gebhart/patrepeval huggingface dataset:
A Versatile PDMS/Paper Hybrid Microfluidic Platform for Sensitive Infectious Disease Diagnosis (2014)

Bacterial meningitis is a serious health concern worldwide. Given that meningitis can be fatal and many meningitis cases occurred in high-poverty areas, a simple, low-cost, highly sensitive method is in great need for immediate and early diagnosis of meningitis. Herein, we report a versatile and cost-effective polydimethylsiloxane (PDMS)/paper hybrid microfluidic device integrated with loop-mediated isothermal amplification (LAMP) for the rapid, sensitive, and instrument-free detection of the main meningitis-causing bacteria, Neisseria meningitidis (N. meningitidis). The introduction of paper into the microfluidic device for LAMP reactions enables stable test results over a much longer period of time than a paper-free microfluidic system. This hybrid system also offers versatile functions, by providing not only on-site qualitative diagnostic analysis (i.e., a yes or no answer), but also confirmatory testing and quantitative analysis in laboratory settings. The limit of detection of N. meningitidis is about 3 copies per LAMP zone within 45 min, close to single-bacterium detection sensitivity. In addition, we have achieved simple pathogenic microorganism detection without a laborious sample preparation process and without the use of centrifuges. This low-cost hybrid microfluidic system provides a simple and highly sensitive approach for fast instrument-free diagnosis of N. meningitidis in resource-limited settings. This versatile PDMS/paper microfluidic platform has great potential for the point of care (POC) diagnosis of a wide range of infectious diseases, especially for developing nations.
[Positional clonage and characterization of the bovine myostatin gene]. (2000)

The double-muscled condition has been intensively selected for in the Belgian Blue cattle breed, where segregation studies have demonstrated the monogenic, autosomal and recessive determinism. This has been confirmed by genetic linkage which located the gene to the centromeric tip of chromosome 2. Our positional cloning strategy, and the discovery of a positional candidate in the mouse, led us to the identification of the causative gene now referred to as the Myostatin gene, since its product downregulates skeletal muscle mass. Disruptive mutations of the gene in cattle have been shown to be responsible for the muscular hypertrophy found in eight european beef breeds. A 15 Kilobases genomic region, including the myostatin gene, has been sequenced and compared in cattle and mice. The murine gene has undergone a complex genetic engineering in order to test different allelic variants in vivo after gene targeting transgenesis.
The TNF family member TL1A induces IL-22 secretion in committed human T<scp>h</scp>17 cells via IL-9 induction (2016)

TL1A contributes to the pathogenesis of several chronic inflammatory diseases, including those of the bowel by enhancing T<sub>H</sub>1, T<sub>H</sub>17, and T<sub>H</sub>2 responses. TL1A mediates a strong costimulation of these T<sub>H</sub> subsets, particularly of mucosal CCR9<sup>+</sup> T cells. However, the signaling pathways that TL1A induces in different T<sub>H</sub> subsets are incompletely understood. We investigated the function of TL1A on human T<sub>H</sub>17 cells. TL1A, together with TGF-β, IL-6, and IL-23, enhanced the secretion of IL-17 and IFN-γ from human CD4<sup>+</sup> memory T cells. TL1A induced expression of the transcription factors BATF and T-bet that correlated with the secretion of IL-17 and IFN-γ. In contrast, TL1A alone induced high levels of IL-22 in memory CD4<sup>+</sup> T cells and committed T<sub>H</sub>17 cells. However, TL1A did not enhance expression of IL-17A in T<sub>H</sub>17 cells. Expression of the transcription factor aryl hydrocarbon receptor, which regulates the expression of IL-22 was not affected by TL1A. Transcriptome analysis of T<sub>H</sub>17 cells revealed increased expression of IL-9 in response to TL1A. Blocking IL-9 receptor antibodies abrogated TL1A-induced IL-22 secretion. Furthermore, TL1A increased IL-9 production by peripheral T<sub>H</sub>17 cells isolated from patients with Crohn's disease. These data suggest that TL1A differentially induces expression of T<sub>H</sub>17 effector cytokines IL-17, -9, and -22 and provides a potential target for therapeutic intervention in T<sub>H</sub>17-driven chronic inflammatory diseases.
Differential access for publicly-posted composite documents with multiple workflow participants (2010)

A novel mechanism for providing and enforcing differential access control for publicly-posted composite documents is proposed. The concept of a document is rapidly changing: individual file-based, traditional formats can no longer accommodate the required mixture of differently formatted parts: individual images, video/audio clips, PowerPoint presentations, html-pages, Word documents, Excel spreadsheets, pdf files, etc. Multi-part composite documents are created and managed in complex workflows, with participants including external consultants, partners and customers distributed across the globe, with many no longer contained within one monolithic secure environment. Distributed over non-secure channels, these documents carry different types of sensitive information: examples include (a) an enterprise pricing strategy for new products, (b) employees' personal records, (c) government intelligence, and (d) individual medical records. A central server solution is often hard or impossible to create and maintain for ad-hoc workflows. Thus, the documents are often circulated between workflow participants over traditional, low security e-mails, placed on shared drives, or exchanged using CD/DVD or USB. The situation is more complicated when multiple workflow participants need to contribute to various parts of such a document with different access levels: for example, full editing rights, read-only, reading of some parts only, etc., for different users. We propose a full scale differential access control approach, enabling public posting of composite documents, to address these concerns.
PMTJ driven STT MRAM with 300mm process (2015)

We will present high performance/low-cost spin transfer torque magnetic random access memory (STT-MRAM) solution based upon 64Mb chip data and scalable magnetic tunneling junction (MTJ) BEOL integration scheme at 55 nm process node. This is the first fully functional STT-MRAM chip fabricated in a top tier foundry using the standard 300 mm CMOS foundry process. We will characterize pMTJ device population performance and provide in-depth analysis of pMTJ driven STT-MRAM technology extendibility. The manufacturability and various applications of STT-MRAM will also be discussed.
Mesenchymal stem cells: a double-edged sword in regulating immune responses (2012)

Mesenchymal stem cells (MSCs) have been employed successfully to treat various immune disorders in animal models and clinical settings. Our previous studies have shown that MSCs can become highly immunosuppressive upon stimulation by inflammatory cytokines, an effect exerted through the concerted action of chemokines and nitric oxide (NO). Here, we show that MSCs can also enhance immune responses. This immune-promoting effect occurred when proinflammatory cytokines were inadequate to elicit sufficient NO production. When inducible nitric oxide synthase (iNOS) production was inhibited or genetically ablated, MSCs strongly enhance T-cell proliferation in vitro and the delayed-type hypersensitivity response in vivo. Furthermore, iNOS(-/-) MSCs significantly inhibited melanoma growth. It is likely that in the absence of NO, chemokines act to promote immune responses. Indeed, in CCR5(-/-)CXCR3(-/-) mice, the immune-promoting effect of iNOS(-/-) MSCs is greatly diminished. Thus, NO acts as a switch in MSC-mediated immunomodulation. More importantly, the dual effect on immune reactions was also observed in human MSCs, in which indoleamine 2,3-dioxygenase (IDO) acts as a switch. This study provides novel information about the pathophysiological roles of MSCs.
Normally OFF Trench CAVET With Active Mg-Doped GaN as Current Blocking Layer (2016)

A normally OFF trench current aperture vertical electron transistor (CAVET) was designed and successfully fabricated with Mg-doped p-GaN current blocking layers. The buried Mg-doped GaN was activated using a postregrowth annealing process. The source-to-drain body diode showed an excellent p-n junction characteristics, blocking over 1 kV, sustaining a maximum blocking electric field of 3.8 MV/cm. Three-terminal breakdown voltages of trench-CAVETs, measured up to 225 V, were limited by dielectric breakdown. This paper highlights the achievement of the well-behaved buried p-n junction that has been a formidable challenge in the success of vertical GaN devices.
Summary of bi-shRNA<sup>furin</sup>/GM-CSF Augmented Autologous Tumor Cell Immunotherapy (FANG™) in Advanced Cancer of the Liver (2014)

Therapies for advanced hepatocellular carcinoma (HCC) are limited. We carried out a phase I trial of a novel autologous whole-cell tumor cell immunotherapy (FANG™), which incorporates a dual granulocyte macrophage colony-stimulating factor (GM-CSF) expressive/bifunctional small hairpin RNA interference (bi-shRNAi) vector. The bi-shRNAi DNA targets furin, which is a proconvertase of transforming growth factors beta (TGFβ) 1 and 2. Safety, mechanism, immunoeffectiveness, and suggested benefit were previously shown [Senzer et al.: Mol Ther 2012;20:679-689; Senzer et al.: J Vaccines Vaccin 2013;4:209]. We now provide further follow-up of a subset of 8 HCC patients. FANG manufacturing was successful in 7 of 8 attempts (one failure due to insufficient cell yield). Median GM-CSF expression was 144 pg/10(6) cells, TGFβ1 knockdown was 100%, and TGFβ2 knockdown was 93% of the vector-transported cells. Five patients were vaccinated (1 or 2.5×10(7) cells/intradermal injection, 6-11 vaccinations). No FANG toxicity was observed. Three of these patients demonstrated evidence of an immune response to the autologous tumor cell sample. Long-term follow-up demonstrated survival of 319, 729, 784, 931+, and 1,043+ days of the FANG-treated patients. In conclusion, evidence supports further assessment of the FANG immunotherapy in HCC.
The power of magnetic levitation-Part 1; A nearly frictionless superconducting bearing invented at Cornell (1990)

A device developed in laboratories at Cornell demonstrates that useful applications of superconducting ceramics are already at hand. The device is a high-speed superconducting bearing that operates by magnetically levitating a rotor. Speeds up to 120,000 revolutions per minute have been achieved without the need for feedback control, and the prospects are good for reaching a million rpm in vacuum. By comparison, currently available magnetic bearings allow speeds of more than 100,000 rpm in a vacuum, but require complex feedback circuits to maintain stability.
An Integrated Protocol for Coverage, Connectivity and Communication (C3) in Wireless Sensor Networks (2013)

Wireless Sensor Networks (WSNs) consume a lot of energy in infrastructure creation and maintenance which also include topology control, i.e., coverage and connectivity. Several sleep-based topology control protocols have been proposed for better performance. While the existing protocols serve their purpose, they still consume high energy. We propose an energy-efficient protocol for Coverage, Connectivity and Communication (C3) in WSNs. The proposed protocol runs in four steps: divide the network into virtual rings using RSSI, define clusters having cluster heads at alternating rings, make dings that are rings inside clusters using triangular tessellation, and start sending data through cluster heads which may involve gateways. It achieves better performance by using near-optimal deployment, load balancing, and energy-efficient communication. Simulation results show that C3 protocol can guarantee 1-connected network, partial coverage of greater than 90% and energy-efficient communication, while consuming 20-25% energy compared to the Layered Diffusion-based Coverage Control (LDCC), and the Coverage and Connectivity Protocol (CCP).
Rapid detection of human HLA transgenes in pigs by fluorescence in situ hybridization (FISH) for adjuvant study of human xenotransplantation (2004)

By FISH, we have detected specific integration sites of the HLA-DP and -DQ transgenes in pig genome and determined mosaic levels and zygosity types of these transgenes. We conclude that FISH is both sensitive and labor-efficient in confirming and differentiating transgenic pigs for multiple rejection-regulatory genes by visualizing individual integration sites in chromosomes or interphase nuclei.
Mcl-1 inhibitors: a patent review (2016)

The myeloid cell leukemia-1 (MCL-1) protein is one of the key anti-apoptotic members of the B-cell lymphoma-2 (BCL-2) protein family. Over-expression of MCL-1 has been closely related to tumor progression as well as to resistance, not only to traditional chemotherapies but also to targeted therapeutics including BCL-2 inhibitors such as ABT-263. Therefore, there has been extensive research and development in the last decade in both academic and industrial settings to address this unmet medical need. Areas covered: This review covers the research and patent literature of the past 10 years in the field of discovery and development of small-molecule inhibitors of the MCL-1 anti-apoptotic protein. Expert opinion: Small-molecule strategies to disrupt the protein-protein interactions between MCL-1 and its pro-apoptotic counterparts, such as BAK and BIM, have recently emerged. Several small-molecules based on different scaffolds describe promising in vitro data as MCL-1 selective inhibitors. While many lead compounds remain at the in vitro preclinical development stage, the two most recent patent applications describe promising in vivo data, and one small molecule inhibitor has recently entered into clinical development. It is such an exciting moment that the long awaited clinical studies will generate some insight into the therapeutic potential of this anti-cancer approach, and possibly facilitate the further development of other early stage inhibitors.
Children with familial hypercholesterolemia display changes in LDL and HDL function: a cross-sectional study (2020)

Abstract Background The functional status of lipoprotein particles contributes to atherogenesis. The tendency of plasma LDL particles to aggregate and the ability of HDL particles to induce and mediate reverse cholesterol transport associate with high and low risk for cardiovascular disease in adult patients, respectively. However, it is unknown whether children with familial hypercholesterolemia (FH) display lipoprotein function alterations. Hypothesis We hypothesized that FH children had disrupted lipoprotein function. Methods We analyzed LDL aggregation susceptibility and HDL-apoA-I exchange to apoA-I ratio (HAE/apoA-I ratio), and activity of four proteins that regulate lipoprotein metabolism (CETP, LCAT, PLTP and PON1) in plasma samples derived from children with FH (n = 47) and from healthy children (n = 56). Potential biological mechanisms behind any variation in lipoprotein functionalities were explored using an NMR-based metabolomics profiling approach. Results LDL aggregation was higher and HAE/apoA-I ratio was lower in FH children than in healthy children. LDL aggregation associated positively with LDL-C and negatively with triglycerides, and HAE/apoA-I ratio associated negatively with LDL-C. Generally, the metabolomic profile for LDL aggregation was a mirror image of that for HAE/apoA-I ratio. Conclusions FH children displayed increased atherogenicity of LDL and disrupted HDL function. These newly observed functional alterations in LDL and HDL may increase the risk for atherosclerotic cardiovascular disease in FH children.
Biosynthesis and insecticidal properties of plant cyclotides: The cyclic knotted proteins from <i>Oldenlandia affinis</i> (2001)

Several members of the Rubiaceae and Violaceae families produce a series of cyclotides or macrocyclic peptides of 29-31 amino acids with an embedded cystine knot. We aim to understand the mechanism of synthesis of cyclic peptides in plants and have isolated a cDNA clone that encodes the cyclotide kalata B1 as well as three other clones for related cyclotides from the African plant Oldenlandia affinis. The cDNA clones encode prepropeptides with a 20-aa signal sequence, an N-terminal prosequence of 46-68 amino acids and one, two, or three cyclotide domains separated by regions of about 25 aa. The corresponding cyclotides have been isolated from plant material, indicating that the cyclotide domains are excised and cyclized from all four predicted precursor proteins. The exact processing site is likely to lie on the N-terminal side of the strongly conserved GlyLeuPro or SerLeuPro sequence that flanks both sides of the cyclotide domain. Cyclotides have previously been assigned an antimicrobial function; here we describe a potent inhibitory effect on the growth and development of larvae from the Lepidopteran species Helicoverpa punctigera.
Uncooled Thermopile Infrared Detector Linear Arrays with Detectivity Greater Than 10(super script9) cmHZ(super script 1/2)/W (1997)

We have fabricated 63-element linear arrays of micromachined thermopile infrared detectors on silicon substrates. Each detector consists of a suspended silicon nitride membrane with 11 thermocouples of sputtered Bi-Te and Bi-Sb-Te films.
Registration of video to geo-referenced imagery (2002)

The ability to locate scenes and objects visible in aerial video imagery with their corresponding locations and coordinates in a reference coordinate system is important in visually-guided navigation, surveillance and monitoring systems. However, a key technical problem of locating objects and scenes in a video with their geo-coordinates needs to be solved in order to ascertain the geo-location of objects seen from the camera platform's current location. We present the key algorithms for the problem of accurate mapping between camera coordinates and geo-coordinates, called geo-spatial registration. Current systems for geo-location use the position and attitude information for the moving platform in some fixed world coordinates to locate the video frames in the reference database. However, the accuracy achieved is only of the order of 100s of pixels. Our approach utilizes the imagery and terrain information contained in the geo-spatial database to precisely align dynamic videos with the reference imagery and thus achieves a much higher accuracy. Applications of geo-spatial registration include aerial mapping, target location and tracking and enhanced visualization such as the overlay of textual/graphical annotations of objects of interest in the current video using the stored annotations in the reference database.
Molecular Mechanisms of Anthracycline-Induced Cardiotoxicity (2016)

Anthracyclines have been an integral part of chemotherapeutic regimen since their discovery in 1960s. Its beneficial effects span from hematological malignancies to solid tumors. Recently, anthracyclines have come under scrutiny due to their cardiotoxic effects. Although medications, such as dexrazoxane proved to curb some of the deleterious cardiac effects, they are unable to fully ameliorate toxicity. A key to combat the unwanted effects of anthracyclines is to understand the underlying mechanism(s). Therefore, this chapter identifies risk factors associated with cardiotoxicity, illuminates the key molecular mechanisms, and suggests some of the therapeutic strategies to attenuate, if not to ameliorate, anthracycline-mediated cardiotoxicity.
Multiuser Pairing in Uplink CoMP MU-MIMO Systems Using Particle Swarm Optimization (2011)

Multi-User Multiple Input Multiple Output (MU- MIMO) technique is introduced into 3rd Generation Partnership Project (3GPP) Long-Term Evolution (LTE) to enhance the system capacity and spectrum efficiency. On the other hand, Coordinated Multi-Point transmission and reception (CoMP) technique which can reduce inter-cell interference (ICI) significantly, has been adopted in LTE-Advanced as one of the promising techniques to increase the throughput of the cell edge user. However, some new problems appear with the promotion of MU-MIMO technique in the CoMP scenario. Considering the necessity that an enhanced algorithm should be proposed to fit the CoMP scenario, this paper presents a novel capacity maximization criterion for multiuser pairing strategy based on particle swarm optimization algorithm for CoMP MU-MIMO in uplink LTE-A system. Under this criterion, this paper gives two kinds of receivers which are zero forcing (ZF) equalizer and minimum mean square error (MMSE) equalizer in the frequency-domain. Simulation results show that the proposed PSO strategy achieves nearly the same performance to the exhaustive search (ES) algorithm in terms of capacity performance, but with lower complexity.
A novel cost-aware multi-objective energy management method for microgrids (2013)

This paper proposes a multi-objective energy management method for microgrids which include local generation sources, grid connection, energy storage units and various loads. Minimization of the energy cost and maximization of batterys lifetime in a microgrid are considered as two main objectives which are optimized simultaneously. To achieve these objectives, microgrids central controller must find the best pattern for charging and discharging the battery. To this purpose, there is a need to have information about time-of-use (TOU) grid electricity rates, forecasted load profile and renewable generation levels. Model predictive control (MPC) policy is then utilized for solving the optimization problem and real-time implementation in a closed-loop framework. The performance and effectiveness of the proposed method is verified by simulating a microgrid model with real yearly data for the demand and renewable generation profiles and TOU rates. It is shown that the saving in energy cost can be increased considerably by applying the proposed MPC algorithm instead of a static energy management approach. Furthermore, the proposed algorithm is capable of regulating the battery usage based on the expected lifetime by considering the battery life span maximization objective.
<title>Real-time determination of interconnect metrology</title> (1996)

Poor control of wire geometry can result in unacceptable variations in signal propagation velocity and cross-talk. A novel laser diffraction technique for the real-time determination of global interconnect metrology is presented and tested on several different types of chips. Analysis of the diffraction patterns produced by He-Cd (lambda equals 442 nm) and He-Ne (lambda equals 633 nm) laser irradiation of the interconnect structure is shown to reveal global information on variations in wiring parameters. The diffraction intensity profile for a commercial microprocessor fabricated using 2 micrometer design rules is used to test the validity of the approach. Standard diffraction theory reveals that the process variation in wire pitch is of the order of 9%, a value confirmed by examination under a phase contrast microscope. In addition to wire pitch variations the diffraction technique is also used for the measurement of the characteristic fractal dimension of the wiring. Initial results indicate that these measurements may provide an extremely rapid method of assessing important wiring figures of merit, such as the on- chip Rent exponent.
The rhodium complex of bis(diphenylphosphinomethyl)dopamine-coated magnetic nanoparticles as an efficient and reusable catalyst for hydroformylation of olefins (2015)

MNPs functionalized with new bis(diphenylphosphinomethyl)dopamine (bpd) for hydroformylation reaction.