gebhart/patrepeval huggingface dataset:
Dynamic fault tolerance in FPGAs via partial reconfiguration (2002)

In this paper we present an on-line, multi-level fault tolerant (FT) technique for system functions and applications mapped to partially and dynamically reconfigurable FPGAs. Our method is based on the roving self testing areas (STARs) fault detection/location strategy presented in Abramovici et al. (1999). In STARs, the area under test uses partial reconfiguration properties to modify the configuration of the area under test without affecting the configuration of the system function and dynamic reconfiguration properties to allow uninterrupted execution of the system function while reconfiguration takes place. In this paper we take this one step further. Once a fault (or multiple faults) is detected we dynamically reconfigure the working area application around the fault with no additional system function interruption (other than the interruption when a STAR moves to a new location). We also apply the concept of partially usable blocks to increase fault tolerance. Our method has been successfully implemented and demonstrated on the ORCA 2CA series FPGAs from Lucent Technologies.
Insights into transcriptional regulation of  -D-N-acetylhexosaminidase, an N-glycan-processing enzyme involved in ripening-associated fruit softening (2014)

Tomato (Solanum lycopersicum) fruit ripening-specific N-glycan processing enzyme, β-D-N-acetylhexosaminidase (β-Hex), plays an important role in the ripening-associated fruit-softening process. However, the regulation of fruit ripening-specific expression of β-Hex is not well understood. We have identified and functionally characterized the fruit ripening-specific promoter of β-Hex and provided insights into its transcriptional regulation during fruit ripening. Our results demonstrate that RIPENING INHIBITOR (RIN), a global fruit ripening regulator, and ABSCISIC ACID STRESS RIPENING 1 (SlASR1), a poorly characterized ripening-related protein, are the transcriptional regulators of β-Hex. Both RIN and SlASR1 directly bound to the β-Hex promoter fragments containing CArG and C₂₋₃(C/G)A cis-acting elements, the binding sites for RIN and SlASR1, respectively. Moreover, β-Hex expression/promoter activity in tomato fruits was downregulated once expression of either RIN or SlASR1 was suppressed; indicating that RIN and SlASR1 positively regulate the transcription of β-Hex during fruit ripening. Interestingly, RIN could also bind to the SlASR1 promoter, which contains several CArG cis-acting elements, and SlASR1 expression was suppressed in rin mutant fruits, indicating that RIN also acts as a positive regulator of SlASR1 expression during fruit ripening. Taken together, these results suggest that RIN, both directly and indirectly, through SlASR1, regulates the transcription of β-Hex during fruit ripening. The fruit ripening-specific promoter of β-Hex could be a useful tool in regulating gene expression during fruit ripening.
Thermostabilization of the <i>Bacillus circulans</i>xylanase by the introduction of disulfide bonds (1994)

The thermostability of the 20 396 Da Bacillus circulans xylanase was increased by the introduction of both intra- and intermolecular disulfide bridges by site-directed mutagenesis. Based on the 3-D structure of the enzyme, sites were chosen where favourable geometry for a bridge existed; in one case, to obtain favourable geometry additional mutations around the cysteine sites were designed by computer modelling. The disulfide bonds introduced into the xylanase were mostly buried and, in the absence of protein denaturants, relatively insensitive to reduction by dithiothreitol. The mutant proteins were examined for residual enzymatic activity after various thermal treatments, and were assayed for enzymatic activity at elevated temperatures to assess their productivity. We have examined one of these mutants by X-ray crystallography. All of the disulfide bond designs tested increased the thermostability of the B. circulans xylanase, but not all enhanced the activity of the enzyme at elevated temperatures.
Identification of miR-185 as a regulator of de novo cholesterol biosynthesis and low density lipoprotein uptake (2013)

Dysregulation of cholesterol homeostasis is associated with various metabolic diseases, including atherosclerosis and type 2 diabetes. The sterol response element binding protein (SREBP)-2 transcription factor induces the expression of genes involved in de novo cholesterol biosynthesis and low density lipoprotein (LDL) uptake, thus it plays a crucial role in maintaining cholesterol homeostasis. Here, we found that overexpressing microRNA (miR)-185 in HepG2 cells repressed SREBP-2 expression and protein level. miR-185-directed inhibition caused decreased SREBP-2-dependent gene expression, LDL uptake, and HMG-CoA reductase activity. In addition, we found that miR-185 expression was tightly regulated by SREBP-1c, through its binding to a single sterol response element in the miR-185 promoter. Moreover, we found that miR-185 expression levels were elevated in mice fed a high-fat diet, and this increase correlated with an increase in total cholesterol level and a decrease in SREBP-2 expression and protein. Finally, we found that individuals with high cholesterol had a 5-fold increase in serum miR-185 expression compared with control individuals. Thus, miR-185 controls cholesterol homeostasis through regulating SREBP-2 expression and activity. In turn, SREBP-1c regulates miR-185 expression through a complex cholesterol-responsive feedback loop. Thus, a novel axis regulating cholesterol homeostasis exists that exploits miR-185-dependent regulation of SREBP-2 and requires SREBP-1c for function.
Infectivity of a Human Respiratory Syncytial Virus Lacking the SH, G, and F Proteins Is Efficiently Mediated by the Vesicular Stomatitis Virus G Protein (2003)

To examine the requirements of the human respiratory syncytial virus (HRSV) SH (small hydrophobic), G (attachment), and F (fusion) proteins for virus infectivity and morphology, we used the prototype A2 strain of HRSV to generate a series of cDNAs from which (i) the SH open reading frame (ORF), (ii) the SH and G ORFs, or (iii) the SH, G, and F ORFs were deleted. Each deleted ORF was replaced as follows: the SH ORF was replaced with that of green fluorescent protein; the G ORF was replaced with that of G(vsv), a chimeric glycoprotein consisting of the vesicular stomatitis Indiana virus (VSIV) G protein ecto- and transmembrane domains coupled to the HRSV F cytoplasmic tail; and the F ORF was replaced with that of marker protein beta-glucuronidase. The number of genes and the intergenic junctions in the constructs were kept as found in A2 virus in order to maintain authentic levels of transcription. Infectious viruses were recovered from all three engineered cDNAs and designated RSdeltash, RSdeltash,g/G(vsv), and RSdeltash,g,f/G(vsv), respectively. Low-pH-induced syncytium formation was observed in cells infected with viruses RSdeltaSH,G/G(vsv) and RSdeltaSH,G,F/G(vsv), indicating that G(vsv) was expressed and functional. Neutralization of infectivity by anti-VSIV G antibodies and inhibition of entry by ammonium chloride showed that RSdeltaSH,G,F/G(vsv) infectivity was mediated by G(vsv) and that an acidification step was required for entry into the host cell, similar to VSIV virions. All three engineered viruses displayed growth kinetics and virus yields similar to a wild-type A2 virus, both in Vero and HEp-2 cells. Abundant virus-induced filaments were observed at the surface of cells infected with each of the three engineered viruses or with virus A2, indicating that neither the SH and G proteins nor the F protein ecto- and transmembrane domains were required for the formation of these structures. This is the first report of the recovery of an infectious HRSV lacking a fusion protein of the Paramyxoviridae family and of manipulation of the HRSV entry pathway via incorporation of a nonparamyxoviral transmembrane glycoprotein.
Polarization perception in humans: on the origin of and relationship between Maxwell’s spot and Haidinger’s brushes (2020)

Under specific conditions of illumination and polarization, differential absorption of light by macular pigments is perceived as the entoptic phenomena of Maxwell's spot (MS) or Haidinger's brushes (HB). To simulate MS and HB, an existing computational model of polarization-dependent properties of the human macula was extended by incorporating neuronal adaptation to stabilized retinal images. The model predicted that polarized light modifies the appearance of MS leading to the perception of a novel phenomenon. The model also predicted a correlation between the observed diameters of MS and HB. Predictions were tested psychophysically in human observers, whose measured differences in the diameters of each entoptic phenomenon generated with depolarized and linearly polarized light were consistent with the model simulations. These findings support a common origin of each phenomenon, and are relevant to the clinical use of polarization stimuli in detecting and monitoring human eye disorders, including macular degeneration. We conclude: (i) MS and HB both result from differential light absorption through a radial diattenuator, compatible with the arrangement of macular pigments in Henle fibres; (ii) the morphology of MS is dependent on the degree of linear polarization; (iii) perceptual differences between MS and HB result from different states of neural adaptation.
Use of whole genome sequencing to identify highly recurrent somatic mutations in Waldenström’s macroglobulinemia. (2012)

8107 Background: Waldenstrom’s Macroglobulinemia (WM) is an IgM secreting lymphoplasmacytic lymphoma. The genetic basis for this disease remains to be clarified. Methods: We performed whole genome sequencing (WGS) using CD19 + selected bone marrow lymphoplasmacytic cells (LPC) from 30 WM patients. For 10 of these patients, paired CD19 + depleted peripheral blood samples were used for WGS as normal controls. Results: The most common somatic variants identified and validated by Sanger sequencing included MYD88 L265P, an activating mutation for IRAK/TRAF6/NFKB and MAPK signaling, which was observed in 27/30 (90%) patients; the N-terminal domain of CXCR4, which included mutations associated with WHIM syndrome and confer constitutive CXCR4 signaling resulting from dysfunctional receptor endocytosis, a finding observed in 8/30 (27%) patients, and ARID1A (5/30; 17%), a tumor suppressor gene. Less common somatic variants were also identified in MUC16 (4/30; 13%), TRAF2 (3/30; 10%), TRRAP (3/30; 10%) and MYBBP1A (2/30; 7%). Conclusions: Using WGS and confirmatory Sanger sequencing, we have identified several somatic variants with oncogenic function, the most common of which include MYD88 L265P, the N-terminal domain of CXCR4, and ARID1A.
Purification of Metallurgical Grade Silicon to Solar Grade for Use in Solar Cell Wafers (2000)

A pyrometallurgical process for manufacturing solar grade silicon (SOG-Si) from metallurgical grade silicon (MG-Si) was developed. Metallic elements in MG-Si such as iron, titanium and aluminum, which show low partition coefficients, were removed by directional solidification practice. Phosphorus removal was carried out by evaporation for high vapor pressure, and boron was changed to boron oxide effectively by water vapor addition, because partition coefficients of phosphorus and boron are close to unity.To satisfy the impurity specification of SOG-Si, each purification process was combined as follows: (first process) dephosphorization by electron beam melting-first step directional solidification-(second process) oxidation of boron and carbon during plasma practice-deoxidation-second step directional solidification.MG-Si (purity level; 99 mass%) was successfully purified to the solar grade impurity level, that is, 6N (99.9999 mass%) except carbon and oxygen elements, by 20 kg scale and 150-300 kg scale equipments. The manufactured ingot was directly sliced to wafers and prepared to solar cells of multicrystalline silicon through the NEDO standard cell production process. The maximum conversion efficiency of solar cells attained to above 14%, which is almost equal to that of solar cells on the market.
Content-Based Image Annotation Refinement (2007)

Automatic image annotation has been an active research topic due to its great importance in image retrieval and management. However, results of the state-of-the-art image annotation methods are often unsatisfactory. Despite continuous efforts in inventing new annotation algorithms, it would be advantageous to develop a dedicated approach that could refine imprecise annotations. In this paper, a novel approach to automatically refining the original annotations of images is proposed. For a query image, an existing image annotation method is first employed to obtain a set of candidate annotations. Then, the candidate annotations are re-ranked and only the top ones are reserved as the final annotations. By formulating the annotation refinement process as a Markov process and defining the candidate annotations as the states of a Markov chain, a content-based image annotation refinement (CIAR) algorithm is proposed to re-rank the candidate annotations. It leverages both corpus information and the content feature of a query image. Experimental results on a typical Corel dataset show not only the validity of the refinement, but also the superiority of the proposed algorithm over existing ones.
Investigation on link performance modeling of advanced receiver employing interference rejection combining in system level evaluation for LTE-Advanced downlink (2012)

This paper investigates an advanced receiver that employs two proposed interference rejection combining (IRC) modeling schemes, one for the covariance matrix and one for channel estimation errors. In a system performance evaluation, the link performance modeling of the IRC receiver, i.e., the output signal-to-interference-plus-noise power ratio (SINR) after IRC reception including the estimation errors, is very important in evaluating the actual performance of the IRC receiver in the system level simulation. This is because these errors affect the suppression of the interference signals for the IRC receiver. The results of simulations assuming the LTE-Advanced downlink with two transmitter and receiver antenna branches show that both proposed schemes accurately approximate the performance of the realistic IRC receiver, which estimates the covariance matrix and channel matrix of the serving cell based on the demodulation reference signal.
Alternative High Performance Polymers for Ablative Thermal Protection Systems (2014)

Ablative thermal protection systems are commonly used as protection from the intense heat during re-entry of a space vehicle and have been used successfully on many missions including Stardust and Mars Science Laboratory both of which used PICA - a phenolic based ablator. Historically, phenolic resin has served as the ablative polymer for many TPS systems. However, it has limitations in both processing and properties such as char yield, glass transition temperature and char stability. Therefore alternative high performance polymers are being considered including cyanate ester resin, polyimide, and polybenzoxazine. Thermal and mechanical properties of these resin systems were characterized and compared with phenolic resin.
Novel edge suppression technique for planar avalanche photodiodes (1999)

We present an advanced drift diffusion simulation of the joint opening effect (JOE) avalanche photodiode (APD). The joint opening effect APD is a new design for achieving edge breakdown suppression in planar avalanche photodiodes. It is a single growth process that achieves center breakdown dominance without the use of guard rings, partial charge sheets, or surface etches. The JOE APD only requires the diffusion of the primary well. Edge breakdown suppression is achieved by partially insulating the electric field growth in the active region from the geometry of the primary well.
Cassette baculovirus vectors for the production of chimeric, humanized, or human antibodies in insect cells (1995)

Plasmid cassette-transfer vectors pBHuC chi and pBHuC gamma l have been designed which enable the construction of recombinant baculoviruses directing the co-expression of complete immunoglobulin in insect cells. We describe the application of these vectors for the expression of a human/mouse chimeric monoclonal antibody of potential immunosuppressive clinical value derived from a mouse anti-human CD29 monoclonal antibody (Mu-K20). The chimeric K20 light and heavy chains produced in sf9 insect cells were correctly processed and assembled into a normal immunoglobulin which is secreted into the culture medium of infected cells. The chimeric mAb Ch-K20-sf9 reproduces in vitro the functional properties of the parental mouse K20, including affinity and inhibition of lymphocyte proliferation. These results demonstrate that the baculovirus/insect cell expression system is suitable for the expression of fully active monoclonal antibodies of therapeutic value. Our generic cassette approach makes this system a very flexible and convenient one for the rapid production of either chimeric, humanized or human mAb with heavy and light chains of any isotype.
Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology (2020)

Among the five candidate citrus promoters characterized in this study, the CitSEP promoter showed a fruit-specific expression pattern, while the CitWAX and CitJuSac promoters exhibited high fruit-preferential expression with strong activity in the fruit, weak activity in floral tissues and low or undetectable activity in other tissues. The CitVO1, CitUNK and PamMybA promoters, while exhibiting strong fruit-preferential expression, also showed consistent weak but detectable activity in leaves and other vegetative tissues. Use of these fruit specific/preferential promoters for genetic engineering can help with precise expression of beneficial genes and help with accurate prediction of the activity of new genes in host fruit plants.
Maximizing Coulombic recovery and solids reduction from primary sludge by controlling retention time and pH in a flat-plate microbial electrolysis cell (2017)

Control of hydraulic retention time and pH of the anode chamber in a flat-plate microbial electrolysis cell can improve Coulombic recovery and sludge stabilization.
A New Approach to Natural Products Discovery Exemplified by the Identification of Sulfated Nucleosides in Spider Venom (2004)

Using a new approach based on the NMR spectroscopic analysis of the entire, unpurified spider venom, we identified a family of unusual sulfated nucleoside derivatives from the venom of the hobo spider, Tegenaria agrestis. These compounds are ribonucleoside mono- and disulfates derived from guanosine and xanthosine, some of which are glycosylated, bearing one or two D-fucose units. The use of NMR spectroscopy to characterize the unfractionated venom was central to the discovery of this heretofore overlooked class of venom components.
Towards ultrasensitive malaria diagnosis using surface enhanced Raman spectroscopy (2016)

We report two methods of surface enhanced Raman spectroscopy (SERS) for hemozoin detection in malaria infected human blood. In the first method, silver nanoparticles were synthesized separately and then mixed with lysed blood; while in the second method, silver nanoparticles were synthesized directly inside the parasites of Plasmodium falciparum. It was observed that the first method yields a smaller variation in SERS measurements and stronger correlation between the estimated contribution of hemozoin and the parasitemia level, which is preferred for the quantification of the parasitemia level. In contrast, the second method yields a higher sensitivity to a low parasitemia level thus could be more effective in the early malaria diagnosis to determine whether a given blood sample is positive.
Instantaneous phase-shift Fizeau interferometer utilizing a synchronous frequency shift mechanism (2008)

An on-axis, vibration insensitive, polarization Fizeau interferometer is realized through the use of a pixelated polarization mask spatial carrier phase shifting technique in conjunction with a high coherence source and a polarization frequency shift device. In this arrangement, differential motion between the test and reference surfaces, in conjunction with the polarization frequency shift device, is used to effectively separate the orthogonally polarized test and reference beam components for interference. With both the test and the reference beams on-axis, the common path cancellation advantages of the Fizeau interferometer are maintained. Additionally, the use of a high coherence source eliminates the need to path match the test and reference arms of the interferometer. Using a 1 mW HeNe source, the optimum camera shutter speed, used when measuring a 4% reflector, was 250 usec, resulting in significantly reduced vibration sensitivity. Experimental results show the performance of this new interferometer to be within the specifications of commercial phase shifting interferometers.
The Lymphoid Cell Surface Receptor NTB-A: A Novel Monoclonal Antibody Target for Leukemia and Lymphoma Therapeutics. (2007)

Abstract NTB-A is a CD2-related cell surface protein expressed primarily on lymphoid cells including B-lymphocytes from Chronic Lymphocytic Leukemia (CLL) and lymphoma patients. We have generated a series of murine and chimeric mAbs against NTB-A and assessed their therapeutic potential for CLL. Selective mAbs to NTB-A were further tested in functional Complement Dependent Cytotoxicity (CDC) and Antibody Dependent Cellular Cytotoxicty (ADCC) assays in cell lines and B lymphocytes freshly isolated from CLL patients. While lower levels of NTB-A were detected in T and NK cells, CDC and ADCC activity was demonstrated primarily in B cells isolated from CLL patients and B lymphoma cell lines. Knockdown of NTB-A by siRNA in target cells results in lower cytotoxicity, demonstrating the specificity of the mAbs. Furthermore, anti-NTB-A mAbs demonstrated anti-tumor activity against CA46 human lymphoma xenografts in nude mice and against systemically disseminated Raji human lymphoma cells in SCID mice. Taken together, these results demonstrate NTB-A as a potential new target for immunotherapy of leukemia and lymphomas.
Suppression of anti-DNA antibody synthesis in vitro by a cross-reactive antiidiotypic antibody. (1987)

An understanding of the regulatory mechanisms that govern the humoral immune response will be facilitated by the availability of techniques for the measurement of specific antibody production in vitro. We have developed an enzyme-linked immunosorbent assay system for the measurement of in vitro anti-DNA antibody production by peripheral blood mononuclear cells (PBMC) from patients with systemic lupus erythematosus. Using this technique, the PBMC from 74% of serologically active SLE patients produced levels of anti-DNA antibodies that were greater than 2 SD above the mean of 18 +/- 9 IU/ml for normal subjects. Furthermore, the addition of 3I, a monoclonal anti-idiotypic antibody that recognizes a cross-reactive determinant on anti-DNA antibodies, was shown to specifically inhibit anti-DNA production in vitro.
Generation and Pruning of Pronunciation Variants to Improve ASR Accuracy (2016)

Speech recognition, especially name recognition, is widely used in phone services such as company directory dialers, stock quote providers or location finders. It is usually challenging due to pronunciation variations. This paper proposes an efficient and robust data-driven technique which automatically learns acceptable word pronunciations and updates the pronunciation dictionary to build a better lexicon without affecting recognition of other words similar to the target word. It generalizes well on datasets with various sizes, and reduces the error rate on a database with 13000+ human names by 42%, compared to a baseline with regular dictionaries already covering canonical pronunciations of 97%+ words in names, plus a well-trained spelling-to-pronunciation (STP) engine.