gebhart/patrepeval huggingface dataset:
Coefficient decimation approach for realizing reconfigurable finite impulse response filters (2008)

A new approach to implement computationally efficient reconfigurable finite impulse response (FIR) filter is presented in this paper. If the coefficients of an FIR filter are decimated by M, i.e., if every M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> coefficient of the filter is kept unchanged and remaining coefficients are changed to zeros, a multi-band frequency response will be obtained. The resulting frequency responses will have centre frequencies at 2pik/M, where k is an integer ranging from 0 to M-1. If these multi-band frequency responses are selectively masked using inherently low complex wide transition-band masking filters, different low-pass, high-pass, bandpass, and bandstop filters can be obtained. If every M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> coefficient is grouped together removing the zero coefficients in between, a decimated frequency response in comparison to the original frequency response is obtained. In this paper, we also show the design of a reconfigurable filter bank using the above approach.
β2-Adrenoreceptor is a regulator of the α-synuclein gene driving risk of Parkinson’s disease (2017)

Copy number mutations implicate excess production of α-synuclein as a possibly causative factor in Parkinson's disease (PD). Using an unbiased screen targeting endogenous gene expression, we discovered that the β2-adrenoreceptor (β2AR) is a regulator of the α-synuclein gene (<i>SNCA</i>). β2AR ligands modulate <i>SNCA</i> transcription through histone 3 lysine 27 acetylation of its promoter and enhancers. Over 11 years of follow-up in 4 million Norwegians, the β2AR agonist salbutamol, a brain-penetrant asthma medication, was associated with reduced risk of developing PD (rate ratio, 0.66; 95% confidence interval, 0.58 to 0.76). Conversely, a β2AR antagonist correlated with increased risk. β2AR activation protected model mice and patient-derived cells. Thus, β2AR is linked to transcription of α-synuclein and risk of PD in a ligand-specific fashion and constitutes a potential target for therapies.
Tissue spectroscopy with electrical impedance tomography: computer simulations (1995)

A method is proposed by which bioelectrical spectroscopy could be combined with electrical impedance tomography (EIT) to provide noninvasive characterization of tissue. Multifrequency (2-200 kHz) EIT measurements were simulated with a numerical model for a volume of porcine liver immersed in an electrolytic tank. From the reconstructed EIT images the tissue characterization method was then applied enabling a plot of complex resistivity to be drawn for any selected pixel in the image. Simulations were performed for a small volume of degraded tissue embedded in the normal tissue to examine its effect on the derived spectroscopic parameters. The method could have an application in transplant surgery for screening organs for tissue degradation.
A convergent synthetic route to the tunicamycin antibiotics. Synthesis of (+)-tunicamycin V (1993)

The tunicamycins are a family of natural products represented generally by structure 1, wherein R indicates one of several long-chain branched, linear, saturated or unsaturated acyl substituents. They elicit a considerable range of biological responses including antimicrobial, antifungal, antiviral, and antitumor activities. Their ability to function as potent inhibitors of oligosaccharide synthesis in eukaryotic cells has established them as unique biochemical probes of the role of glycosylation on protein structure and function. In this work, we describe a concise synthetic route to the tunicamycins, illustrated by the preparation of (+)-tunicamycin V (1-V).
The Novel Costimulatory Programmed Death Ligand 1/B7.1 Pathway Is Functional in Inhibiting Alloimmune Responses In Vivo (2011)

The programmed death ligand 1 (PDL1)/programmed death 1 (PD1) costimulatory pathway plays an important role in the inhibition of alloimmune responses as well as in the induction and maintenance of peripheral tolerance. It has been demonstrated recently that PDL1 also can bind B7.1 to inhibit T cell responses in vitro. Using the bm12 into B6 heart transplant model, we investigated the functional significance of this interaction in alloimmune responses in vivo. PD1 blockade unlike PDL1 blockade failed to accelerate bm12 allograft rejection, suggesting a role for an additional binding partner for PDL1 other than PD1 in transplant rejection. PDL1 blockade was able to accelerate allograft rejection in B7.2-deficient recipients but not B7.1-deficient recipients, indicating that PDL1 interaction with B7.1 was important in inhibiting rejection. Administration of the novel 2H11 anti-PDL1 mAb, which only blocks the PDL1-B7.1 interaction, aggravated chronic injury of bm12 allografts in B6 recipients. Aggravated chronic injury was associated with an increased frequency of alloreactive IFN-γ-, IL-4-, and IL-6-producing splenocytes and a decreased percentage of regulatory T cells in the recipients. Using an in vitro cell culture assay, blockade of the interaction of PDL1 on dendritic cells with B7.1 on T cells increased IFN-γ production from alloreactive CD4(+) T cells, whereas blockade of dendritic cell B7.1 interaction with T cell PDL1 did not. These data indicate that PDL1 interaction with B7.1 plays an important role in the inhibition of alloimmune responses in vivo and suggests a dominant direction for PDL1 and B7.1 interaction.
Genetically Encoded Azide Containing Amino Acid in Mammalian Cells Enables Site-Specific Antibody–Drug Conjugates Using Click Cycloaddition Chemistry (2015)

Antibody-drug conjugates (ADC) have emerged as potent antitumor drugs that provide increased efficacy, specificity, and tolerability over chemotherapy for the treatment of cancer. ADCs generated by targeting cysteines and lysines on the antibody have shown efficacy, but these products are heterogeneous, and instability may limit their dosing. Here, a novel technology is described that enables site-specific conjugation of toxins to antibodies using chemistry to produce homogeneous, potent, and highly stable conjugates. We have developed a cell-based mammalian expression system capable of site-specific integration of a non-natural amino acid containing an azide moiety. The azide group enables click cycloaddition chemistry that generates a stable heterocyclic triazole linkage. Antibodies to Her2/neu were expressed to contain N6-((2-azidoethoxy)carbonyl)-l-lysine at four different positions. Each site allowed over 95% conjugation efficacy with the toxins auristatin F or a pyrrolobenzodiazepine (PBD) dimer to generate ADCs with a drug to antibody ratio of >1.9. The ADCs were potent and specific in in vitro cytotoxicity assays. An anti Her2/neu conjugate demonstrated stability in vivo and a PBD containing ADC showed potent efficacy in a mouse tumor xenograph model. This technology was extended to generate fully functional ADCs with four toxins per antibody. The high stability of the azide-alkyne linkage, combined with the site-specific nature of the expression system, provides a means for the generation of ADCs with optimized pharmacokinetic, biological, and biophysical properties.
Dominant negative mutants of human T-cell leukemia virus type I Rex and human immunodeficiency virus type 1 Rev fail to multimerize in vivo (1993)

Human T-cell leukemia virus type I (HTLV-I) Rex and human immunodeficiency virus type 1 (HIV-1) Rev are essential gene products required for the replication of these two pathogenic human retroviruses. Both Rex and Rev act at a posttranscriptional level by binding to highly structured RNA-response elements, the Rex-response element in HTLV-I and the Rev-response element in HIV-1. Using a sensitive in vivo assay of protein-protein interaction, we now demonstrate that the HTLV-I Rex and HIV-1 Rev proteins readily form homomultimeric complexes in the absence of their cognate RNA-response elements yet fail to form heteromultimeric complexes with each other. Dominant negative mutations have been identified in both the rex and rev genes which presumably specify a critical activation or effector domain in each of these viral transactivators. Surprisingly, these dominant negative mutants of Rex and Rev fail to interact in vivo. These findings raise the possibility that the binding of nonfunctional monomers rather than functional multimers underlies the transdominant phenotype of these Rex and Rev mutants. Further, it seems likely that the assembly of functional and stable multimers of Rex and Rev in vivo may depend not only on the intrinsic multimerization domains of these proteins but also on the binding of a bridging cellular cofactor to the related activation domains present in each viral transactivator.
Effects of prostaglandin synthetase inhibitors, salt overload and renomedullary dissection on the hypoxia stimulated erythropoietin production in rats. (1980)

The effect of prostaglandin synthetase inhibitors, aspirin and indomethacin, salt overload and salt depletion, as well as renomedullary dissection on serum Ep level in rats exposed to acute hypoxia was studied. Male rats were given aspirin or saline for seven days prior to the exposure to hypoxia. Other group of animals was fed salt free diet for the same period of time. Indomethacin was given on two consecutive days and renomedullary dissection was performed three weeks before exposure to hypoxia. Ep level was indirectly determined by measuring the 48 h 59Fe incorporation into RBC of mice with posthypoxic polycythemia. Hypoxia induced Ep production was diminished after blocking the PG synthesis using PG synthesis inhibitors. Salt overload, procedure known to decrease PG synthesis, had the same effect. Further on, dissection of the renal medulla, the main source of renal PG, decreased Ep production. The results indicate that PG are part of the mechanism which controls Ep production.
?'(?)???: A Tale of Two Anomalies (2002)

The radiative decays of the pseudoscalar mesons $P=(\pi^0,\eta,\eta')$ are of special interest as they provide an experimental window on the electromagnetic and colour chiral $U_A(1)$ anomalies. $\pi^0\to\gamma\gamma$ is well described by the electromagnetic $U_A(1)$ anomaly under the assumption that $\pi^0$ is a Goldstone boson for spontaneously broken chiral symmetry, but the analogous results for $\eta'(\eta)\to\gamma\gamma$ are complicated by the colour $U_A(1)$ anomaly in QCD. This paper reviews the theory of $\eta'(\eta)\to\gamma\gamma$ decays, emphasising the role of the colour $U_A(1)$ anomaly and the renormalisation group. The relation to the Witten-Veneziano mass formula for the $\eta'$ and the QCD topological susceptibility is derived. The implications for the phenomenological analysis of $P\to\gamma\gamma$ are described and a proposal is made for a comprehensive re-analysis of existing data on $P\to\gamma\gamma$, $P\to V\gamma$, where $V=(\rho,\omega, \phi)$ is a light $1^-$ meson, $\eta'(\eta)\to \pi\pi\gamma$, $\psi\to\eta'(\eta)\gamma$, etc. Other applications, to the muon anomalous magnetic moment $g_\m-2$ and the determination of the photon structure function $g_1^\gamma$ in polarised deep inelastic scattering, are also briefly discussed.
Adjunctive Aripiprazole in Major Depressive Disorder (2008)

clinicaltrials.gov Identifiers: NCT00095823 and NCT00095758.
Matching Images to Models for Registration and Object Detection via Clustering (1982)

A new technique is presented for matching image features to maps or models. The technique forms all possible pairs of image features and model features which match on the basis of local evidence alone. For each possible pair of matching features the parameters of an RST (rotation, scaling, and translation) transformation are derived. Clustering in the space of all possible RST parameter sets reveals a good global transformation which matches many image features to many model features. Results with a variety of data sets are presented which demonstrate that the technique does not require sophisticated feature detection and is robust with respect to changes of image orientation and content. Examples in both cartography and object detection are given.
A preliminary clinical evaluation of the Mauch hydraulic foot-ankle system (1981)

A preliminary clinical evaluation was conducted by the United States Veterans Administration on eight prototype Mauch hydraulic foot/ankle systems over a period of two years (June 1977-October 1979). One above-knee, three below-knee, and one bilateral above-knee/below-knee subjects were fitted. Both of the above-knee amputees were Mauch S-N-S hydraulic knee users. The purpose of this study was: 1. To determine if this system provides the functions of the natural anatomical ankle around all three main axes; mediolateral, anteroposterior, and vertical. 2. To determine its applicability as to level of amputation, its benefits to bilateral amputees, and its compatibility with crustacean and pylon prostheses/standard knee designs. 3. To determine ease of installation, alignment, and adjustment procedures by a prosthetist and any new gait training techniques by a therapist. The results of the study revealed that this system does simulate the anatomical ankle in activities such as walking on uneven terrain, descending stairs step over step, running, ascending and descending inclines step over step, and a variety of sports activities including skiing. Fifty units have been produced and are being clinically tested in a nation-wide clinical application study conducted by the VA Rehabilitation Engineering Center (formerly V.A.P.C.).
Hold Your Horses: Impulsivity, Deep Brain Stimulation, and Medication in Parkinsonism (2007)

Deep brain stimulation (DBS) of the subthalamic nucleus markedly improves the motor symptoms of Parkinson's disease, but causes cognitive side effects such as impulsivity. We showed that DBS selectively interferes with the normal ability to slow down when faced with decision conflict. While on DBS, patients actually sped up their decisions under high-conflict conditions. This form of impulsivity was not affected by dopaminergic medication status. Instead, medication impaired patients' ability to learn from negative decision outcomes. These findings implicate independent mechanisms leading to impulsivity in treated Parkinson's patients and were predicted by a single neurocomputational model of the basal ganglia.
Human vascular smooth muscle cells contain functional estrogen receptor. (1994)

We have demonstrated for the first time that human VSMCs express E2-receptor mRNA and protein and that the E2 receptor in VSMCs is capable of estrogen-dependent gene activation. These data suggest a mechanism by which estrogen may directly alter VSMC function.
Overlapping promoters transcribed by bacillus subtilis sigma 55 and sigma 37 RNA polymerase holoenzymes during growth and stationary phases. (1984)

A 471-base pair HindIII DNA fragment of Bacillus subtilis contains two overlapping promoters which are recognized in vitro by sigma 55- and sigma 37-containing RNA polymerase holoenzymes from B. subtilis. In vitro transcript analyses and S1 nuclease mapping experiments with in vivo RNA indicate that both enzymes initiate transcription from the same putative +1 site. Physiological studies with the promoter-containing DNA fragment inserted into the expression probe plasmid pCED6 and quantitative S1 nuclease mapping experiments with RNA isolated from various stages of growth indicate that expression from these overlapping promoters is greater during the early stationary phase than during growth. We propose that the cryptic gene controlled by these promoters is transcribed by the sigma 55 enzyme during growth and by the sigma 37 enzyme during early stationary phase.
Scaling all-pairs overlay routing (2009)

This paper presents and experimentally evaluates a new algorithm for efficient one-hop link-state routing in full-mesh networks. Prior techniques for this setting scale poorly, as each node incurs quadratic (n2) communication overhead to broadcast its link state to all other nodes. In contrast, in our algorithm each node exchanges routing state with only a small subset of overlay nodes determined by using a quorum system. Using a two round protocol, each node can find an optimal one-hop path to any other node using only n1.5 per-node communication. Our algorithm can also be used to find the optimal shortest path of arbitrary length using only n1.5 logn per-node communication. The algorithm is designed to be resilient to both node and link failures. We apply this algorithm to a Resilient Overlay Network (RON) system, and evaluate the results using a large-scale, globally dis-tributed set of Internet hosts. The reduced communication overhead from using our improved full-mesh algorithm allows the creation of all-pairs routing overlays that scale to hundreds of nodes, without reducing the system’s ability to rapidly find optimal routes.
Validation coverage analysis for complex digital designs (1996)

The functional validation of a state-of-the-art digital design is usually performed by simulation of a register-transfer-level model. The degree to which the test vector suite covers the important tests is known as the coverage of the suite. Previous coverage metrics have relied on measures such as the number of simulated cycles or number of toggles on a circuit node, which are indirect metrics at best. This paper proposes a new method of analyzing coverage based on projecting a minimized control finite-state graph onto control signals for the datapath part of the design to yield a meaningful metric and provide detailed feedback about missing tests. The largest hurdle is state-space explosion. We describe two methods of dealing with this in a practical manner and give results of applying this coverage analysis to parts of the node controller of the Stanford FLASH multiprocessor.
An overview of membrane transport proteins in Saccharomyces cerevisiae (1995)

All eukaryotic cells contain a wide variety of proteins embedded in the plasma and internal membranes, which ensure transmembrane solute transport. It is now established that a large proportion of these transport proteins can be grouped into families apparently conserved throughout organisms. This article presents the data of an in silicio analysis aimed at establishing a preliminary classification of membrane transport proteins in Saccharomyces cerevisiae. This analysis was conducted at a time when about 65% of all yeast genes were available in public databases. In addition to approximately 60 transport proteins whose function was at least partially known, approximately 100 deduced protein sequences of unknown function display significant sequence similarity to membrane transport proteins characterized in yeast and/or other organisms. While some protein families have been well characterized by classical genetic experimental approaches, others have largely if not totally escaped characterization. The proteins revealed by this in silicio analysis also include a putative K+ channel, proteins similar to aquaporins of plant and animal origin, proteins similar to Na+-solute symporters, a protein very similar to electroneural cation-chloride cotransporters, and a putative Na+-H+ antiporter. A new research area is anticipated: the functional analysis of many transport proteins whose existence was revealed by genome sequencing.
Empirical Measurements of Disk Failure Rates and Error Rates (2007)

The SATA advertised bit error rate of one error in 10 terabytes is frightening. We moved 2 PB through low-cost hardware and saw five disk read error events, several controller failures, and many system reboots caused by security patches. We conclude that SATA uncorrectable read errors are not yet a dominant system-fault source - they happen, but are rare compared to other problems. We also conclude that UER (uncorrectable error rate) is not the relevant metric for our needs. When an uncorrectable read error happens, there are typically several damaged storage blocks (and many uncorrectable read errors.) Also, some uncorrectable read errors may be masked by the operating system. The more meaningful metric for data architects is Mean Time To Data Loss (MTTDL.)
Human telomerase reverse transcriptase (hTERT) gene expression in thyroid neoplasms. (1999)

Ten percent of fine-needle aspirations (FNAs) of the thyroid are deemed "indeterminate" or "suspicious" for malignancy by the cytopathologist, but most of these lesions are benign. Therefore, additional markers of malignancy may prove to be a useful adjunct. The catalytic component of telomerase, human telomerase reverse transcriptase (hTERT), has been found to be reactivated in immortalized cell lines. Reverse transcription-PCR of the hTERT gene revealed expression in 15 (79%) of 19 malignant thyroid neoplasms, including 6 of 6 follicular carcinomas and 9 of 13 papillary carcinomas. In contrast, hTERT gene expression was detected in only 5 (28%) of 18 benign thyroid nodules, including 2 of 7 follicular adenomas and 3 of 11 hyperplastic nodules. All five benign thyroids exhibiting hTERT gene expression had lymphocytic thyroiditis. No normal thyroids exhibited hTERT gene expression. Telomerase enzyme activity was examined in all 37 nodules and was found to correlate with hTERT gene expression in 35 (95%) nodules. The two cases in which telomerase activity and hTERT expression results were discrepant were in two papillary carcinomas that were telomerase activity negative and hTERT positive. Finally, we have demonstrated that hTERT gene expression can be measured in in vivo FNA samples. These results suggest that hTERT expression may be more accurate than telomerase activity in distinguishing benign from malignant and may be measured in FNA samples from suspicious thyroid lesions.
Estimation of optical pathlength through tissue from direct time of flight measurement (1988)

Quantitation of near infrared spectroscopic data in a scattering medium such as tissue requires knowledge of the optical pathlength in the medium. This can now be estimated directly from the time of flight of picosecond length light pulses. Monte Carlo modelling of light pulses in tissue has shown that the mean value of the time dispersed light pulse correlates with the pathlength used in quantitative spectroscopic calculations. This result has been verified in a phantom material. Time of flight measurements of pathlength across the rat head give a pathlength of 5.3 +/- 0.3 times the head diameter.
Field effect in epitaxial graphene on a silicon carbide substrate (2007)

The authors report a strong field effect observed at room temperature in epitaxially synthesized, as opposed to exfoliated, graphene. The graphene formed on the silicon face of a 4H silicon carbide substrate was photolithographically patterned into isolated active regions for the semimetal graphene-based transistors. Gold electrodes and a polymer dielectric were used in the top-gate transistors. The demonstration of a field effect mobility of 535cm2∕Vs was attributed to the transistor geometry that maximizes conductance modulation, although the mobility is lower than observed in exfoliated graphene possibly due to grain boundaries caused by the rough morphology of the substrate surface.