gebhart/patrepeval huggingface dataset:
shRNAs Targeting Hepatitis C: Effects of Sequence and Structural Features, and Comparision with siRNA (2007)

Hepatitis C virus (HCV) is a leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. Currently available treatment options are of limited efficacy, and there is an urgent need for development of alternative therapies. RNA interference (RNAi) is a natural mechanism by which small interfering RNA (siRNA) or short hairpin RNA (shRNA) can mediate degradation of a target RNA molecule in a sequence-specific manner. In this study, we screened in vitro-transcribed 25-bp shRNAs targeting the internal ribosome entry site (IRES) of HCV for the ability to inhibit IRES-driven gene expression in cultured cells. We identified a 44-nt region at the 3'-end of the IRES within which all shRNAs efficiently inhibited expression of an IRES-linked reporter gene. Subsequent scans within this region with 19-bp shRNAs identified even more potent molecules, providing effective inhibition at concentrations of 0.1 nM. Experiments varying features of the shRNA design showed that, for 25-bp shRNAs, neither the size of the loop (4-10 nt) nor the sequence or pairing status of the ends affects activity, whereas in the case of 19-bp shRNAs, larger loops and the presence of a 3'-UU overhang increase efficacy. A comparison of shRNAs and siRNAs targeting the same sequence revealed that shRNAs were of comparable or greater potency than the corresponding siRNAs. Anti-HCV activity was confirmed with HCV subgenomic replicons in a human hepatocyte line. The results indicate that shRNAs, which can be prepared by either transcription or chemical synthesis, may be effective agents for the control of HCV.
A New Biconcave Contact Lens for Vitrectomy in Eyes With Intraocular Lens Implantation (2011)

The authors report a new biconcave contact lens capable of providing superior surgical views of eyes during vitrectomy and intraocular lens implantation under both fluid-filled and air-filled conditions. The new biconcave lens is made of a glass with a high refractive index (nd = 1.883). The lens is placed on the cornea using a regular lens ring for the floating vitrectomy lens system. During vitrectomy, the new biconcave lens provides a view as clear as that of the commercially available flat-concave lens when the vitreous cavity is filled with fluid. The lens also provides a more magnified view than the commercially sold biconcave lens during fluid-air exchange, with no need for replacement. The new biconcave vitrectomy lens spares the surgeon the trouble of replacing different refractive lenses during the fluid-air exchange procedure in an eye undergoing intraocular lens implantation, and may be helpful for vitreous surgery.
Update on EMD and Hilbert-Spectra Analysis of Time Series (2003)

This method is especially well suited for analyzing time-series data that represent nonstationary and nonlinear physical phenomena. The method is based principally on the concept of empirical mode decomposition (EMD), according to which any complicated signal (as represented by digital samples) can be decomposed into a finite number of functions, called "intrinsic mode functions" (IMFs), that admit well-behaved Hilbert transforms. The local energies and the instantaneous frequencies derived from the IMFs through Hilbert transforms can be used to construct an energy-frequency-time distribution, denoted a Hilbert spectrum.
ChemInform Abstract: Synthesis and Anticancer Activity of Sclerophytin‐Inspired Hydroisobenzofurans. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Statistical modelling of polarisation induced fading in interferometric fibre sensors (1991)

The probability functions associated with the polarisation parameters of an optical fibre interferometer, and the concomitant polarisation fading problems which arises have been experimentally and theoretically investigated. Good agreement between experimental results and theoretical models are obtained.
Multi-Layer Virtual Network Embedding (2018)

Network virtualization (NV), considered as a key enabler for overcoming the ossification of the Internet allows multiple heterogeneous virtual networks to co-exist over the same substrate network. Resource allocation problems in NV have been extensively studied for single layer substrates such as IP or Optical networks. However, little effort has been put to address the same problem for multi-layer IP-over-optical networks. The increasing popularity of multi-layer networks for deploying backbones combined with their unique characteristics ( e.g., topological flexibility of the IP layer) calls for the need to carefully investigate the resource provisioning problems arising from their virtualization. In this paper, we address the problem of multi-layer virtual network embedding (MULE; similar to multi-layer networks, this hybrid species brings the best of two species together.) on IP-over-optical networks. We propose two solutions to MULE: 1) an integer linear program formulation for the optimal solution (OPT-MULE) and 2) a heuristic to address the computational complexity of the optimal solution (FAST-MULE). We demonstrate through extensive simulations that on average our heuristic performs within $\boldsymbol \approx 1.47\boldsymbol \times $ of optimal solution while executing several orders of magnitude faster. Simulation results also show that FAST-MULE incurs ≈66% less cost on average than the state-of-the-art heuristic while accepting ≈60% more virtual network requests on average.
Long-term Hematopoietic Transfer of the Anti-Cancer and Lifespan-Extending Capabilities of A Genetically Engineered Blood System by Transplantation of Bone Marrow Mononuclear Cells (2023)

Abstract A causal relationship exists among the aging process, organ decay and dis-function, and the occurrence of various diseases including cancer. A genetically engineered mouse model, termed Klf1 K74R/K74R or Klf1 (K74R), carrying mutation on the well-conserved sumoylation site of the hematopoietic transcription factor KLF1/ EKLF has been generated that possesses extended lifespan and healthy characteristics including cancer resistance. We show that the healthy longevity characteristics of the Klf1 (K74R) mice, as exemplified by their higher anti- cancer capability, are likely gender-, age- and genetic background-independent. Significantly, the anti-cancer capability, in particular that against melanoma as well as hepatocellular carcinoma, and lifespan-extending property of Klf1 (K74R) mice could be transferred to wild-type mice via transplantation of their bone marrow mononuclear cells at young age of the latter. Furthermore, NK(K74R) cells carry higher in vitro cancer cell-killing ability than wild type NK cells. Targeted/global gene expression profiling analysis has identified changes of the expression of specific proteins, including the immune checkpoint factors PDCD and CD274, and cellular pathways in the leukocytes of the Klf1 (K74R) that are in the directions of anti-cancer and/or anti-aging. This study demonstrates the feasibility of developing a transferable hematopoietic/ blood system for long-term anti-cancer and, potentially, for anti-aging.
Treatment of Polycythemia Vera (2006)

The selection of treatment for patients with polycythemia vera (PV) still is the subject of much discussion among hematologists. It is emphasized that important physiologic and pathogenic components of the illness relate not only to the erythroid cell, but also to the megakaryocyte. Both play essential roles in causing complications of the disease. Hematologists agree that the mainstay in treatment remains phlebotomy, a basic pillar of the concept of PRIMUM NON NOCERE. In general, the target levels for the hematocrit have been accepted as <or= 45% for men and <or= 42% for women. Low-dose aspirin, 80 to 100 mg daily, should be used as a basic component of therapy. The selection of the type of treatment for those patients who require some form of myelosuppression owing to the frequency of phlebotomy and/or its complications provides the basis for major discussion, confrontation, and disagreement. For the most part, alkylating agents are avoided owing to the established risk of secondary leukemia, but these drugs and radioactive phosphorous ( (32)P) still play a role in treating the very elderly patient or for those who have significant comorbid conditions. Whereas hydroxyurea remains the most frequently prescribed drug, limitations to its use as a therapeutic agent of choice include questions regarding its effectiveness, toxicity, and potential leukemogenicity. Interferon offers a rational choice of treatment owing to its broad physiologic effects on hematopoiesis. Whereas its effect in treating patients with PV is unequivocal, it is associated with side effects even when used properly. Moreover, it has only modest effect on Janus kinase 2 (JAK2) expression. Clearly, the best treatment for patients with PV is still sought. Perhaps more explicit exploitation of the JAK2 abnormality found in PV (and other myeloproliferative diseases) may provide more effective agents in the future.
Arterial compliance probe for calibration free pulse pressure measurement (2016)

Cardiovascular diseases are the leading cause of death around the world. Non-invasive estimation of arterial parameters is significant in the early detection of cardiovascular diseases. In this work, we present an arterial compliance probe for calibration-free evaluation of carotid pulse pressure. This novel cuffless measurement technique uses dual magnetic plethysmograph (MPG) transducers for carotid local pulse wave velocity (PWV) measurement and single element ultrasound transducer for measuring arterial dimensions. Proposed arterial compliance probe can acquire two blood pulse waveforms and arterial diameter parameters simultaneously, which are then utilized in cycle-to-cycle estimation of arterial local PWV and pulse pressure without any subject or population specific calibration. The design of compliance probe and measurement system was verified by in-vivo trials. Accurate local PWV measurement and calibration free estimation of carotid pulse pressure was also validated by in-vivo studies. Initial results indicate a strong potential of MPG - Ultrasound arterial compliance probe in continuous, cuffless evaluation of blood pressure (BP) from superficial arteries.
A micro gas chromatograph with integrated bi-directional pump for quantitative analyses (2014)

This paper describes a micro gas chromatography (μGC) system that comprises a Knudsen pump with bidirectional capability (KP2), a two-stage preconcentrator-focuser (PCF2) and a separation column. In this valveless system, the bi-directionality of the pump allows flow reversal in the multi-stage preconcentrator. The KP2, PCF2, and separation column are arranged in a 4.3 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> stack, and used with a commercial flame ionization detector. In preliminary experiments, the μGC system demonstrated quantitative separation of benzene, toluene, and xylene (BTX) in ambient room air.
Micro Inertial Reference System for Microspacecraft (1998)

This paper reports on the development of a silicon bulk micromachined vibratory gyroscope designed for a micro inertial reference system for microspacecraft applications.
Mechanical and compaction properties of graphite nanoplatelet-modified asphalt binders and mixtures (2019)

This paper presents an experimental investigation of the properties of asphalt binders and mixtures modified with graphite nanoplatelets (GNPs). The focus is on studying the effects of GNP addition on low-temperature rheological and fracture properties of asphalt binders and mixtures and on compaction effort of asphalt mixtures. This is the first time that these effects are investigated and significant findings are reported. The study considers three types of GNP materials, including graphite nanoplatelets and sub-microscale graphite flakes. The cost of these materials is reasonably low, which makes them suitable for large-scale applications, unlike other types of graphite and graphene materials. The experimental results indicate that the addition of GNPs leads to considerable improvements of low-temperature strength and fracture properties of asphalt binders and mixtures. While the properties of asphalt binders at intermediate temperatures are minimally affected, for some combinations of binders and GNPs the increase in low-temperature strength is over 100%. A similar effect is observed for some of the asphalt mixtures investigated, in which the low-temperature fracture energy almost doubles. The laboratory compaction experiments show that the number of gyrations required for achieving a target density can be reduced by as much as 20–40% by adding a small percentage of GNPs into asphalt binders. The results of this experimental study indicate that GNP-modified asphalt binders and mixtures have significant potential for increasing the durability of asphalt pavements in cold regions, by reducing the compaction effort and improving the low-temperature strength and fracture properties of asphalt materials.
Context Lenses - Document Visualization and Navigation Tools for Rapid Access to Detail. (2001)

We introduce visualization and navigation tools -Context Lenses (CL) -which use a condensed representation of a document to provide a global overview of the distribution of key items as well as a focus view of their immediate context. The Context Lens is a focus+context dynamic information filtering tool allowing users to optimally choose how to access a particular piece of information. CLs support efficient information finding tasks by allowing rapid skimming of documents and document collections. Certain tasks can be accomplished using only the context information provided in the context lens, eliminating the need to access the actual document. Thus, use of a CL can eliminate the need to scroll within a document, or – in a distributed environment – to download the document. This hints at interesting applications for the display of search results and document collections on wireless PDAs. We present a user study about two different Context Lenses.
Targeted PMP22 TATA-box editing by CRISPR/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice (2019)

Charcot-Marie-Tooth 1A (CMT1A) is the most common inherited neuropathy without a known therapy, which is caused by a 1.4 Mb duplication on human chromosome 17, which includes the gene encoding the peripheral myelin protein of 22 kDa (PMP22). Overexpressed PMP22 protein from its gene duplication is thought to cause demyelination and subsequently axonal degeneration in the peripheral nervous system (PNS). Here, we targeted TATA-box of human PMP22 promoter to normalize overexpressed PMP22 level in C22 mice, a mouse model of CMT1A harboring multiple copies of human PMP22. Direct local intraneural delivery of CRISPR/Cas9 designed to target TATA-box of PMP22 before the onset of disease, downregulates gene expression of PMP22 and preserves both myelin and axons. Notably, the same approach was effective in partial rescue of demyelination even after the onset of disease. Collectively, our data present a proof-of-concept that CRISPR/Cas9-mediated targeting of TATA-box can be utilized to treat CMT1A.
Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides (2012)

Alternative splicing of the pyruvate kinase M gene involves a choice between mutually exclusive exons 9 and 10. Use of exon 10 to generate the M2 isoform is crucial for aerobic glycolysis (the Warburg effect) and tumour growth. We previously demonstrated that splicing enhancer elements that activate exon 10 are mainly found in exon 10 itself, and deleting or mutating these elements increases the inclusion of exon 9 in cancer cells. To systematically search for new enhancer elements in exon 10 and develop an effective pharmacological method to force a switch from PK-M2 to PK-M1, we carried out an antisense oligonucleotide (ASO) screen. We found potent ASOs that target a novel enhancer in exon 10 and strongly switch the splicing of endogenous PK-M transcripts to include exon 9. We further show that the ASO-mediated switch in alternative splicing leads to apoptosis in glioblastoma cell lines, and this is caused by the downregulation of PK-M2, and not by the upregulation of PK-M1. These data highlight the potential of ASO-mediated inhibition of PK-M2 splicing as therapy for cancer.
Combating digital document forgery using new secure information hiding algorithm (2008)

The recent digital revolution has facilitated communication, data portability and on-the-fly manipulation. Unfortunately, this has brought along some critical security vulnerabilities that put digital documents at risk. The problem is in the security mechanism adopted to secure these documents by means of encrypted passwords; however, this security shield does not actually protect the documents which are stored intact. We propose a solution to this real world problem through a 1D hash algorithm coupled with 2D irFFT (irreversible fast Fourier transform) to encrypt digital documents in the 2D spatial domain. This method is described elsewhere in [1]. Further by applying an imperceptible information hiding technique we can add another security layer which is resistant to noise and to a certain extent JPEG compression. We support this assertion by showing a practical example which is drawn from our set of experiments. Our proposal not only points out forgery but also lets a jury or a forensics expert have access to the original document despite being manipulated. This would undoubtedly be very useful in cases of disputes or claims.
Selective Breeding of Two Lines of Guinea Pigs Differing in Bronchial Sensitivity to Acetylcholine and Histamine Exposure (1991)

We developed two lines of guinea pigs, one as model animals for bronchial asthma with bronchial hypersensitivity and the other with hyposensitivity as a control. In the last four years, the bronchial hypersensitive line (BHS) and hyposensitive line (BHR), both derived from Hartley strain guinea pigs, have been selected by using bronchial reactivity to acetylcholine and to histamine as parameters. Both lines have reached the F6 generation. The following results were obtained with the two lines: 1) Sib and cous in matings, and mating of selected consanguineous individuals were adopted in breeding BHS and BHR. The breeding started with six families, each, but in the F6 generation the number of families decreased to two in each line. 2) Appearance rates of hyper- or hyposensitivity to acetylcholine and histamine increased with successive generations in both lines, which had been completely separated by the F6 generation. 3) Coefficients of inbreeding in BHS and BHR in the F6 generation ranged from 42% to 45% in the former and 42% in the latter. 4) Heritabilities (h2) of BHS and BHR for the appearance rates of sensitivity to acetylcholine were presumed to be 0.54 in the former and 0.69 in the latter. 5) No difference in the body weight of 0, 20, and 40 day-old BHS was observed in any generation. On the other hand, the body weight of 20 and 40 day-old BHR tended to decrease with successive generations. 6) Mean litter sizes of BHS and BHR in each of the generations ranged from 2.24 to 3.47 animals in the former and from 2.63 to 3.38 animals in the latter.(ABSTRACT TRUNCATED AT 250 WORDS)
Validation of matching (2016)

We introduce a technique to compute probably approximately correct (PAC) bounds on precision and recall for matching algorithms. The bounds require some verified matches, but those matches may be used to develop the algorithms. The bounds can be applied to network reconciliation or entity resolution algorithms, which identify nodes in different networks or values in a data set that correspond to the same entity. For network reconciliation, the bounds do not require knowledge of the network generation process.
Characterization of Melanin-Concentrating Hormone from Rat Hypothalamus* (1989)

A melanin-concentrating hormone (MCH)-like peptide was isolated from rat hypothalamus by acid extraction, gel filtration chromatography, immunoaffinity chromatography using antiserum directed against salmon MCH, and two steps of HPLC using octadecyl columns. Several zones of immunoreactivity were isolated, and Edman degradation in a gas phase sequencer indicated that the amino acid sequence of all zones was identical. Rat hypothalamic MCH is a nonadecapeptide which differs from salmon MCH by an N-terminal extension of two amino acids and four additional substitutions. Rat MCH has the following primary structure: Asp-Phe-Asp-Met-Leu-Arg-Cys-Met-Leu-Gly-Arg-Val-Tyr-Arg-Pro-Cys-Trp-Gln- Val.
The LCPDI: A Compact and Robust Phase-Shifting Point-Diffraction Interferometer Based on Dye-Doped LC Technology (2006)

Abstract Point-diffraction interferometers, by design, are much less sensitive to environmental disturbances than dual-path interferometers, but, until very recently, have not been capable of phase shifting. The liquid crystal point diffraction interferometer (LCPDI) utilizes a dye-doped, liquid crystal (LC), electro-optical device that functions as both the point-diffraction source and the phase-shifting element, yielding a phase-shifting diagnostic device that is significantly more compact and robust while also using fewer optical elements than conventional dual-path interferometers. These attributes make the LCPDI of special interest for diagnostic applications in the scientific, commercial, military, and industrial sectors, where vibration insensitivity, power requirements, size, weight, and cost are critical issues. Until very recently, LCPDI devices have used a plastic microsphere embedded in the LC fluid layer as the point-diffraction source. The process for fabricating microsphere-based LCPDI devices is low-yield, labor-intensive, very “hands-on,” and great care and skill are required to produce devices with adequate interference fringe contrast for diagnostic measurements. With the goal in mind of evolving the LCPDI beyond the level of a laboratory prototype, we have developed “second-generation” LCPDI devices in which the reference diffracting elements are an integral part of the substrates by depositing a suitable optical material (vapor-deposited thin films or photoresist) directly on the substrate surface. These “structured” substrates eliminate many of the assembly difficulties and performance limitations of previous LCPDI devices as well as open the possibility of mass-producing LCPDI devices at low cost by the same processes used to manufacture commercial LC displays. Keywords: interferometryliquid crystalphase-shiftingphotoresistpoint diffraction Acknowledgments This work is supported by the U.S. Department of Energy Office of Inertial Confinement Fusion under Cooperative Agreement No. DE-FC52-92SF19460 and the University of Rochester. The support of DOE does not constitute an endorsement by DOE of the views expressed in this article. This work was also supported by the NASA Glenn Research Center Microgravity Fluid Physics Division under Grant # NAG3-2348. Notes *Measured in a 22-µm path cell, 543-nm, 1-khz applied field.