gebhart/patrepeval huggingface dataset:
Conserved Structural Regions Involved in the Catalytic Mechanism of Escherichia coli K-12 WaaO (RfaI) (1998)

Escherichia coli K-12 WaaO (formerly known as RfaI) is a nonprocessive alpha-1,3 glucosyltransferase, involved in the synthesis of the R core of lipopolysaccharide. By comparing the amino acid sequence of WaaO with those of 11 homologous alpha-glycosyltransferases, four strictly conserved regions, I, II, III, and IV, were identified. Since functionally related transferases are predicted to have a similar architecture in the catalytic sites, it is assumed that these four regions are directly involved in the formation of alpha-glycosidic linkage from alpha-linked nucleotide diphospho-sugar donor. Hydrophobic cluster analysis revealed a conserved domain at the N termini of these alpha-glycosyltransferases. This domain was similar to that previously reported for beta-glycosyltransferases. Thus, this domain is likely to be involved in the formation of beta-glycosidic linkage between the donor sugar and the enzyme at the first step of the reaction. Site-directed mutagenesis analysis of E. coli K-12 WaaO revealed four critical amino acid residues.
Green resource allocation with QoS provisioning for cooperative cellular network (2011)

Relay-based cooperative transmission in cellular network has been an area of tremendous research recently. Transmission via relays introduces power consumption at both the source and relay stations which may lead to less efficient system in terms of power consumption. Because of increasing energy cost for cellular systems and concern over environmental issues, an energy efficient design of resource allocation scheme in cooperative cellular network is of prime importance. In this paper, we propose a novel resource allocation scheme in order to maximize the energy aware system performance. The proposed low-complexity scheme allocates powers for base station and relay by using a strategy that minimizes required transmit power per unit achieved throughput and at the same time guarantees a predefined quality of service (QoS) which is specified in terms of minimum end-to-end data rate required by each user. Simulation results show that proposed scheme outperforms existing power allocation schemes by decreasing required power to guarantee the QoS without increasing system outage penalty, which is essential for green communication systems.
Lack of correlation between the response to a proliferation inhibitor and other transformation markers in a mutant liver cell line. (1981)

A rat liver factor, which has been found previously to inhibit proliferation of untransformed rat liver cell lines but not of transformed liver cell lines, did not inhibit proliferation of the chemically transformed rat liver cell line, W-8. Moreover, a temperature-sensitive mutant derived from W-8 (TS-223), which exhibits an untransformed phenotype at 39.5-41 degrees and a transformed phenotype at 36 degrees, was not affected by the liver factor at either temperature. Since the factor can be incubated at 41 degrees for 4 days without loss of activity, it would seem that the regulation of cell proliferation is not necessarily linked with the expression of other markers of transformed cells.
Message communications of particular message types between compute nodes using DMA shadow buffers (2023)

Message communications of particular message types between compute nodes using DMA shadow buffers includes: receiving a buffer identifier specifying an application buffer having a message of a particular type for transmission to a target compute node through a network; selecting one of a plurality of shadow buffers for a DMA engine on the compute node for storing the message, each shadow buffer corresponding to a slot of an injection FIFO buffer maintained by the DMA engine; storing the message in the selected shadow buffer; creating a data descriptor for the message stored in the selected shadow buffer; injecting the data descriptor into the slot of the injection FIFO buffer corresponding to the selected shadow buffer; selecting the data descriptor from the injection FIFO buffer; and transmitting the message specified by the selected data descriptor through the data communications network to the target compute node.
A Randomized Placebo-Controlled Trial of Sarilumab in Hospitalized Patients with Covid-19 (2021)

ABSTRACT BACKGROUND Sarilumab (anti-interleukin-6 receptor-α monoclonal antibody) may attenuate the inflammatory response in Covid-19. METHODS We performed an adaptive, phase 2/3, randomized, double-blind, placebo-controlled trial of intravenous sarilumab 200 mg or 400 mg in adults hospitalized with Covid-19. The phase 3 primary analysis population (cohort 1) was patients with critical Covid-19 receiving mechanical ventilation (MV) randomized to sarilumab 400 mg or placebo. The primary end point for phase 3 was the proportion of patients with ≥1-point improvement in clinical status from baseline to day 22. RESULTS Four-hundred fifty-seven (457) and 1365 patients were randomized and treated in phases 2 and 3, respectively. Among phase 3 critical patients receiving MV (n=289; 34.3% on corticosteroids), the proportion with ≥1-point improvement in clinical status (alive not receiving MV) at day 22 was 43.2% in sarilumab 400 mg and 35.5% in placebo (risk difference [RD] +7.5%; 95% confidence interval [CI], –7.4 to 21.3; P=0.3261), representing a relative risk improvement of 21.7%. Day 29 all-cause mortality was 36.4% in sarilumab 400 mg versus 41.9% in placebo (RD –5.5%; 95% CI, –20.2 to 8.7; relative risk reduction 13.3%). In post hoc analyses pooling phase 2 and 3 critical patients receiving MV, the hazard ratio (HR) for death in sarilumab 400 mg compared with placebo was 0.76 (95% CI, 0.51 to 1.13) overall, improving to 0.49 (95% CI, 0.25 to 0.94) in patients receiving corticosteroids at baseline. CONCLUSION In hospitalized patients with Covid-19 receiving MV, numerical benefits with sarilumab did not achieve statistical significance, but benefit may be greater in patients receiving corticosteroids. A larger study is required to confirm this observed numerical benefit. ( ClinicalTrials.gov number, NCT04315298 )
On the Value of Transmitter Information (2007)

Coherent signaling over a fading channel requires the receiver to have knowledge of the current fading state (CSIR). In order to proactively prevent outages, the transmitter requires knowledge of the fading state (CSIT) to perform power control. Typically, the channel state is estimated by using a training signal, and the channel state information contains some error. In this work, we examine the performance of a symmetric, single-input, multiple-output (SIMO) channel in which both the transmitter and the receiver have independent, imperfect estimates of the channel. We give expressions for mutual information and outage probability, and we use those expressions to evaluate the diversity order of the system for a constant target rate. We show that diversity order is dominated by the transmitter error and that the diversity order is equal to that of a system with perfect CSIR
Improving cover type identification in speckled SAR images by prefiltering and sequential classification (1988)

Synthetic aperture radar utilizes coherent microwaves to produce images of the earth's surface. Due to the interference of coherent wavelets, the images appear speckled. This reduces the performance of per-pel classifiers. One way to increase the performance is to filter the image first, then classify the filtered image. For this purpose, several novel filters that have been reported in the literature are investigated. These are the geometric filter, adaptive LMMSE filter, and linear approximation filter. For comparison, conventional mean and median filters are also considered. It is found that the mean filter with seven iterations gives the best result. The overall performance increased from 65.2 to 88.9 percent. The capability of these filters to preserve edges in the original image are also assessed. It is seen that the geometric and median filters are the best in preserving edges, and that the linear approximation and adaptive LMMSE filters are the best in discriminating roads. Prefiltering the image effectively provides contextual information to the per-pel classifier. An alternate approach is to directly design a contextual classifier. A new contextual classifier based on sequential decision theory is proposed. With this classifier, it is found that the overall performance increases to 89.5 percent.
Analysis of Steroid‐Induced Genes in the Rat Preoptic Area‐Anterior Hypothalamus Using a Differential‐Display Reverse Transcriptase‐Polymerase Chain Reaction (2001)

Steroid hormones modulate a variety of physiological functions in the hypothalamus. We attempted to identify steroid-regulated genes in the rat preoptic area-anterior hypothalamus by comparing differentially expressed mRNAs. Adult female rats were ovariectomized and, 1 week later, a silastic capsule containing 17beta-oestradiol (180 microg/ml) was subcutaneously implanted. After 2 days, a single injection of progesterone (1 mg) was administered at 10.00 h and rats were killed at 17.00 h on the same day. Differential-display polymerase chain reaction followed by Northern blot analysis showed that 10 clones were differentially regulated. Using homology search in Genbank, three genes were identified as sodium, potassium-ATPase beta1, protein kinase C-binding Nell-homologue protein and evectin-1. Further characterization of 10 clones showed that the expression patterns were tissue-specific and differentially regulated during puberty. Among these, mRNAs for protein kinase C-binding Nell-homologue protein, evectin-1 and human CGI-118 protein-like gene were induced after vagina opening, and differentially expressed during the oestrous cycle. Taken together, several steroid-regulated genes identified in the present study may play an important role in regulating hypothalamic functions, including puberty and the oestrous cycle.
Active protection against PCB physical tampering (2016)

A printed circuit board (PCB) acts as the backbone of any electronic system hardware by providing mechanical support and electrical connections to its active and passive components. Traditionally, the PCB of a system has been considered trusted and robust during field operation. However, there are numerous recent reports on physical tampering of PCB in the field for malicious alteration of its functionality (e.g. adding/replacing a component through soldering, snooping a trace, and bypassing a connection). Through such alteration, an adversary can leak secret information from PCB or bypass security protection implemented in a system. This paper presents a novel approach to detect tampering in a PCB after it is deployed and to actively prevent system operation when tampering is detected. To our knowledge, this is the first report on active protection against PCB tampering in field. The proposed autonomous monitoring and prevention can enable active defense against physical tampering of electronic hardware, thus maintaining the integrity of a system against various security issues arising from such tampering.
Dielectric-loaded surface plasmon polariton waveguides on a finite-width metal strip (2010)

We investigate the guiding properties of a dielectric-loaded surface plasmon polariton waveguide on a finite-width metal strip. The guided mode is characterized by leakage radiation microscopy for different metal strip widths. We show a strong mode attenuation for metal strip widths below 1.75 μm at telecom wavelength λ=1.55 μm. We estimate the minimal width using numerical methods and propose an original interpretation. Good agreement with the measured data is achieved. The determination of this critical width is a prerequisite for designing miniaturized plasmonics devices.
Smad 3 May Regulate Follicular Growth in the Mouse Ovary1 (2002)

Although Smad 3 is known to serve as a signaling intermediate for the transforming growth factor beta (TGFbeta) family in nonreproductive tissues, its role in the ovary is unknown. Thus, we used a recently generated Smad 3-deficient (Smad 3-/-) mouse model to test the hypothesis that Smad 3 alters female fertility and regulates the growth of ovarian follicles from the primordial stage to the antral stage. In addition, we tested whether Smad 3 affects the levels of proteins that control apoptosis, survival, and proliferation in the ovarian follicle. To test this hypothesis, breeding studies were conducted using Smad 3-/- and wild-type mice. In addition, ovaries were collected from Smad 3-/- and wild-type mice on Postnatal Days 2-90. One ovary from each animal was used to estimate the total number of primordial, primary, and antral follicles. The other ovary was used for immunohistochemical analysis of selected members of the B-cell lymphoma/leukemia-2 family of protooncogenes (Bax, Bcl-2, Bcl-x), proliferating cell nuclear antigen (PCNA), and cyclin-dependent kinase 2 (Cdk-2). The results indicate that Smad 3-/- mice have reduced fertility compared with wild type mice. The results also indicate that Smad 3 may not affect the size of the primordial follicle pool at birth, but it may regulate growth of primordial follicles to the antral stage. Further, the results indicate that Smad 3 may regulate the expression of Bax and Bcl-2, but not Bcl-x, Cdk-2, and PCNA. Collectively, these data suggest that Smad 3 may play an important role in the regulation of ovarian follicle growth and female fertility.
ChemInform Abstract: Novel Renin Inhibitors Containing Analogues of Statine Retro‐Inverted at the C‐Termini: Specificity at the P2 Histidine Site. (1987)

Abstract Starting with the epoxides (I), the 1,3‐diamines (III) are prepared by reaction with sodium azide and subsequent reduction.
SHG properties of K/sub 3/Li/sub 2-x/Nb/sub 5+x/O/sub 15+2x/ single crystals grown by the micro-pulling-down method (1996)

Summary form only given. Potassium lithium niobate (K/sub 3/Li/sub 2-x/Nb/sub 5+x/O/sub 15+2x/: KLN) has been expected as a hopeful material for SHG blue laser because of its excellent features such as a large nonlinear coefficients, high optical damage resistance, and wide noncritical phase-matching characteristics at room temperature. We have studied SHG properties of /spl mu/-pulling down (PD)-grown KLN single crystals both along and perpendicular to the growth axis.
Learnable Descriptors for Visual Search (2020)

This work proposes LDVS, a learnable binary local descriptor devised for matching natural images within the MPEG CDVS framework. LDVS descriptors are learned so that they can be sign-quantized and compared using the Hamming distance. The underlying convolutional architecture enjoys a moderate parameters count for operations on mobile devices. Our experiments show that LDVS descriptors perform favorably over comparable learned binary descriptors at patch matching on two different datasets. A complete pair-wise image matching pipeline is then designed around LDVS descriptors, integrating them in the reference CDVS evaluation framework. Experiments show that LDVS descriptors outperform the compressed CDVS SIFT-like descriptors at pair-wise image matching over the challenging CDVS image dataset.
A Virtual Synchronous Generator Strategy for a Grid-Connected qZSI (2019)

In this paper, a virtual synchronous generation (VSG) strategy is proposed for a three-phase quasi-impedance source inverter (qZSI). The main objective of the scheme is to provide inertia and damping to the inverter operation in order to add those characteristics to the system in the form of ancillary services, thus contributing a more stable operation of the microgrid where the inverter is operating. The generated references are received by linear control loops on the dc and ac sides of the three-phase qZSI. In the development of this work, the theoretical foundations of the proposal are shown. Also, to prove that the strategy helps to improve the response of the system, simulated results of the qZSI connected to a weak grid are displayed, showing data of the inverter operating in a traditional form (without inertia) and as a VSG, to make comparisons.
Multi-Resolution Mixtures of Principal Components (1998)

The main contribution of this thesis is a new method of image compression based on a recently developed adaptive transform called Mixtures of Principal Components (MPC). Our multi-resolution extension of MPC-called Multi-Resolution Mixtures of Principal Components (MR-MPC) compresses and decompresses images in stages. The first stage processes the original images at very low resolution and is followed by stages that process the encoding errors of the previous stages at incrementally higher resolutions. To evaluate our multi-resolution extension of MPC we compared it with MPC and with the excellent performing wavelet based scheme called SPIHT. Fifty chest radiographs were compressed and compared to originals in two ways. First, Peak Signal to Noise Ratio (PSNR) and five distortion factors from a perceptual distortion measure called PQS were used to demonstrate that our multi-resolution extension of MPC can achieve rate distortion performance that is 220% to 720% better than MPC and much closer to that of SPIHT. And second, in a study involving 724 radiologists' evaluations of compressed chest radiographs, we found that the impact of MR-MPC and SPIHT at 25:1, 50:1, 75:1 on subjective image quality scores was less than the difference of opinion between four radiologists.
Analyzing behavioral data for improving search experience (2014)

Yandex is one of the largest internet companies in Europe, operating Russia's most popular search engine, generating 62\% of all search traffic in Russia, what means processing about 220 million queries from about 22 million users daily. Clearly, the amount and the variety of user behavioral data which we can monitor at search engines is rapidly increasing. Still, we do not always recognize its potential to help us solve the most challenging search problems and do not immediately know the ways to deal with it most effectively both for search quality evaluation and for its improvement. My talk will focus on various practical challenges arising from the need to "grok" search engine users and do something useful with the data they most generously, though almost unconsciously share with us. I will also present some answers to that by overviewing our latest research on user model based retrieval quality evaluation, implicit feedback mining and personalization. I will also summarize the experience we gained from organizing three data mining challenges at the series of workshops on using search click data (WSCD) organized in the scope of WSDM 2012 -- 2014 conferences. These challenges provided a unique opportunity to consolidate and scrutinize the work from search engines' industrial labs on analyzing behavioral data. Each year we publicly shared a fully anonymized dataset extracted from Yandex query logs and asked participants to predict editorial relevance labels of documents using search logs (in 2011), detect search engine switchings in search sessions (in 2012) and personalize web search using the long-term (user history based) and short-term (session-based) user context (in 2013).
Role of ω-hydroxylase in adenosine-mediated aortic response through MAP kinase using A2A-receptor knockout mice (2011)

Previously, we have shown that A(2A) adenosine receptor (A(2A)AR) knockout mice (KO) have increased contraction to adenosine. The signaling mechanism(s) for A(2A)AR is still not fully understood. In this study, we hypothesize that, in the absence of A(2A)AR, ω-hydroxylase (Cyp4a) induces vasoconstriction through mitogen-activated protein kinase (MAPK) via upregulation of adenosine A(1) receptor (A(1)AR) and protein kinase C (PKC). Organ bath and Western blot experiments were done using isolated aorta from A(2A)KO and corresponding wild-type (WT) mice. Isolated aortic rings from WT and A(2A)KO mice were precontracted with submaximal dose of phenylephrine (10(-6) M), and concentration responses for selective A(1)AR, A(2A)AR agonists, angiotensin II and cytochrome P-450-epoxygenase, 20-hydroxyeicosatrienoic acid (20-HETE) PKC, PKC-α, and ERK1/2 inhibitors were obtained. 2-p-(2-Carboxyethyl)-phenethylamino-5'-N-ethylcarboxamidoadenosine hydrochloride (CGS-21680, A(2A)AR agonist) induced concentration-dependent relaxation in WT, which was blocked by methylsulfonyl-propargyloxyphenylhexanamide (cytochrome P-450-epoxygenase inhibitor; 10(-5) M) and also with removal of endothelium. A(1) agonist, 2-chloro-N(6)-cyclopentyladenosine (CCPA) produced higher contraction in A(2A)KO aorta than WT (49.2 ± 8.5 vs. 27 ± 5.9% at 10(-6) M, P < 0.05). 20-HETE produced higher contraction in A(2A)KO than WT (50.6 ± 8.8 vs. 21.1 ± 3.3% at 10(-7) M, P < 0.05). Contraction to CCPA in WT and A(2A)KO aorta was inhibited by PD-98059 (p42/p44 MAPK inhibitor; 10(-6) M), chelerythrine chloride (nonselective PKC blocker; 10(-6) M), Gö-6976 (selective PKC-α inhibitor; 10(-7) M), and HET0016 (20-HETE inhibitor; 10(-5) M). Also, contraction to 20-HETE in WT and A(2A)KO aorta was inhibited by PD-98059 and Gö-6976. Western blot analysis indicated the upregulation of A(1)AR, Cyp4a, PKC-α, and phosphorylated-ERK1/2 in A(2A)KO compared with WT (P < 0.05), while expression of Cyp2c29 was significantly higher in WT. CCPA (10(-6) M) increased the protein expression of PKC-α and phosphorylated-ERK1/2, while HET0016 significantly reduced the CCPA-induced increase in expression of these proteins. These data suggest that, in the absence of A(2A)AR, Cyp4a induces vasoconstriction through MAPK via upregulation of A(1)AR and PKC-α.
AAV2/1 CD74 Gene Transfer Reduces β-amyloidosis and Improves Learning and Memory in a Mouse Model of Alzheimer's Disease (2015)

Modulation of the amyloid-β (Aβ) trafficking pathway heralds a new therapeutic frontier for Alzheimer's disease (AD). As CD74 binds to the amyloid-β precursor protein (APP) and can suppresses Aβ processing, we investigated whether recombinant adeno-associated virus (AAV) delivery of CD74 could reduce Aβ production and affect disease outcomes. This idea was tested in a mouse AD model. Cotransduction of AAV-tetracycline-controlled transactivator (tTA) and AAV-tet-response element (TRE)-CD74 resulted in CD74 expression, reduced Aβ production in mouse neurons containing the human APP with familial AD-linked mutations. Stereotaxic injection of AAV-TRE-GFP or CD74 into the hippocampi of an AD mouse, defined as a TgCRND8 × calmodulin-dependent protein kinase II derived promoter-tTA double-transgenic, reduced Aβ loads and pyramidal neuronal Aβ accumulation in the hippocampus. Immunofluorescent studies showed that APP colocalization with Lamp1 was increased in CD74-expressing neurons. Moreover, Morris water maze tasks demonstrated that mice treated with AAV-TRE-CD74 showed improved learning and memory compared to AAV-TRE-GFP control animals. These results support the idea that CD74-induced alteration of Aβ processing could improve AD-associated memory deficits as shown in mouse models of human disease.