machine interactive process. The proposed system can expand its knowledge base. A special representation of this knowledge base is proposed in order to record a great amount of data in a suitable way. A fast multistroke handwritten isolated character recognition system is presented. The test of this system was performed on a PC based prototype while the realization of a parallel transputer based working machine is in progress. Experimental results obtained applying these machines to handwritten numerals recognition are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lowering of Tumor Interstitial Fluid Pressure Reduces Tumor Cell Proliferation in a Xenograft Tumor Model (2006)

High tumor interstitial fluid pressure (TIFP) is a characteristic of most solid tumors. TIFP may hamper adequate uptake of macromolecular therapeutics in tumor tissue. In addition, TIFP generates mechanical forces affecting the tumor cortex, which might influence the growth parameters of tumor cells. This seems likely as, in other tissues (namely, blood vessels or the skin), mechanical stretch is known to trigger proliferation. Therefore, we hypothesize that TIFP-induced stretch modulates proliferation-associated parameters. Solid epithelial tumors (A431 and A549) were grown in Naval Medical Research Institute nude mice, generating a TIFP of about 10 mm Hg (A431) or 5 mm Hg (A549). Tumor drainage of the central cystic area led to a rapid decline of TIFP, together with visible relaxation of the tumor cortex. It was found by sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blot analysis that TIFP lowering yields a decreased phosphorylation of proliferation-associated p44/42 mitogen-activated protein kinase and tumor relaxation. In confirmation, immunohistochemical staining showed a decrease of tumor-associated proliferation marker Ki-67 after TIFP lowering. These data suggest that the mechanical stretch induced by TIFP is a positive modulator of tumor proliferation.
Spatial Control of Multiphoton Electron Excitations in InAs Nanowires by Varying Crystal Phase and Light Polarization (2017)

We demonstrate the control of multiphoton electron excitations in InAs nanowires (NWs) by altering the crystal structure and the light polarization. Using few-cycle, near-infrared laser pulses from an optical parametric chirped-pulse amplification system, we induce multiphoton electron excitations in InAs nanowires with controlled wurtzite (WZ) and zincblende (ZB) segments. With a photoemission electron microscope, we show that we can selectively induce multiphoton electron emission from WZ or ZB segments of the same wire by varying the light polarization. Developing ab initio GW calculations of first to third order multiphoton excitations and using finite-difference time-domain simulations, we explain the experimental findings: While the electric-field enhancement due to the semiconductor/vacuum interface has a similar effect for all NW segments, the second and third order multiphoton transitions in the band structure of WZ InAs are highly anisotropic in contrast to ZB InAs. As the crystal phase of NWs can be precisely and reliably tailored, our findings open up for new semiconductor optoelectronics with controllable nanoscale emission of electrons through vacuum or dielectric barriers.
Demonstration of 8-Step Single-Photon Quantum Walk using 32 x 32 Reconfigurable Silicon Photonics Switch (2020)

We implemented a reconfigurable quantum-walk circuit on a 32*32 silicon photonics switch system. The 1 to 8-step quantum walk exhibited a long-term stability over 45 hours with clear single-photon interference for 10-nm-bandwidth heralded single photons.
Interferon‐alpha up‐regulates bcl‐2 expression and protects B‐CLL cells from apoptosis in vitro and in vivo (1994)

The bcl-2 oncoprotein, which is involved in the t(14,18) translocation, protects cells against apoptosis. We examined the effects of interferon-alpha (IFN-alpha) on bcl-2 protein expression and apoptosis in B-chronic lymphocytic leukaemia (B-CLL) cells. None of 12 patients with B-CLL examined expressed the t(14,18) translocation; however, all these, and seven other patients, expressed significant levels of bcl-2 protein. In vitro, IFN-alpha (500 U/ml over 18 h) increased bcl-2 expression on CLL cells (to 200 +/- 23% of control MCF, as determined by indirect immunofluorescence and flow cytometry, n = 10, P < 0.001). All of eight patients who received IFN-alpha (3 megaunits subcutaneously three times a week) demonstrated an increase in bcl-2 expression on circulating malignant cells. CLL cells undergo apoptotic cell death when cultured in vitro (35.6 +/- 10.3% DNA fragmentation after 18 h, n = 10). In the presence of IFN-alpha, however, DNA fragmentation was reduced to 6.6 +/- 5.8% (n = 10, P < 0.001). IFN-alpha also protected CLL cells against apoptosis induced by hydrocortisone and gamma irradiation (reducing DNA fragmentation from 63.9 +/- 12.6% to 10.8 +/- 4.5% and from 80 +/- 2.9% to 5.4 +/- 1.6%, respectively, P < 0.001 for both). The protective effect of IFN-alpha was dose dependent, and maintained for up to 24 h. Our data demonstrate that bcl-2 expression and apoptosis of CLL cells can be influenced by cytokines. In addition, it seems unlikely that the observed clinical responses to IFN-alpha in patients with CLL are due to a direct effect on the malignant cells.
Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive (2021)

Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, learning, and memory. Previous sequencing studies have demonstrated that aging alters gene expression in the PFC, however the extent to which these changes are conserved across species and are meaningful in neurodegeneration is unknown. Identifying conserved, age-related genetic and morphological changes in the brain allows application of the wealth of tools available to study underlying mechanisms in model organisms such as Drosophila melanogaster. RNA sequencing data from human PFC and fly heads were analyzed to determine conserved transcriptome signatures of age. Our analysis revealed that expression of 50 conserved genes can accurately determine age in Drosophila (R2 = 0.85) and humans (R2 = 0.46). These transcriptome signatures were also able to classify Drosophila into three age groups with a mean accuracy of 88% and classify human samples with a mean accuracy of 69%. Overall, this work identifies 50 highly conserved aging-associated genetic changes in the brain that can be further studied in model organisms and demonstrates a novel approach to uncovering genetic changes conserved across species from multi-study public databases.
ChemInform Abstract: Novel Pathways for the Formation of Phenylpyrroles. (1990)

Abstract 3‐Chloropropyl phenyl ketone (I) is converted to the oxime (III) which undergoes base‐induced cyclization to give the dihydro‐1,2‐oxazine (IV) as the main product.
Effect of reactive pharmacy intervention on quality of hospital prescribing. (1990)

Most reactive pharmacy interventions concerned prescribing errors with a limited potential for medical harm, but a small number of detected errors with a major potential for medical harm; cost savings were not appreciable.
Swelling-driven rolling and anisotropic expansion of striped gel sheets (2013)

Swelling of spatially patterned gel films promises many new opportunities for understanding and exploiting differential growth as a means to define three-dimensional (3D) configurations of thin sheets. Here, we consider the swelling-driven deformation of sheets patterned with alternating parallel strips of material with high and low equilibrium extents of swelling, and the dependence of this process on film thickness, strip width, and swelling contrast. Temperature-responsive, photo-crosslinkable hydrogels are prepared from poly(N-isopropyl acrylamide) (PNIPAm) copolymers with pendent benzophenone groups that allow the degree of crosslinking to be programmed by the dose of UV light. Photo-patterned multi-strips deform by rolling around the axis perpendicular to the interface between high- and low-swelling regions, due to a balance between stretching energy in the transition region and bending of the entire sheet. However, when the strip width falls below a critical size proportional to the film thickness, the patterned sheets instead remain flat, undergoing greater expansion along the direction normal to the interfaces than in the direction parallel. This configuration suggests possibilities for patterning anisotropic growth, and also provides fruitful information on the contrast in modulus between the regions.
IgM in a human neuropathy related to paraproteinemia binds to a carbohydrate determinant in the myelin-associated glycoprotein and to a ganglioside. (1984)

The IgM in three patients with paraproteinemia and peripheral neuropathy was shown to bind to human myelin-associated glycoprotein (MAG) that had been purified to homogeneity by gel filtration on Sepharose CL-6B. The antigenic determinant reacting with the IgM from all three patients was in the carbohydrate part of the MAG molecule. In addition, the IgM from the same three patients bound to a single ganglioside of human sciatic nerve. The results indicate that the IgM paraproteins in these patients react with a carbohydrate determinant that is shared between MAG and a peripheral nerve ganglioside.