gebhart/patrepeval huggingface dataset:
Identification and cDNA cloning of single-stranded DNA binding proteins that interact with the region upstream of the human c-myc gene. (1994)

We have previously reported that a c-myc protein complex binds to the region upstream of the c-myc gene, where exist an origin of cellular DNA replication (ori) and a transcriptional enhancer. Both functions require a 21 bp long sequence, while the c-myc protein complex recognizes a 7 bp consensus therein. It was recently reported that single-stranded DNA binding proteins bound specifically to sequences that play roles in DNA replication or transcription. We examined for proteins binding to the single-stranded DNAs of the 21 bp element (myc(H-P)21). In a band shift assay with HL60 cells nuclear extract, probes of either the plus strand or the minus strand gave rise to specific signals. Mutation introduced within a short consensus (A/TCTA/TA/TT) present in both strands completely abolished binding in either case. Southwestern blotting analysis showed that proteins of molecular weight 105, 80, 50, 45, 40, 39.5 and 14 kDa bound sequence-specifically to either strand and 22 kDa to minus strand to the cognate A/TCTA/TA/TT consensus. These single-stranded DNA binding proteins were named MSSP, c-myc gene single strand binding proteins. We attempted to isolate the cDNAs encoding these proteins by screening a human cDNA library with the plus single-stranded oligonucleotide as a probe. Among several positive clones, we have characterized one, termed MSSP-1. MSSP-1 produced in E. coli as a fusion protein with GST specifically interacted with single-stranded TCTTAT (plus myc(H-P)21) and ACT-ATT (in minus myc(H-P)21), the consensus of which can be referred to as A/TCTA/TA/TT. Sequence analysis of MSSP-1 cDNA revealed that two domains thereof are homologous to the RNA binding motifs common to several ribonucleoproteins. Interestingly, the MSSP-1/GST fusion protein specifically recognized myc(H-P)21 not only in single-stranded but also in double-stranded forms. Binding properties of MSSP-1 imply its functions in DNA replication. Furthermore, when the AT stretch in the SV40 ori core was substituted by TCTTAT, MSSP-1 promoted viral DNA replication depending on the consensus sequences.
Techno‐economics of the production of mixed alcohols from lignocellulosic biomass via high‐temperature gasification (2010)

Abstract This techno‐economic study investigates the production of mixed alcohols from lignocellulosic biomass using an entrained flow slagging gasifier. Similar analyses for 2000 dry tonne per day plants have been performed at the National Renewable Energy Laboratory using indirect, and direct dry ash gasifiers. The use of a high‐temperature entrained flow gasifier differs from the previous studies because it eliminates equipment for tar and methane reformation. The conversion targets for tar reforming in the previous studies, and for alcohol synthesis in all of the studies, are based on DOE's research goals for 2012. The conversion cost increased compared to both of the previous studies, assuming the achievement of the 2012 research targets. Feed handling, high oxygen demand, and a high gasifier capital cost are primarily responsible for the high cost projected by this study. It is understood that the achievement of research targets, maturity, reliability, relative complexities, and redundancy requirements will be the other keys to commercialization. The effect of key assumptions and uncertainties were evaluated using sensitivity analysis. © 2010 American Institute of Chemical Engineers Environ Prog, 2010
Small-Fiber Neuropathy Nav1.8 Mutation Shifts Activation to Hyperpolarized Potentials and Increases Excitability of Dorsal Root Ganglion Neurons (2013)

Idiopathic small-fiber neuropathy (I-SFN), clinically characterized by burning pain in distal extremities and autonomic dysfunction, is a disorder of small-caliber nerve fibers of unknown etiology with limited treatment options. Functional variants of voltage-gated sodium channel Nav1.7, encoded by SCN9A, have been identified in approximately one-third of I-SFN patients. These variants render dorsal root ganglion (DRG) neurons hyperexcitable. Sodium channel Nav1.8, encoded by SCN10A, is preferentially expressed in small-diameter DRG neurons, and produces most of the current underlying the upstroke of action potentials in these neurons. We previously demonstrated two functional variants of Nav1.8 that either enhance ramp current or shift activation in a hyperpolarizing direction, and render DRG neurons hyperexcitable, in I-SFN patients with no mutations of SCN9A. We have now evaluated additional I-SFN patients with no mutations in SCN9A, and report a novel I-SFN-related Nav1.8 mutation I1706V in a patient with painful I-SFN. Whole-cell voltage-clamp recordings in small DRG neurons demonstrate that the mutation hyperpolarizes activation and the response to slow ramp depolarizations. However, it decreases fractional channels resistant to fast inactivation and reduces persistent currents. Current-clamp studies reveal that mutant channels decrease current threshold and increase the firing frequency of evoked action potentials within small DRG neurons. These observations suggest that the effects of this mutation on activation and ramp current are dominant over the reduced persistent current, and show that these pro-excitatory gating changes confer hyperexcitability on peripheral sensory neurons, which may contribute to pain in this individual with I-SFN.
Brain concentrations of benzodiazepines are elevated in an animal model of hepatic encephalopathy. (1990)

Brain extracts from rats with hepatic encephalopathy due to thioacetamide-induced fulminant hepatic failure contained 4- to 6-fold higher concentrations of substances that inhibit radioligand binding to benzodiazepine receptors than corresponding control rat extracts. Both isocratic and gradient-elution HPLC indicated that this inhibitory activity was localized in 3-8 peaks with retention times corresponding to deschlorodiazepam, deschlorolorazepam, lorazepam, oxazepam, diazepam, and N-desmethyldiazepam. The presence of diazepam and N-desmethyldiazepam was confirmed by mass spectroscopy. Both mass spectroscopic and radiometric techniques indicated that the concentrations of N-desmethyldiazepam and diazepam in brain extracts from encephalopathic rats were 2-9 and 5-7 times higher, respectively, than in control brain extracts. While benzodiazepines have been identified previously in mammalian and plant tissues, this report demonstrates that concentrations of these substances are increased in a pathophysiological condition. These findings provide a rational basis for the use of benzodiazepine receptor antagonists in the management of hepatic encephalopathy in humans.
Studies with Arylhydrazono-3-oxopropanals:A novel route to synthesis of substituted pyrazoles, oxoalkanonitrile and glyoxalonitrile containing sulfa drug moieties (2008)

El acoplamiento de las enaminonas 1 con sales de diazonio da los hidrazonopropanales 3a-h. El compuesto 3 reacciona con &-bromoacetofenona o a-cloroacetanilida rindiendo 5 y 8. Estos compuestos se ciclan suavemente, dando 6 y 9 respectivamente. Por reaccion con fenilhidrazina se obtienen las difenilhidrazonas 10, que ciclan a los arilazopirazoles 11 en piridina a reflujo. Sin embargo, la reaccion de 3c-f con hidrato de hidracina rinde los pirazoles 12. La reaccion de 3 con hidrocloruro de fenilhidrazina da 11. Finalmente, la reaccion de 3c con hidrocloruro de hidroxilamina rinde la aldoxima 14, que por calefaccion en piridina a reflujo da 15 en lugar de 16.
Robust Algorithms for Object Localization (2021)

Object localization using sensed data features and corresponding model features is a fundamental problem in machine vision. We reformulate object localization as a least squares problem: the optimal pose estimate minimizes the squared error (discrepancy) between the sensed and predicted data. The resulting problem is non-linear and previous attempts to estimate the optimal pose using local methods such as gradient descent suffer from local minima and, at times, return incorrect results. In this paper, we describe an exact, accurate and efficient algorithm based on resultants, linear algebra, and numerical analysis, for solving the nonlinear least squares problem associated with localizing two-dimensional objects given two-dimensional data. This work is aimed at tasks where the sensor features and the model features are of different types and where either the sensor features or model features are points. It is applicable to localizing modeled objects from image data, and estimates the pose using all of the pixels in the detected edges. The algorithm's running time depends mainly on the type of non-point features, and it also depends to a small extent on the number of features. On a SPARC 10, the algorithm takes a few microseconds for rectilinear features, a few milliseconds for linear features, and a few seconds for circular features.
A Bayesian approach to introducing anatomo-functional priors in the EEG/MEG inverse problem (1997)

In this paper, we present a new approach to the recovering of dipole magnitudes in a distributed source model for magnetoencephalographic (MEG) and electroencephalographic (EEG) imaging. This method consists in introducing spatial and temporal a priori information as a cure to this ill-posed inverse problem. A nonlinear spatial regularization scheme allows the preservation of dipole moment discontinuities between some a priori noncorrelated sources, for instance, when considering dipoles located on both sides of a sulcus. Moreover, we introduce temporal smoothness constraints on dipole magnitude evolution, at time scales smaller than those of cognitive processes. These priors are easily integrated into a Bayesian formalism, yielding a maximum a posteriori (MAP) estimator of brain electrical activity. Results from EEG simulations of our method are presented and compared with those of classical quadratic regularization and a now popular generalized minimum-norm technique called low-resolution electromagnetic tomography (LORETA).
3G – 4G – 5G: How Baw Filter Technology Enables a Connected World (2019)

5G is highly anticipated by service providers, phone manufacturers and consumers. 5G marks a dramatic increase in data rates. The number of frequency bands requiring high performance filters increases significantly. BAW is particularly well suited for new bands below 6 GHz, many of which have very wide bandwidth and close-by neighbors. The only path forward to achieve full connectivity in LTE 4G + 5G wireless is RF integration; complexity of the antenna systems and the resulting coexistence challenges will dictate it. The article discusses trends for BAW, wide bandwidth and miniaturization.
Activities of Masked 2′,3′-Dideoxynucleoside Monophosphate Derivatives against Human Immunodeficiency Virus in Resting Macrophages (2000)

The anti-human immunodeficiency virus (HIV) activity of aryloxyphosphoramidate protides of a number of anti-HIV nucleoside analogues was assessed in resting primary monocyte-macrophages (M/M). While 2',3'-dideoxythymidine (d4T), 2',3'-dideoxyadenosine (ddA), and 2',3'-dideoxy-2',3'-didehydroadenosine (d4A) protides showed an anti-HIV activity that was 25- to 625-fold greater than the parent nucleotides d4T, ddA, and d4A, respectively, other aryloxyphosphoramidate protides showed similar or even lower anti-HIV activities than their parent compounds. This variable anti-HIV effect is most likely related to the different dynamics of intracellular nucleoside monophosphate release from the protides. Our results indicate the potential advantage of therapeutic use of this approach for some nucleotide analogues to affect HIV replication in M/M, one of the major reservoirs of HIV in vivo.
Human Herpesvirus 8 Envelope Glycoprotein K8.1A Interaction with the Target Cells Involves Heparan Sulfate (2001)

Human herpesvirus-8 (HHV-8) or Kaposi's sarcoma-associated herpesvirus K8.1 gene encodes for two immunogenic glycoproteins, gpK8.1A and gpK8.1B, originating from spliced messages. The 228-amino-acid (aa) gpK8.1A is the predominant form associated with the virion envelope, consisting of a 167-aa region identical to gpK8.1B and a 61-aa unique region (L. Zhu, V. Puri, and B. Chandran, Virology 262:237-249, 1999). HHV-8 has a broad in vivo and in vitro cellular tropism, and our studies showed that this may be in part due to HHV-8's interaction with the ubiquitous host cell surface molecule, heparan sulfate (HS). Since HHV-8 K8.1 gene is positionally colinear to the Epstein-Barr virus (EBV) gene encoding the gp350/gp220 protein involved in EBV binding to the target cells, gpK8.1A's ability to interact with the target cells was examined. The gpK8.1A without the transmembrane and carboxyl domains (DeltaTMgpK8.1A) was expressed in a baculovirus system and purified. Radiolabeled purified DeltaTMgpK8.1A protein bound to the target cells, which was blocked by unlabeled DeltaTMgpK8.1A. Unlabeled DeltaTMgpK8.1A blocked the binding of [(3)H]thymidine-labeled purified HHV-8 to the target cells. Binding of radiolabeled DeltaTMgpK8.1A to the target cells was inhibited in a dose-dependent manner by soluble heparin, a glycosaminoglycan (GAG) closely related to HS, but not by other GAGs such as chondroitin sulfate A and C, N-acetyl heparin and de-N-sulfated heparin. Cell surface absorbed DeltaTMgpK8.1A was displaced by soluble heparin. Radiolabeled DeltaTMgpK8.1A also bound to HS expressing Chinese hamster ovary (CHO-K1) cells, and binding to mutant CHO cell lines deficient in HS was significantly reduced. The DeltaTMgpK8.1A specifically bound to heparin-agarose beads, which was inhibited by HS and heparin, but not by other GAGs. Virion envelope-associated gpK8.1A was specifically precipitated by heparin-agarose beads. These findings suggest that gpK8.1A interaction with target cells involves cell surface HS-like moieties, and HHV-8 interaction with HS could be in part mediated by virion envelope-associated gpK8.1A.
EFFECTS OF PLANT GROWTH PROMOTING BACTERIA ON YIELD, GROWTH, LEAF WATER CONTENT, MEMBRANE PERMEABILITY, AND IONIC COMPOSITION OF STRAWBERRY UNDER SALINE CONDITIONS (2010)

Plant growth promoting effects of Bacillus subtilis EY2, Bacillus atrophaeus EY6, Bacillus spharicus GC subgroup B EY30, Staphylococcus kloosii EY37 and Kocuria erythromyxa EY43 were tested on strawberry cv. ‘Fern’ in terms of fruit yield, growth, chlorophyll reading value, leaf relative water content (LRWC), membrane permeability and ionic composition of leaves and roots under saline conditions. Compared with 0 mM sodium chloride (NaCl) treatment, the average decrease of yield and LRWC were 51.6% and 21.0%, respectively, when 35 mM NaCl was applied. However, EY30, EY37, and EY43 treatments under saline condition (35 mM NaCl) significantly increased fruit yield (54.4%, 51.7% and 94.9%) compared with 35 mM NaCl treatment without plant growth promoting bacteria (PGPB). The LRWC increased from 72.0% in 35 mM NaCl treatment to 88.4%, 86.6%, 84.2%, 83.5%, and 86.2% by EY2, EY6, EY30, EY37, and EY43 applications, respectively. The lowest membrane permeability among the bacterial strains was obtained from EY37 treatment (37) while it was 33 and 58 in 0 mM NaCl and 35 mM NaCl treatments, respectively. The concentration of all plant tissue nutrients investigated [nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg)] with the exception of root phosphorus (P) and Mg concentration significantly decreased with 35 mM salt treatment. Nitrogen content of leaves varied between 3.04 and 3.14% in bacterial treatments under saline conditions while it was 2.71% in 35 mM NaCl treatment. In contrast sodium (Na) and chloride (Cl) of leaves and Cl content of roots were significantly decreased by root inoculation with all bacterial treatments in comparison to 35 mM NaCl treatment with no inoculation. Treatment with Bacillus EY30, Staphylococcus EY37 and Kocuria EY43 to strawberry plants can ameliorative the deleterious effect of salt stress on fruit yield, growth and nutrition. These results demonstrate that PGPB treatment could be offer an economic and simple means to increased plant resistance for salinity stress.
A multi-analyte serum test for the early diagnosis of non-small cell lung cancer. (2010)

1554 Background: Non-small cell lung cancer (NSCLC) is the second most diagnosed cancer in the United States and the most common cause of cancer related death. Currently, there are no screening methods that have been proven to reduce mortality, including low-dose spiral computerized tomography (CT). In this study we appraised a wide assortment of biomarkers previously demonstrated to have diagnostic or prognostic value for NSCLC with the intent of establishing a multi-analyte serum test capable of identifying patients with early-stage disease. Methods: Levels of 47 biomarkers were evaluated in serum from 92 NSCLC and 43 non-cancer controls using Luminex and ELISA-based immunoassays. Multivariate statistical methods were then used to define a diagnostic panel of biomarkers for NSCLC that we then tested on serum from a second patient cohort consisting of 33 NSCLC, 15 benign lung disease and 40 COPD patients. Results: Of the initial 47 biomarkers, 14 had an AUC greater than 0.65. Multivariate analysis of the 14 narrowed them down to a panel of 6: TNF-α, CYFRA 21.1, IL-1ra, MMP-2, MCP-1, and sE-selectin. When this panel was tested on the original cohort of patients, it correctly classified 132 of 135 patients with 99% sensitivity and 95% specificity. When tested on the second cohort, the panel successfully classified 75 of 88. The panel did very well on COPD patients, but struggled in classifying those with surgically resected benign lung nodules. Conclusions: Here we report the development of a 6-analyte serum test that possesses excellent test performance characteristics for classifying patients with NSCLC against a patient cohort comprised of various high-risk individuals. When used on the second group of patients, the test had trouble classifying patients with benign lung disorders such as caseating granulomas as benign. This may be due to a general inflammatory state of these individuals. The panel did have excellent classification in stage I lung cancer and those with COPD. With modifications and broader validation, the ultimate goal of this biomarker panel is to function either independently or in conjunction with low- dose spiral CT-based screening protocols for early detection of lung cancer. No significant financial relationships to disclose.
Existence of both IL-1 alpha and beta in normal human amniotic fluid: unique high molecular weight form of IL-1 beta. (1988)

We investigated the possible existence of IL-1 in human amniotic fluid (AF). Since AF from most full-term deliveries appeared to contain an inhibitor(s) for thymocyte proliferation, AFs were fractionated by gel filtration prior to IL-1 assay. IL-1 activities eluted in two peaks at positions of 90,000-60,000 MW and 20,000-15,000 MW. Growth inhibitory activity eluted at the position of 70,000-50,000 MW, and its effect appeared to be non-specific because these fractions inhibited the growth of various cell lines. Using isoelectric focusing (IEF) techniques, pI values of 6.8-7.3 for the higher MW IL-1 as well as 4.9-5.5 and 6.7-7.0 for the lower MW IL-1 were obtained. Antibody against human IL-1 alpha partially neutralized the activity of the lower MW IL-1, though it exhibited little effect on the higher MW IL-1. In contrast, antibody against human IL-1 beta almost completely neutralized the activity of the higher MW IL-1 and partially neutralized the activity of the lower MW IL-1. These results suggest that most of the higher MW IL-1 is beta-type, and the lower MW IL-1 is a mixture of alpha and beta-types. IL-1 beta appeared to exist as a complex (combined with AF components) or as an aggregate of the lower MW IL-1 forms. These findings indicate that both IL-1 alpha and IL-1 beta are present in normal human AF from full-term deliveries, though IL-1 beta exists as a higher MW form aggregated with an unknown molecule.
A Method for Determining X‐ray Elastic Constants for the Measurement of Residual Stress (2003)

Abstract: The X‐ray diffraction method is arguably the most convenient method of measuring residual stresses in terms of cost, spatial resolution, measurement time and the accuracy of measurement. The normal methods for calibrating X‐ray diffractometers are not conveniently applied to automated scanning systems, however, and so a new approach is required. In this study, a scanning X‐ray diffractometer was calibrated and the X‐ray elastic constant for a steel alloy was determined using a customised four‐point bending rig. The bending rig, in turn, was calibrated by dead loading. This study also described a simple alternative method for determining the X‐ray elastic constant, without the use of specialised software. After calibration, the error band of the diffractometer was found to be less than ±10 MPa. As this is ±5% of the yield stress for a typical steel, this level of accuracy was deemed to be acceptable for the measurement of residual stress.
Implantation-induced strains in silicon studied by X-ray interferometry and topography (1978)

Abstract The dose dependence and annealing of lateral strains induced by 80 keV argon implants in silicon have been studied by X-ray interferometry and X-ray diffraction topography in the range 1014-1017 ions/cm2 and 20–900°C, respectively. Volume expansion has been observed in the as-implanted state, but for bombardment to doses much larger than that required to produce an amorphous layer, an essentially stress-free state is obtained. Annealing at 600°C results in a stress-free state for all doses considered. Samples implanted up to doses required to form an amorphous layer, and slightly higher, show a rapid reverse-annealing above 600°C, accompanied by a reversal of sign of the strain.
Targeting myeloid leukemia with a DT390-mIL-3 fusion immunotoxin: ex vivo and in vivo studies in mice (1999)

The IL-3 receptor was expressed on a high frequency of myeloid leukemia cells and also on hematopoietic and vascular cells. We previously showed that a recombinant IL-3 fusion immunotoxin (DT(390)IL-3) expressed by splicing the murine IL-3 gene to a truncated diphtheria toxin (DT(390)) gene selectively killed IL-3R(+) expressing cells and was not uniformly toxic to uncommitted BM progenitor cells (Chan,C.-H., Blazar,B.R., Greenfield,L., Kreitman,R.J. and Vallera,D.A., 1996, Blood, 88, 1445-1456). Thus, we explored the feasibility of using DT(390)IL-3 as an anti-leukemia agent. DT(390)IL-3 was toxic when administered to mice at doses as low as 0.1 microg/day. The dose limiting toxicity appeared to be related to platelet and bleeding effects of the fusion toxin. Because of these effects, DT(390)IL-3 was studied ex vivo as a means of purging contaminating leukemia cells from BM grafts in a murine autologous BM transplantation. In this setting, as few as 1000 IL-3R-expressing, bcr/abl transformed myeloid 32Dp210 leukemia cells were lethal. An optimal purging interval of 10 nM/l for 8 h eliminated leukemia cells from 32Dp210/BM mixtures given to lethally irradiated (8 Gy) C3H/HeJ syngeneic mice. Mice given treated grafts containing BM and a lethal dose of 32Dp210 cells survived over 100 days while mice given untreated grafts did not survive (P < 0.00001). DT(390)IL-3 may prove highly useful for ex vivo purging of lethal malignant leukemia cells from autologous BM grafts.