gebhart/patrepeval huggingface dataset:
tRNA genes rapidly change in evolution to meet novel translational demands (2013)

Changes in expression patterns may occur when organisms are presented with new environmental challenges, for example following migration or genetic changes. To elucidate the mechanisms by which the translational machinery adapts to such changes, we perturbed the tRNA pool of Saccharomyces cerevisiae by tRNA gene deletion. We then evolved the deletion strain and observed that the genetic adaptation was recurrently based on a strategic mutation that changed the anticodon of other tRNA genes to match that of the deleted one. Strikingly, a systematic search in hundreds of genomes revealed that anticodon mutations occur throughout the tree of life. We further show that the evolution of the tRNA pool also depends on the need to properly couple translation to protein folding. Together, our observations shed light on the evolution of the tRNA pool, demonstrating that mutation in the anticodons of tRNA genes is a common adaptive mechanism when meeting new translational demands. DOI: http://dx.doi.org/10.7554/eLife.01339.001.
Amplification of the MLL gene on double minutes, a homogeneously staining region, and ring chromosomes in five patients with acute myeloid leukemia or myelodysplastic syndrome (2000)

Gene amplification is one of the mechanisms for activating proto-oncogenes resulting in an enhanced expression of the corresponding gene product. By fluorescence in situ hybridization (FISH), amplification of the proto-oncogene MLL has been described only in seven patients with acute myeloid leukemia (AML). We report five new patients (four had de novo AML, one had a de novo myelodysplastic syndrome) displaying different mechanisms of MLL amplification, suspected by G-banding and confirmed by FISH analysis. In two patients, MLL was amplified on double-minute chromosomes (dmins). In both cases, an interstitial deletion in 11q23 including the MLL gene was associated with the occurrence of the dmins containing MLL. As a rarely described mechanism, MLL amplification in the form of size-variable ring chromosomes was observed in two patients. Remodeling of the ring chromosomes leads to multiple copies of MLL and obviously provided a selective growth advantage. In one of the two cases with ring chromosomes, the centromeric α-satellite DNA of the ring chromosome was not detectable. Our fifth patient showed the unique finding of MLL amplification within a uniformly (homogeneously?) stained region in interaction with amplified ribosomal DNA sequences. Also, one of the patients with ring chromosomes exhibited the amplification of ribosomal DNA on the ring chromosomes. The transcriptionally active genes for ribosomal RNA could probably enhance the expression of MLL. In one of our five patients, we found the new combination of concomitant amplification of the proto-oncogenes MLL and MYC. Genes Chromosomes Cancer 27:380–386, 2000. © 2000 Wiley-Liss, Inc.
Gincosan (A Combination of Ginkgo biloba and Panax ginseng ): The Effects on Mood and Cognition of 6 and 12 Weeks' Treatment in Post-menopausal Women (2004)

As memory and concentration impairments are a frequent complaint in post-menopausal women, this well-defined population was selected to investigate the effect on mood and cognition of chronic treatment with Gincosan. In a double-blind placebo controlled study, post-menopausal women aged 51-66 were randomly assigned to 12 weeks' treatment with Gincosan (320mg/day), containing 120mg Ginkgo biloba, and 200mg Panax ginseng (n = 30), or matched placebo (n = 27). They were given measurements of mood, somatic anxiety, sleepiness, and menopausal symptoms and a battery of cognitive tests before treatment and after 6 and 12 weeks of treatment. There were no significant effects of Gincosan treatment on ratings of mood, bodily symptoms of somatic anxiety, menopausal symptoms, or sleepiness or on any of the cognitive measures of attention, memory or frontal lobe function. Thus, after chronic administration, Gincosan appeared to have no beneficial effects in post-menopausal women.
‘Big issues’ in neurodevelopment for children and adults with congenital heart disease (2019)

It is established that neurodevelopmental disability (NDD) is common in neonates undergoing complex surgery for congenital heart disease (CHD); however, the trajectory of disability over the lifetime of individuals with CHD is unknown. Several 'big issues' remain undetermined and further research is needed in order to optimise patient care and service delivery, to assess the efficacy of intervention strategies and to promote best outcomes in individuals of all ages with CHD. This review article discusses 'gaps' in our knowledge of NDD in CHD and proposes future directions.
Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism (2014)

Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multidrug-resistant tuberculosis in decades. Though BDQ has shown excellent efficacy in clinical trials, its early bactericidal activity during the first week of chemotherapy is minimal. Here, using microfluidic devices and time-lapse microscopy of Mycobacterium tuberculosis, we confirm the absence of significant bacteriolytic activity during the first 3-4 days of exposure to BDQ. BDQ-induced inhibition of ATP synthesis leads to bacteriostasis within hours after drug addition. Transcriptional and proteomic analyses reveal that M. tuberculosis responds to BDQ by induction of the dormancy regulon and activation of ATP-generating pathways, thereby maintaining bacterial viability during initial drug exposure. BDQ-induced bacterial killing is significantly enhanced when the mycobacteria are grown on non-fermentable energy sources such as lipids (impeding ATP synthesis via glycolysis). Our results show that BDQ exposure triggers a metabolic remodelling in mycobacteria, thereby enabling transient bacterial survival.
Antimicrobial stewardship programs in adult intensive care units in Latin America: Implementation, assessments, and impact on outcomes (2021)

MS-ICUs with more comprehensive ASPs showed significant improvement in antimicrobial utilization.
Predicting the optimal position and direction of a ubiquitous ECG using a multi-scale model of cardiac electrophysiology (2011)

In this study, we determined the optimal position and direction of a one-channel bipolar electrocardiogram (ECG), used ubiquitously in healthcare. To do this, we developed a three-dimensional (3D) electrophysiological model of the heart coupled with a torso model that can generate a virtual body surface potential map (BSPM). Finite element models of the atria and ventricles incorporated the electrophysiological dynamics of atrial and ventricular myocytes, respectively. The torso model, in which the electric wave pattern on the cardiac tissue is reflected onto the body surface, was implemented using a boundary element method. Using the model, we derived the optimal positions of two electrodes, 5 cm apart, of the bipolar ubiquitous ECG (U-ECG) for detecting the P, R, and T waves. This model can be used as a simulation tool to design U-ECG device for use for various arrhythmia and normal patients.
A 23-watt single-frequency vertical-external-cavity surface-emitting laser (2014)

We report on a single-frequency semiconductor disk laser which generates 23.6 W output power in continuous wave operation, at a wavelength of 1013 nm. The high output power is a result of optimizing the chip design, thermal management and the cavity configuration. By applying passive stabilization techniques, the free-running linewidth is measured to be 407 kHz for a sampling time of 1 ms, while undercutting 100 kHz in the microsecond domain.
First templates of human brain kurtosis sources: relevance of microscopic kurtosis from Correlation Tensor MRI at 3 Tesla (2023)

The Correlation Tensor MRI (CTI) framework has been recently formulated to disentangle anisotropic, isotropic, and microscopic kurtosis sources without a priori assumptions from Double-Diffusion-Encoding (DDE) data. In this work, group average maps (templates) are presented for the first time, thereby mapping the contrasts for anisotropic and isotropic kurtosis, and non-vanishing positive microscopic kurtosis in grey and white matter. The relative weight of the microscopic kurtosis within the total kurtosis, and the bias associated with neglecting this component under the Multiple Gaussian Component assumption are investigated and suggest that this component significantly contributes to the total diffusional kurtosis.
FPGA based stereo imaging system with applications in computer gaming (2009)

A real-time stereo imaging system is described. It incorporates dual image acquisition chains on a single FPGA device and is able to provide real-time synchronized video output from twin CMOS imaging sensors. The platform is designed to provide hardware support for future implementations of advanced face analysis algorithms. In the context of computer gaming applications this system can provide real-time capture of a game players facial actions and expressions serving as an enabling technology for next generation gaming. Potential applications include (i) generating 3D real-time responsive game avatars and (ii) employing real-time face data for next-generation game UI.
Efficacy of a prehospital self-expanding polyurethane foam for noncompressible hemorrhage under extreme operational conditions (2015)

Under a range of military operational conditions, foam treatment resulted in a survival advantage relative to the control group. This supports the feasibility of foam treatment as a prehospital hemostatic bridge to surgery for severely bleeding causalities.
Using self‐synthesized aminopropyl‐terminated polydimethylsiloxane to toughen epoxy resin: The role of molecular weight of polydimethylsiloxane (2015)

Aminopropyl‐terminated polydimethylsiloxane (APDMS) with different molecular weights ( ) were synthesized by 1,3‐ bis (3‐aminopropyl)‐1,1,3,3‐tetramethyldisiloxane (BADS) and dimethylcyclosiloxane ( D n ). Fourier‐transform infrared shows the increase in APDMS and the decrease in NH 2 content in the products with the increasing ratio of D n /BADS. 1 H NMR further confirmed the conclusion obtained by Fourier‐transform infrared spectra, and the APDMS resulted from 1 H NMR were 1,106 (APDMS1), 1,987 (APDMS2), 2,690 (APDMS3), and 4,313 (APDMS4) g/mol. These APDMS were then blended with the epoxy resin (diglycidyl ether of bisphenol A) system to improve its toughness. Mechanical tests revealed that the impact strength of the epoxy resin was improved by APDMS1 and APDMS2, which has lower . The toughening effect decreased when APDMS4 was used. It was suggested that the APDMS with high was easier to agglomerate, which in turn resulted in lower toughening efficiency. This was also confirmed by scanning electron microscopy results. J. VINYL ADDIT. TECHNOL., 23:305–311, 2017. © 2015 Society of Plastics Engineers
Different contributions of chemokine N‐terminal features attest to a different ligand binding mode and a bias towards activation of ACKR3/CXCR7 compared with CXCR4 and CXCR3 (2017)

These results suggest a different interaction mechanism between this atypical receptor and its ligands and illustrate its strong propensity to activation.
Learning from the 2009 H1N1 pandemic: prospects for more broadly effective influenza vaccines (2011)

Calls to develop a universal influenza vaccine have increased in the wake of the 2009 H1N1 influenza pandemic. This demand comes at a time when analyses of the human antibody repertoire, informed by structures of complexes between broadly neutralizing antibodies and influenza hemagglutinin, have revealed the target of a class of broadly neutralizing antibodies. Recent studies suggest a path forward to more broadly protective influenza vaccines.
Deadbeat-Direct Torque and Flux Control of Interior Permanent Magnet Synchronous Machines With Discrete Time Stator Current and Stator Flux Linkage Observer (2011)

This paper presents a discrete time deadbeat-direct torque and flux controller (DB-DTFC) for interior permanent magnet synchronous machines (IPMSMs). A Gopinath-style discrete time flux linkage observer is developed which contains two different flux estimation methods based on current and voltage models for flux linkage. This observer produces correctly estimated flux linkages needed for accurate DB-DTFC implementation. In order to eliminate the sampling delay due to a characteristic of digital control computation, a complex vector model-based rotor reference frame current observer is also developed. Combining the discrete time current and flux linkage observers, the correct single time step (deadbeat) air-gap torque and stator flux linkage control at the (constant) switching frequency is achieved and experimentally evaluated.
<title>Visual surveillance of human activity</title> (1998)

W<SUP>4</SUP> is a real time visual surveillance system for detecting and tracking people and monitoring their activities in an outdoor environment. It operates on monocular grayscale video imagery, or on video imagery from an IR camera.Unlike many of systems for tracking people, W<SUP>4</SUP> makes no use of color cues. Instead, W<SUP>4</SUP> employs a combination of shape analysis and tracking to create models of people's appearance so that they can be tracked through interactions such as occlusions. W<SUP>4</SUP> is capable of simultaneously tracking multiple people even with occlusion. It runs at 20 Hz for 320 X 240 resolution images on a dual-pentium 200 PC.
Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162 (2021)

Wild-type human glutathione peroxidase 4 (GPX4) was co-expressed with SBP2 (selenocysteine insertion sequence-binding protein 2) in human HEK cells to achieve efficient production of this selenocysteine-containing enzyme on a preparative scale for structural biology. The protein was purified and crystallized, and the crystal structure of the wild-type form of GPX4 was determined at 1.0 Å resolution. The overall fold and the active site are conserved compared with previously determined crystal structures of mutated forms of GPX4. A mass-spectrometry-based approach was developed to monitor the reaction of the active-site selenocysteine Sec46 with covalent inhibitors. This, together with the introduction of a surface mutant (Cys66Ser), enabled the crystal structure determination of GPX4 in complex with the covalent inhibitor ML162 [(S)-enantiomer]. The mass-spectrometry-based approach described here opens the path to further co-complex crystal structures of this potential cancer drug target in complex with covalent inhibitors.
A role for leucine in regulation of protein turnover in working rat hearts (1980)

Effect of leucine on protein turnover was examined in perfused hearts provided with 1 (0.2 mM) or 5 times (1 mM) plasma levels of leucine and normal plasma levels of other amino acids. When hearts were perfused as Langendorff or working preparations with buffer that contained 15 mM glucose, protein degradation was 2-3 times faster than protein synthesis. As a result, the heart was in marked negative nitrogen balance. Addition of 1 mM leucine significantly improved the nitrogen balance (24-33%) by stimulating protein synthesis in Langendorff preparations (25%) and inhibiting protein degradation in both preparations (14-29%). The stimulatory effect of leucine on protein synthesis was associated with a reduction in levels of ribosomal subunits. In hearts supplied physiological levels of glucose, lactate, beta-hydroxybutyrate, insulin, and glucagon, protein synthesis was more nearly equal to protein degradation. Provision of 1 mM leucine stimulated protein synthesis only in Langendorff preparations (32%) but did not have a significant effect on protein degradation in either preparation. Although leucine did not have a significant effect on either protein synthesis or degradation in working hearts, nitrogen balance became positive with addition of 1 mM leucine. These results suggest that leucine may exert an effect on myocardial nitrogen balance in vivo under conditions that elevate plasma leucine concentrations.
Non-vanishing Berry curvature driven large anomalous Hall effect in non-collinear antiferromagnet Mn3Ge (2015)

It has been established that the anomalous Hall effect roughly scales with the magnetization of a ferromagnet.Therefore, it should disappear for an antiferromagnet due to its zero net magnetic moment. However, recent theoretical works have predicted that a large anomalous Hall effect can be accomplished in some of the non-collinear antiferromagnets resulting from a non-vanishing Berry-phase curvature. Here we show that the non-collinear antiferromagnet Mn3Ge with practically zero net magnetic moment exhibits a large anomalous Hall effect comparable to that of ferromagnetic metals, the magnitude of the anomalous conductivity is 500 per Ohm per cm at 2 K and about 50 per Ohm per cm at at room temperature. The inverse triangular spin-alignment in Mn3Ge ensures a non-vanishing Berry curvature, leading to the observed effect.
A Convergent Approach to 1,3-Dithiolan-2-ones and an Unexpected Synthesis of Lactones (2022)

A convergent route to 1,3-dithiolan-2-ones based on the radical addition of xanthates to allylic acetates is described. The process is modular, uses inexpensive starting materials and reagents, and is atom economical, since both sulfur atoms of the xanthate end up in the products. With adducts derived from xanthates bearing an ester group, an unexpected transformation leading to lactones was uncovered.
Perceptron Learning in Optical Neural Computers (2020)

A neural computer consists of simple nonlinear processing units, “neurons”, and a large number of linear interconnections between neurons. In implementing a neural computer it is necessary to provide sufficient interconnections and neurons to address the problems to which the network will be applied and to allow for modification of the interconnections in order to search for the interconnection pattern which implements a desired transformation. Optical holography is well suited to implementations of neural computers since it can provide a large number of interconnections relatively simply. The perceptron is an example of a supervised adaptive neural model which can be implemented using photorefractive crystals. The rudimentary perceptron algorithm is interesting because it relies directly on the dynamics of the photorefractive response. Since the dimension of the input can be fairly large, this algorithm may be of use in certain applications.
Pulmonary Safety and Tolerability of Inhaled Levodopa (CVT-301) Administered to Patients with Parkinson's Disease (2017)

Acute and longitudinal assessment of pulmonary function showed that CVT-301 treatment was not associated with acute airflow obstruction in this population. CVT-301 was generally safe and well tolerated.
Wake on wireless (2002)

The demand for an all-in-one phone with integrated personal information management and data access capabilities is beginning to accelerate. While personal digital assistants (PDAs) with built-in cellular, WiFi, and Voice-Over-IP technologies have the ability to serve these needs in a single package, the rate at which energy is consumed by PDA-based phones is very high. Thus, these devices can quickly drain their own batteries and become useless to their owner.In this paper, we introduce a technique to increase the battery lifetime of a PDA-based phone by reducing its idle power, the power a device consumes in a "standby" state. To reduce the idle power, we essentially shut down the device and its wireless network card when the device is not being used---the device is powered only when an incoming call is received. Using this technique, we can increase the battery lifetime by up to 115%.In this paper, we describe the design of our "wake-on-wireless" energy-saving strategy and the prototype device we implemented. To evaluate our technique, we compare it with alternative approaches. Our results show that our technique can provide a significant lifetime improvement over other technologies.
Acceleration of ML iterative algorithms for CT by the use of fast start images (2012)

This report develops a new strategy for the acceleration of a maximum likelihood (ML) iterative reconstruction algorithm for CT, by selecting a starting image which is closer to the solution of the ML algorithm than the commonly used filtered backprojection image. The starting image is obtained by passing both the acquired projection data and the reconstructed volume though a novel de-noising algorithm which uses the same image penalty function as the ML reconstruction. Clinical examples suggest that a savings of 5-10 iterations of the separable paraboloidal surrogates algorithm per volume is possible when using this new acceleration strategy.
Augmentation of Muscle Blood Flow by Ultrasound Cavitation Is Mediated by ATP and Purinergic Signaling (2017)

URL: http://clinicaltrials.gov. Unique identifier: NCT01566890.
Electrochemical Investigations of Novel Solid Redox Polymerization Electrodes (1989)

Electrochemical investigations of a group of novel solid redox polymerization electrodes, recently discovered in our laboratory, indicate that these materials are excellent candidates for all-solid-state, thin-film, energy-storage systems.Some of the advantages offered by the batteries based on these solid cathodes include high energy density and rate capability, extensive utilization of cathode capacity, ease of fabrication, low cost, and superior reliability and safety.In addition, these materials are .reversible to lithium and sodium (as well as many alkaline earth and transition metals), allowing for a much greater choice of anode materials, in stark contrast to cells based on analogous intercalation compounds.Further, and in particular, a great advantage of redox polymerization electrodes is the ability to alter the physical, chemical, and electrochemical properties of these materials in a very predictable manner through manipulation of various functional groups, electron-withdrawing heteroatoms, and the molecular architecture.
Medicinal Chemistry and Pharmacology of Cyclic ADP‐Ribose (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Data from Tumor Subtype-Specific Cancer–Testis Antigens as Potential Biomarkers and Immunotherapeutic Targets for Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;Cancer–testis (CT) antigens are potential targets for cancer immunotherapy because of their restricted expression in immune-privileged germ cells and various malignancies. Current application of CT-based immunotherapy has been focused on CT expression–rich tumors such as melanoma and lung cancers. In this study, we surveyed CT expression using The Cancer Genome Atlas (TCGA) datasets for ten common cancer types. We show that CT expression is specific and enriched within certain cancer molecular subtypes. For example, &lt;i&gt;HORMAD1, CXorf61, ACTL8&lt;/i&gt;, and &lt;i&gt;PRAME&lt;/i&gt; are highly enriched in the basal subtype of breast cancer; &lt;i&gt;MAGE&lt;/i&gt; and &lt;i&gt;CSAG&lt;/i&gt; are most frequently activated in the magnoid subtype of lung adenocarcinoma; and &lt;i&gt;PRAME&lt;/i&gt; is highly upregulated in the ccB subtype of clear cell renal cell carcinoma. Analysis of CT gene expression and DNA methylation indicates that some CTs are regulated epigenetically, whereas others are controlled primarily by tissue- and subtype-specific transcription factors. Our results suggest that although for some CT expression is associated with patient outcome, not many are independent prognostic markers. Thus, CTs with shared expression pattern are heterogeneous molecules with distinct activation modes and functional properties in different cancers and cancer subtypes. These data suggest a cancer subtype–orientated application of CT antigen as biomarkers and immunotherapeutic targets. &lt;i&gt;Cancer Immunol Res; 2(4); 371–9. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;