gebhart/patrepeval huggingface dataset:
Model for the biosynthesis, transport and regulation of the non-ribosomal peptide siderophore in <i>B</i>. <i>xenovorans</i> LB400 based on bioinformatic analyses. (2016)

&lt;p&gt;A, The amino acids are modified by MbaH, MbaC and MbaE enzymes and assembled by MbaA and MbaB NRPS that synthetize the siderophore. The siderophore is exported through MbaN transporter localized in the inner membrane (IM). The siderophore binds iron(III) in the extracellular space, forming the ferrisiderophore complex. The complex is recognized by MbaD in the outer membrane (OM) and imported through the inner membrane by the MbaIJL ABC transporter. From the cytoplasmic ferrisiderophore complex the iron is released by MbaK. MbaO MFS transporter may be involved in siderophore transport, but its function is unknown. B, The transcriptional expression of the &lt;i&gt;mba&lt;/i&gt; gene cluster from &lt;i&gt;B&lt;/i&gt;. &lt;i&gt;xenovorans&lt;/i&gt; LB400 is repressed by iron. In presence of iron, dimerized Fur binds to the Fur box present in the &lt;i&gt;mbaF&lt;/i&gt; and &lt;i&gt;mbaD&lt;/i&gt; genes and prevents their transcription. In absence of iron, Fur inactivation released ECF sigma factor binding site of &lt;i&gt;mbaF&lt;/i&gt; gene, which allows the transcription of the &lt;i&gt;mbaF&lt;/i&gt; gene. MbaF factor binds to the MbaF boxes in the &lt;i&gt;mbaG&lt;/i&gt;, &lt;i&gt;mbaN&lt;/i&gt;, &lt;i&gt;mbaA&lt;/i&gt; and &lt;i&gt;mbaP&lt;/i&gt; genes promoters for their expression. The &lt;i&gt;mbaP&lt;/i&gt; gene transcription is also expressed in iron-rich condition. The LysR-type transcriptional regulator MbaP binds to the LysR binding site present in the &lt;i&gt;mbaP&lt;/i&gt; and &lt;i&gt;mbaO&lt;/i&gt; genes allowing their expression.&lt;/p&gt;
Supplementary Fig. from Decreased levels of UMP kinase as a mechanism of fluoropyrimidine resistance (2023)

Supplementary Fig. from Decreased levels of UMP kinase as a mechanism of fluoropyrimidine resistance
Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Focused Update (2018)

Purpose To update key recommendations of the American Society of Clinical Oncology/College of American Pathologists human epidermal growth factor receptor 2 (HER2) testing in breast cancer guideline. Methods Based on the signals approach, an Expert Panel reviewed published literature and research survey results on the observed frequency of less common in situ hybridization (ISH) patterns to update the recommendations. Recommendations Two recommendations addressed via correspondence in 2015 are included. First, immunohistochemistry (IHC) 2+ is defined as invasive breast cancer with weak to moderate complete membrane staining observed in > 10% of tumor cells. Second, if the initial HER2 test result in a core needle biopsy specimen of a primary breast cancer is negative, a new HER2 test may (not "must") be ordered on the excision specimen based on specific clinical criteria. The HER2 testing algorithm for breast cancer is updated to address the recommended work-up for less common clinical scenarios (approximately 5% of cases) observed when using a dual-probe ISH assay. These scenarios are described as ISH group 2 ( HER2/chromosome enumeration probe 17 [CEP17] ratio ≥ 2.0; average HER2 copy number < 4.0 signals per cell), ISH group 3 ( HER2/CEP17 ratio < 2.0; average HER2 copy number ≥ 6.0 signals per cell), and ISH group 4 ( HER2/CEP17 ratio < 2.0; average HER2 copy number ≥ 4.0 and < 6.0 signals per cell). The diagnostic approach includes more rigorous interpretation criteria for ISH and requires concomitant IHC review for dual-probe ISH groups 2 to 4 to arrive at the most accurate HER2 status designation (positive or negative) based on combined interpretation of the ISH and IHC assays. The Expert Panel recommends that laboratories using single-probe ISH assays include concomitant IHC review as part of the interpretation of all single-probe ISH assay results. Find additional information at www.asco.org/breast-cancer-guidelines .
Interleukin-1α and -1β Promoter Polymorphisms in Taiwanese Patients with Dementia (2007)

Our data suggest a protective role of the IL-1alpha -889 CT genotype in VaD susceptibility among Taiwanese aged over 70 years.
Developmentally regulated polyadenylation of two discrete messenger ribonucleic acids for müllerian inhibiting substance. (1992)

Mullerian inhibiting substance (MIS) is a 140-kilodalton homodimeric glycoprotein that causes regression of the Mullerian ducts in male embryos, and may also have a role in both males and females in the regulation of germ cell maturation. We examined the ontogeny of MIS messenger RNA (mRNA) in rat testes from midgestation through adulthood and found two discrete MIS mRNA species that are developmentally regulated. The larger 2.0-kilobase species is abundant at embryonic day 14, then decreases in late gestation, and is barely detectable after birth. The smaller 1.8-kilobase species is first noted at embryonic day 18 and is the major species detected postnatally. Both species are abundant just prior to birth, at embryonic day 21, then decrease markedly after birth. This variation in MIS mRNA levels correlates with the developmental expression of MIS protein. A series of oligonucleotide-directed ribonuclease H mapping experiments determined that the two mRNA species differ at their 3' ends in the extent of polyadenylation. Thus, differential polyadenylation of MIS mRNA may be an additional mechanism for regulating MIS expression during fetal and postnatal development.
Accurate physical compact models of high-voltage/power semiconductor devices for efficient design of performance-optimized circuits and systems (2014)

2014 International Conference on Solid State Devices and Materials,Accurate physical compact models of high-voltage/power semiconductor devices for efficient design of performance-optimized circuits and systems
Tunable two-photon pumped lasing using a holographic polymer-dispersed liquid-crystal grating as a distributed feedback element (2003)

A holographic polymer-dispersed liquid-crystal (H-PDLC) grating film was employed as an angle-dependent and narrow spectral-band feedback control element for two-photon pumped lasing in a dye solution, 4-[N-(2-hydroxyethyl)-N-(methyl)amino phenyl]-4′-(6-hydroxyhexyl sulfonyl) stilbene (APSS) in dimethyl sulphoxide. The grating film contained about 80 layers of liquid-crystal domains periodically dispersed in an ∼15 μm thick polymer film, featuring a maximum reflectance of 75% at 561 nm position with an ∼9 nm spectral bandwidth. The output lasing wavelength could be tuned from 561.5 to 548.5 nm and the lasing bandwidth changed from 5 to 3 nm when the incidence angle on the grating film varied from 0° to 22°. The overall lasing efficiency was measured to be 10%.
Essential Gene Identification and Drug Target Prioritization in Aspergillus fumigatus (2007)

Aspergillus fumigatus is the most prevalent airborne filamentous fungal pathogen in humans, causing severe and often fatal invasive infections in immunocompromised patients. Currently available antifungal drugs to treat invasive aspergillosis have limited modes of action, and few are safe and effective. To identify and prioritize antifungal drug targets, we have developed a conditional promoter replacement (CPR) strategy using the nitrogen-regulated A. fumigatus NiiA promoter (pNiiA). The gene essentiality for 35 A. fumigatus genes was directly demonstrated by this pNiiA-CPR strategy from a set of 54 genes representing broad biological functions whose orthologs are confirmed to be essential for growth in Candida albicans and Saccharomyces cerevisiae. Extending this approach, we show that the ERG11 gene family (ERG11A and ERG11B) is essential in A. fumigatus despite neither member being essential individually. In addition, we demonstrate the pNiiA-CPR strategy is suitable for in vivo phenotypic analyses, as a number of conditional mutants, including an ERG11 double mutant (erg11BDelta, pNiiA-ERG11A), failed to establish a terminal infection in an immunocompromised mouse model of systemic aspergillosis. Collectively, the pNiiA-CPR strategy enables a rapid and reliable means to directly identify, phenotypically characterize, and facilitate target-based whole cell assays to screen A. fumigatus essential genes for cognate antifungal inhibitors.
Growth of Ga x In1 − x Sb solid solution single crystals by the Czochralski method (2009)

Ga x In1 − x Sb solid solution single crystals (x = 0.03–0.09) have been grown. The dislocation density and electrophysical parameters are measured. A technique for the growth Ga x In1 − x Sb single crystals by the Czochralski method with GaSb polycrystal feed is developed. The conditions for the growth Ga0.08In0.92Sb single crystals with a more homogeneous distribution of Ga along the bulk are determined.
Adaptive Optical Wireless OFDM System with Controlled Asymmetric Clipping (2007)

Optical wireless (OW) technology is attractive for short-range high-speed transmission, especially in RF sensitive environments or where secure applications are desired. We consider transmission over a broadband OW channel, present in the non-directed line-of-sight (LOS) link. For communication, we assume a system concept based on a modulation-adaptive OFDM (DMT). Such system offers efficient channel capacity exploitation, while avoiding inconvenient pointing and tracking mechanisms. Moreover, it allows deployment of simple optical components and efficient electrical signal processing. We first show that the dynamically adaptive system can provide great transmission rate enhancements compared to the statically designed one, even assuming a very conservative constraint on the electrical signal waveform (i.e., no clipping). Then, we show that significant further improvements can be achieved by tolerating some clipping, at the cost of accepting a minor increase of the symbol error rate.
CRANIAL MIGRATION OF A BACLOFEN PUMP CATHETER ASSOCIATED WITH SUBARACHNOID HEMORRHAGE (2009)

Cephalad catheter migration is a rare phenomenon. The mechanism of rostral migration remains unclear. The forces that propel a free fragment of catheter under these circumstances seem to be sufficient to cause a small vessel to rupture and bleed. Given the lack of an observed arterial injury, we postulate that venous bleeding caused this hemorrhage.
Aggregated and Monomeric α-Synuclein Bind to the S6′ Proteasomal Protein and Inhibit Proteasomal Function (2003)

The accumulation of aggregated alpha-synuclein is thought to contribute to the pathophysiology of Parkinson's disease, but the mechanism of toxicity is poorly understood. Recent studies suggest that aggregated proteins cause toxicity by inhibiting the ubiquitin-dependent proteasomal system. In the present study, we explore how alpha-synuclein interacts with the proteasome. The proteasome exists as a 26 S and a 20 S species. The 26 S proteasome is composed of the 19 S cap and the 20 S core. Aggregated alpha-synuclein strongly inhibited the function of the 26 S proteasome. The IC(50) of aggregated alpha-synuclein for ubiquitin-independent 26 S proteasomal activity was 1 nm. Aggregated alpha-synuclein also inhibited 26 S ubiquitin-dependent proteasomal activity at a dose of 500 nm. In contrast, the IC(50) of aggregated alpha-synuclein for 20 S proteasomal activity was > 1 microm. This suggests that aggregated alpha-synuclein selectively interacts with the 19 S cap. Monomeric alpha-synuclein also inhibited proteasomal activity but with lower affinity and less potency. Recombinant monomeric alpha-synuclein inhibited the activity of the 20 S proteasomal core with an IC(50) > 10 microm, exhibited no inhibition of 26 S ubiquitin-dependent proteasomal activity at doses up to 5 microm, and exhibited only partial inhibition (50%) of the 26 S ubiquitin-independent proteasomal activity at doses up to 10 mm. Binding studies demonstrate that both aggregated and monomeric alpha-synuclein selectively bind to the proteasomal protein S6', a subunit of the 19 S cap. These studies suggest that proteasomal inhibition by aggregated alpha-synuclein could be mediated by interaction with S6'.
Energy Harvesting Based On Printed Organic Photovoltaic Cells for RFID Applications (2019)

This work discusses the possibility of using printed organic photovoltaic cells in order to increase the performance of UHF RFID sensor tags. As a proof of concept, an organic photovoltaic (OPV) cell was used to power the chip SL900A that incorporates a sensor front-end interface capable of measuring voltages, currents, resistances, and capacitances. Several read range measurements were realized using other types of power sources and compared to OPV. Results based on the OPV cell showed a significant enhancement in the tag read range (up to 80%) under low light conditions which opens the door for several IoT applications.
Laboratory- and community-based health outcomes in people with transtibial amputation using crossover and energy-storing prosthetic feet: A randomized crossover trial (2018)

ClinicalTrials.gov NCT02440711.
New CMOS compatible junction-isolatedlateral base resistance controlled thyristor (1994)

A new 550V lateral base resistance controlled thyristor structure is proposed and its operation is rigorously characterised by two-dimensional numerical simulation in the off-state, on-state, and turn-off transient mode. Simulations indicate a 40% lower forward voltage drop over a comparable LIGBT, and a superior switching property over other competing lateral thyristor structures.
Efficient two-level mesh based simulation of PRAMS (2002)

We consider time-processor optimal simulations of PRAM models on coated block meshes. A coated block mesh consists of n-processor blocks and /spl pi//spl times//spl pi/ or /spl radic/(/spl pi/)/spl times//spl radic/(/spl pi/)/spl times//spl radic/(/spl pi/) router blocks. The router blocks form a 2-dimensional or a 3-dimensional regular mesh, and the processor and memory blocks are located on the surface of the block mesh. As a generalization of the coated mesh, the 2-dimensional and 3-dimensional coated block meshes simulate EREW, CREW, and CRCW PRAM models time-processor optimally with moderate simulation cost. Using proper amount of parallel slackness, the cost can be decreased clearly below 2 routing steps per simulated PRAM processor. The coated block mesh is actually an instance of a more general two-level construction technique, which uses a seemingly inefficient but scalable solution on top of a non-scalable but efficient solution. Within blocks (chips) brute force techniques are applied, whereas the mesh structure on top makes the whole construction modular, simple, and scalable. The parameter /spl pi/ provides a method to balance the construction with respect to the two techniques. Keywords: PRAM, shared memory machine, simulation, time-processor optimal, mesh, interconnection network.
SARM1 deficiency promotes rod and cone photoreceptor cell survival in a model of retinal degeneration (2020)

Retinal degeneration is the leading cause of incurable blindness worldwide and is characterised by progressive loss of light-sensing photoreceptors in the neural retina. SARM1 is known for its role in axonal degeneration, but a role for SARM1 in photoreceptor cell degeneration has not been reported. SARM1 is known to mediate neuronal cell degeneration through depletion of essential metabolite NAD and induction of energy crisis. Here, we demonstrate that SARM1 is expressed in photoreceptors, and using retinal tissue explant, we confirm that activation of SARM1 causes destruction of NAD pools in the photoreceptor layer. Through generation of <i>rho</i> <sup><i>-/-</i></sup> <i>sarm1</i> <sup><i>-/-</i></sup> double knockout mice, we demonstrate that genetic deletion of SARM1 promotes both rod and cone photoreceptor cell survival in the rhodopsin knockout (<i>rho</i> <sup><i>-/-</i></sup> ) mouse model of photoreceptor degeneration. Finally, we demonstrate that SARM1 deficiency preserves cone visual function in the surviving photoreceptors when assayed by electroretinography. Overall, our data indicate that endogenous SARM1 has the capacity to consume NAD in photoreceptor cells and identifies a previously unappreciated role for SARM1-dependent cell death in photoreceptor cell degeneration.
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health (2021)

We describe the anaerobic conversion of inositol stereoisomers to propionate and acetate by the abundant intestinal genus Anaerostipes. A inositol pathway was elucidated by nuclear magnetic resonance using [<sup>13</sup>C]-inositols, mass spectrometry and proteogenomic analyses in A. rhamnosivorans, identifying 3-oxoacid CoA transferase as a key enzyme involved in both 3-oxopropionyl-CoA and propionate formation. This pathway also allowed conversion of phytate-derived inositol into propionate as shown with [<sup>13</sup>C]-phytate in fecal samples amended with A. rhamnosivorans. Metabolic and (meta)genomic analyses explained the adaptation of Anaerostipes spp. to inositol-containing substrates and identified a propionate-production gene cluster to be inversely associated with metabolic biomarkers in (pre)diabetes cohorts. Co-administration of myo-inositol with live A. rhamnosivorans in western-diet fed mice reduced fasting-glucose levels comparing to heat-killed A. rhamnosivorans after 6-weeks treatment. Altogether, these data suggest a potential beneficial role for intestinal Anaerostipes spp. in promoting host health.
User-Centric Interference Nulling in Downlink Multi-Antenna Heterogeneous Networks (2015)

Heterogeneous networks (HetNets) have strong interference due to spectrum reuse. This affects the signal-to-interference ratio (SIR) of each user, and hence is one of the limiting factors of network performance. However, in previous works, interference management approaches in HetNets are mainly based on interference level, and thus cannot effectively utilize the limited resource to improve network performance. In this paper, we propose a user-centric interference nulling (IN) scheme in downlink two-tier HetNets to improve network performance by improving each user's SIR. This scheme has three design parameters: the maximum degree of freedom for IN (IN DoF), and the IN thresholds for the macro and pico users, respectively. Using tools from stochastic geometry, we first obtain a tractable expression of the coverage (equivalently outage) probability. Then, we characterize the asymptotic behavior of the outage probability in the high reliability regime. The asymptotic results show that the maximum IN DoF can affect the order gain of the asymptotic outage probability, while the IN thresholds only affect the coefficient of the asymptotic outage probability. Moreover, we show that the IN scheme can linearly improve the outage performance, and characterize the optimal maximum IN DoF which minimizes the asymptotic outage probability.
Effect of N-Desalkylquetiapine/Quetiapine Plasma Level Ratio on Anxiety and Depression in Bipolar Disoder: A Prospective Observational Study (2017)

Our findings confirm the efficacy of quetiapine on depressive symptoms, and the available data support that quetiapine's antidepressant activity is mediated by the active metabolite norquetiapine, and it exemplifies the case of an active metabolite that can make a drug like quetiapine originally introduced as an antipsychotic a useful antidepressant agent.
Figure S1 from Kindlin-2 Regulates the Growth of Breast Cancer Tumors by Activating CSF-1–Mediated Macrophage Infiltration (2023)

&lt;p&gt;This figure contains tumor staining with individual markers to support Figure 3F and Figure 3I&lt;/p&gt;
An Enantiospecific Polyene Cyclization Initiated by an Enantiomerically Pure Bromonium Ion (2013)

Dimethylaluminum triflate-mediated activation of tetrafluorobenzoates of enantiomerically pure bromohydrins results in enantiospecific polyene cyclizations. The initiation of cyclization by enantiomerically pure bromonium ions and subsequent propagation is not subject to catastrophic erosion of enantiomeric purity by any intramolecular or intermolecular bromonium ion-to-alkene transfer.
Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study (2011)

This study suggests that the exposure of estrogens to hPR A as well as hPR B, and more particularly to hPR A alone, is a risk factor for breast cancer.
Acoustic Effect And The Polarization Of Adjacent Bits In Soliton Communication Lines (1993)

One of the main mechanisms that limits the bit rate and transmission distance in soliton communication lines is the so called “long-range” interaction of solitons [1]. The physical reason of this interaction is the electrostrictional excitation of the acoustic waves by light pulses and back-influence of the acoustic wave on solitons [2]. In soliton communication lines the interaction of solitons with the acoustic wave results in the additional to the Gordon-Haus effect [3] timing jitter of solitons [4,5]. Although the timing jitter of solitons can be significantly reduced by guiding filters [6], the detailed investigation of the acoustic effect is still important because the guiding filters cannot totally suppress the timing jitter.
Manufacture of high-performance fiber Bragg for dispersion compensation (2004)

Significant progress has been achieved in the manufacture of chirped fiber Bragg gratings for dispersion compensation. Iterative correction technique further improves their quality and enables consistent fabrication of gratings with unprecedented performance.
Trapping in 1nm EOT high-k / MG (2008)

PFET's with EOT ~1 nm shows a large hysteresis at high field in the Id-Vg characteristics, while nothing is sensed for nmos devices. An advanced charge pumping technique proves that this hysteresis in pmos is caused by hole traps in the high-k. Furthermore, we show how NBTI defects are affected correlated with such hole traps. We will demonstrate how optimization of the nitridation process can strongly reduce the hole trap density. Phase separation in the HfSiON can be detected by this simple hole trap measurements.
ChemInform Abstract: Stereochemistry of Phenylpiracetam and Its Methyl Derivative: Improvement of the Pharmacological Profile (2015)

Abstract Review: 29 refs.
DNA Repair and Free Radicals, New Insights into the Mechanism of Spore Photoproduct Lyase Revealed by Single Amino Acid Substitution (2008)

The major DNA photoproduct in UV-irradiated Bacillus subtilis spores is the thymine dimer named spore photoproduct (SP, 5-(alpha-thyminyl)-5,6-dihydrothymine). The SP lesion has been found to be efficiently repaired by SP lyase (SPL) a very specific enzyme that reverses the SP to two intact thymines, at the origin of the great resistance of the spores to UV irradiation. SPL belongs to a superfamily of [4Fe-4S] iron-sulfur enzymes, called "Radical-SAM." Here, we show that the single substitution of cysteine 141 into alanine, a residue fully conserved in Bacillus species and previously shown to be essential for spore DNA repair in vivo, has a major impact on the outcome of the SPL-dependent repair reaction in vitro. Indeed the modified enzyme catalyzes the almost quantitative conversion of the SP lesion into one thymine and one thymine sulfinic acid derivative. This compound results from the trapping of the allyl-type radical intermediate by dithionite, used as reducing agent in the reaction mixture. Implications of the data reported here regarding the repair mechanism and the role of Cys-141 are discussed.
ChemInform Abstract: Palladium‐Promoted Synthesis of Ionophore Antibiotics. Strategy and Assembly of the Homochiral Tetrahydrofuran and Tetrahydropyran Portions of Tetronomycin. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.