gebhart/patrepeval huggingface dataset:
Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes. (1988)

Three group I introns of bacteriophage T4 have been compared with respect to their sequence and structural properties. The introns include the td intervening sequence, as well as the two newly described introns in the nrdB and sunY genes of T4. The T4 introns are very closely related, containing phylogenetically conserved sequence elements that allow them to be folded into a core structure that is characteristic of eukaryotic group IA introns. Similarities extend outward to the exon sequences surrounding the three introns. All three introns contain open reading frames (ORFs). Although the intron ORFs are not homologous and occur at different positions, all three ORFs are looped-out of the structure models, with only the 3' ends of each of the ORFs extending into the secondary structure. This arrangement invites interesting speculations on the regulation of splicing by translation. The high degree of similarity between the T4 introns and the eukaryotic group I introns must reflect a common ancestry, resulting either from vertical acquisition of a primordial RNA element or from horizontal transfer.
Modal tomography for adaptive optics (1999)

Multiple Laser Guide Stars can be used to retrieve the three-dimensional distribution of the perturbing layers on the coming wavefront in Adaptive Optics system and to derive corrections for conical anisoplanatism. We outline the basic an- alytical details of a modal approach to this problem. The ad- vantages of this approach with respect to the traditional zonal one are pointed out along with a preliminary discussion of the way the involved matrices are to be treated in order to minimize noise propagation problems.
Surface enhanced Raman scattering (SERS) of citrate ion adsorbed on colloidal silver (1980)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Kerker, O. Siiman, L. A. Bumm, and D.-S. Wang, "Surface enhanced Raman scattering (SERS) of citrate ion adsorbed on colloidal silver," Appl. Opt. 19, 3253-3255 (1980) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A hybrid strategy of offline adaptive planning and online image guidance for prostate cancer radiotherapy (2010)

Offline adaptive radiotherapy (ART) has been used to effectively correct and compensate for prostate motion and reduce the required margin. The efficacy depends on the characteristics of the patient setup error and interfraction motion through the whole treatment; specifically, systematic errors are corrected and random errors are compensated for through the margins. In online image-guided radiation therapy (IGRT) of prostate cancer, the translational setup error and inter-fractional prostate motion are corrected through pre-treatment imaging and couch correction at each fraction. However, the rotation and deformation of the target are not corrected and only accounted for with margins in treatment planning. The purpose of this study was to investigate whether the offline ART strategy is necessary for an online IGRT protocol and to evaluate the benefit of the hybrid strategy. First, to investigate the rationale of the hybrid strategy, 592 cone-beam-computed tomography (CBCT) images taken before and after each fraction for an online IGRT protocol from 16 patients were analyzed. Specifically, the characteristics of prostate rotation were analyzed. It was found that there exist systematic inter-fractional prostate rotations, and they are patient specific. These rotations, if not corrected, are persistent through the treatment fraction, and rotations detected in early fractions are representative of those in later fractions. These findings suggest that the offline adaptive replanning strategy is beneficial to the online IGRT protocol with further margin reductions. Second, to quantitatively evaluate the benefit of the hybrid strategy, 412 repeated helical CT scans from 25 patients during the course of treatment were included in the replanning study. Both low-risk patients (LRP, clinical target volume, CTV = prostate) and intermediate-risk patients (IRP, CTV = prostate + seminal vesicles) were included in the simulation. The contours of prostate and seminal vesicles were delineated on each CT. The benefit of margin reduction to compensate for both rotation and deformation in the hybrid strategy was evaluated geometrically. With the hybrid strategy, the planning margins can be reduced by 1.4 mm for LRP, and 2.0 mm for IRP, compared with the standard online IGRT only, to maintain the same 99% target volume coverage. The average relative reduction in planning target volume (PTV) based on the internal target volume (ITV) from PTV based on CTV is 19% for LRP, and 27% for IRP.
Umbilical cord blood progenitor cell transplantation. The International Conference Workshop on Cord Blood Transplantation, Indianapolis, November 1993. (1994)

Haemopoietic progenitor cells are present in umbilical cord blood (UCB) and have been used to restore haemopoiesis in children after myeloablative therapy. UCB may possess a number of advantages over bone marrow and peripheral blood as a source of allogeneic progenitor cells, e.g. a lower incidence of graft-versus-host disease and a decreased risk of transmission of infection and there is considerable interest in the establishment of large cord blood banks for use in unrelated transplants. The International Conference Workshop on Cord Blood Transplantation was held in Indianapolis in November 1993 and provided a timely opportunity to review the clinical and laboratory data relating to the use of UCB in transplantation. The results from 34 UCB transplants have been reported to the International Cord Blood Transplant Registry. Engraftment was achieved in 27 of 31 evaluable patients. Graft-versus-host disease > grade 1 occurred only in children transplanted from a one haplotype matched donor; 22 patients survive at a median of 1.5 years. Further sessions at the meeting reviewed the haemopoietic cell content of UCB, the capacity for expansion of early cells and the origin (fetal and/or maternal) and function of lymphoid cells within the graft. The conference ended with a discussion of the practicalities of cord blood banking including collection, cryopreservation, storage, HLA-typing and screening for genetic and infectious diseases.
On Short Forward Error-Correcting Codes for Wireless Communication Systems (2007)

For real-time wireless communications, short forward error-correcting (FEC) codes are indispensable due to the strict delay requirement. In this paper we study the performance of short FEC codes. Reed-Solomon (RS) codes and concatenated zigzag (CZ) codes are chosen as representatives of classical algebraic codes and modern simple iterative decodable codes, respectively. Additionally, we use random binary linear codes as a baseline reference for comparison. Our main results (demonstrated by both simulation and ensemble distance spectrum analysis) are as follows: 1) Short RS codes are as good as random binary linear codes; 2) Carefully designed short low-density parity-check (LDPC) codes are almost as good as random binary linear codes when high decoding complexity can be tolerated; 3) Low complexity belief propagation decoders incur considerable performance loss at short coding lengths.
Re-framing salmon aquaculture in the aftermath of the ISAV crisis in Chile (2020)

Globally, aquaculture is expanding rapidly, with salmon becoming one of the most dynamic and fast-growing production systems in the world. Despite its commercial success, Chilean salmon production has navigated through severe economic and sanitary crises; followed by consecutive policy changes. Between 2007 and 2009, the rapid spread and the multiple effects of the Infectious Salmon Anemia virus (ISAV) marked a tipping point in the trajectory of the salmon aquaculture in southern Chile. This paper examines the discursive mechanisms through which the Chilean salmon aquaculture industry is currently being re-framed in the aftermath of the ISAV crisis, with a focus on searching for the emergence of ecosystem-related elements post crisis. The analysis shows that Chilean salmon aquaculture is being re-framed by the reproduction of three main discourses: biosecurity, sustainable protein and The Promise of Patagonia. The paper concludes that despite the staggering effects of the ISAV crisis on the national salmon production and on coastal communities more than a decade ago, new discourses are focused on the legitimization to growth, in the absence of integrated marine ecosystem-related elements, indicating a crucial gap toward environmental sustainability in salmon aquaculture.
Regulated expression of green fluorescent protein in Debaryomyces hansenii (2004)

The broad range of environmental conditions under which Debaryomyces hansenii can grow, and its production of lipolytic and proteolytic enzymes, have promoted its widespread use. The present work represents a preliminary characterization of D. hansenii for heterologous expression and secretion of green fluorescent protein (GFP). Six heterologous expression vectors were used to address protein production efficiency under regulated expression conditions. Protein expression in D. hansenii seems to be similar to that in Saccharomyces cerevisiae, with transcription being controlled by almost all of the S. cerevisiae and D. hansenii inducible promoters tested, with the exception of the alcohol dehydrogenase 2 gene promoter from S. cerevisiae. Extracellular protein levels in D. hansenii were lower than in S. cerevisiae when Saccharomyces signal peptides were used.
Optical trapping of dielectric nanoparticles in resonant cavities (2010)

We theoretically investigate the opto-mechanical interactions between a dielectric nanoparticle and the resonantly enhanced optical field inside a high $Q$, small-mode-volume optical cavity. We develop an analytical method based on open system analysis to account for the resonant perturbation due to particle introduction and predict trapping potential in good agreement with three-dimensional (3D) finite-difference time-domain (FDTD) numerical simulations. Strong size-dependent trapping dynamics distinctly different from free-space optical tweezers arise as a consequence of the finite cavity perturbation. We illustrate single nanoparticle trapping from an ensemble of monodispersed particles based on size-dependent trapping dynamics. We further discover that the failure of the conventional dipole approximation in the case of resonant cavity trapping originates from a new perturbation interaction mechanism between trapped particles and spatially localized photons.
Predicting Gaze in Egocentric Video by Learning Task-dependent Attention Transition (2018)

We present a new computational model for gaze prediction in egocentric videos by exploring patterns in temporal shift of gaze fixations (attention transition) that are dependent on egocentric manipulation tasks. Our assumption is that the high-level context of how a task is completed in a certain way has a strong influence on attention transition and should be modeled for gaze prediction in natural dynamic scenes. Specifically, we propose a hybrid model based on deep neural networks which integrates task-dependent attention transition with bottom-up saliency prediction. In particular, the task-dependent attention transition is learned with a recurrent neural network to exploit the temporal context of gaze fixations, e.g. looking at a cup after moving gaze away from a grasped bottle. Experiments on public egocentric activity datasets show that our model significantly outperforms state-of-the-art gaze prediction methods and is able to learn meaningful transition of human attention.
Increased serum soluble CD14, ICAM-1 and E-selectin correlate with disease activity and prognosis in systemic lupus erythematosus (2000)

To improve monitoring of immunological and disease activity, we determined soluble markers of activity of the monocyte/macrophage system (sCD14) and the vascular endothelium (sE-selectin, sICAM-1) in patients with systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) in comparison to patients with infections or sepsis. Concentrations of sCD14, sICAM-1 and sE-selectin (soluble CD14, ICAM-1 and E-selectin, respectively) were measured in serum samples from patients with SLE and pSS, patients with sepsis, different infectious diseases and healthy controls using ELISA systems. Elevated levels of sE-selectin and sICAM-1 were detected in patients with SLE as well as sepsis, in contrast to patients with a localized infection (SLE and sepsis, respectively, versus infection P<0.001; Kruskal-Wallis test). Levels of sCD14 were persistently elevated in sera from patients with SLE, whereas these values decreased rapidly after effective therapy in patients with sepsis or infection. A continuous elevation of all of these three parameters was associated with a fatal outcome in patients with sepsis as well as in patients with SLE. Combined elevation of sCD14, sICAM-1 and sE-selectin correlates with the prognosis in patients with active SLE and indicates a remarkable immune activation involving the monocyte/macrophage system and the endothelium comparable to an activation found only in patients with sepsis.
Learning from natural variation across the proteomes of single cells (2022)

Biological functions arise from protein interactions, which are reflected in the natural variation of proteome configurations across individual cells. Emerging single-cell proteomics methods may decode this variation and empower inference of biological mechanisms with minimal assumptions.
Ligand Dependent and Independent Activation of the Androgen Receptor (2001)

Androgens play a pivotal role in the embryonic development, growth, and function of many tissues within male species. The cells of these tissues are influenced by androgens through the binding and resultant conformational changes in the androgen receptor (AR). The importance of the role played by ARs in the life of androgen dependent tissues is evidenced in the genetic diseases that produce alterations in the AR, resulting in alterations in the male phenotype. Most of the available knowledge regarding the function of androgens and the role of AR has been obtained from studies of the prostate gland. These studies have elucidated the importance of androgens in the maintenance of homeostasis. The prostate provides a physiologic tissue model of AR action. The study of prostate cancer also provides a pathophysiologic model for the investigation of androgens and AR. Androgen ablation therapies in prostate cancer take advantage of the continued requirement of the androgen-AR relationship in the immortalized tumor cells. Unfortunately, these therapies often fail with time, and the disease progresses to an androgen refractory and/or androgen independent stage. Recent studies have begun to pull back the veil regarding the pathophysiology of these refractory cells and the role of AR in their growth.
Para-hydrogen induced polarization of amino acids, peptides and deuterium–hydrogen gas (2011)

Signal Amplification by Reversible-Exchange (SABRE) is a method of hyperpolarizing substrates by polarization transfer from para-hydrogen without hydrogenation. Here, we demonstrate that this method can be applied to hyperpolarize small amounts of all proteinogenic amino acids and some chosen peptides down to the nanomole regime and can be detected in a single scan in low-magnetic fields down to 0.25 mT (10 kHz proton frequency). An outstanding feature is that depending on the chemical state of the used catalyst and the investigated amino acid or peptide, hyperpolarized hydrogen-deuterium gas is formed, which was detected with (1)H and (2)H NMR spectroscopy at low magnetic fields of B(0) = 3.9 mT (166 kHz proton frequency) and 3.2 mT (20 kHz deuterium frequency).
G-quadruplex ligands mediate downregulation of DUX4 expression (2020)

Abnormal DUX4 expression in skeletal muscles plays a key role in facioscapulohumeral muscular dystrophy (FSHD) pathogenesis, although the molecular mechanisms regulating DUX4 expression are not fully defined. Using bioinformatic analysis of the genomic DUX4 locus, we have identified a number of putative G-quadruplexes (GQs) forming sequences. Their presence was confirmed in synthetic oligonucleotiode sequences derived from the enhancer, promoter and transcript of DUX4 through circular dichroism and nuclear magnetic resonance analysis. We further examined the binding affinity of a naturally occurring GQ stabilizing compound, berberine, to these non-canonical genetic structures using UV-Vis and fluorescence spectroscopy. Subsequent in vitro study in FSHD patient myoblasts indicated that berberine treatment reduced DUX4 expression and also expression of genes normally switched on by DUX4. Further investigation in a mouse model overexpressing exogenous DUX4 confirmed the therapeutic effects of berberine in downregulating DUX4 protein expression, inhibiting muscle fibrosis, and consequently rescuing muscle function. Our data demonstrate for the first time that GQs are present in the DUX4 locus and that the GQ interactive ligand reduces DUX4 expression suggesting potential role of GQs in FSHD pathogenesis. Our work provides the basis of a novel therapeutic strategy for the treatment of FSHD.
Characterization of phosphatidylinositol-specific phospholipase C from cultured vascular smooth muscle cells (1991)

Phosphoinositide-specific phospholipase C (PLC) activities have been partially purified from cultured vascular smooth muscle cells and analyzed for substrate specificity, calcium and pH requirements, and molecular weight. The purification procedure involved DEAE-cellulose and heparin-Sepharose chromatographies followed by Mono Q and size exclusion high performance liquid chromatography. This technique resolves multiple peaks of activity using phosphatidylinositol (PI) and PI 4,5-bisphosphate (PIP2) as substrates. The major peak was purified to near homogeneity as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PLC activity in vascular smooth muscle cells can be divided into two types based on their calcium and pH requirements, substrate preferences, and molecular weights. The low molecular weight PLC hydrolyzes both PI and PIP2, has a molecular mass of 58 kDa, requires the most calcium for full activation, and has a PI-pH profile that shifts slightly with calcium concentration. Screening a cDNA library with oligonucleotides directed against several of the known PLCs identified a highly expressed PLC cDNA that is 99% homologous to PLC-alpha, suggesting that this low molecular weight peak in fact corresponds to PLC-alpha. The high molecular mass peak (157 kDa) shows much greater activity against PI than PIP2, is active at lower calcium concentrations, and has a PI-pH optimum of 5.0 regardless of calcium concentration. Each of the PIP2 PLC activities is strongly dependent on the relative levels of calcium and pH in the assay buffer. These observations suggest that vascular smooth muscle contains both a high and low molecular weight PLC whose activities are affected markedly by the changes in calcium and pH accompanying hormonal stimulation of the cell.
A 0.54 pJ/b 20 Gb/s Ground-Referenced Single-Ended Short-Reach Serial Link in 28 nm CMOS for Advanced Packaging Applications (2013)

High-speed signaling over high density interconnect on organic package substrates or silicon interposers offers an attractive solution to the off-chip bandwidth limitation problem faced in modern digital systems. In this paper, we describe a signaling system co-designed with the interconnect to take advantage of the characteristics of this environment to enable a high-speed, low area, and low-power die to die link. Ground-Referenced Signaling (GRS) is a single-ended signaling system that eliminates the major problems traditionally associated with single-ended design by using the ground plane as the reference and signaling above and below ground. This design employs a novel charge pump driver that additionally eliminates the issue of simultaneous switching noise with data independent current consumption. Silicon measurements from a test chip implementing two 16-lane links, with forwarded clocks, in a standard 28 nm process demonstrate 20 Gb/s operation at 0.54 pJ/bit over 4.5 mm organic substrate channels at a nominal 0.9 V power supply voltage. Timing margins at the receiver are <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${>}$</tex></formula> 0.3 UI at a BER of <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${<}$</tex> </formula> 10 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{-12}$</tex> </formula> . We estimate BER <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${<}$</tex> </formula> 10 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{-25}$</tex> </formula> at the eye center.
Effect of garment design on piezoelectricity harvesting from joint movement (2016)

The harvesting of piezoelectricity through the human body involves the conversion of mechanical energy, mostly generated by the repeated movements of the body, to electrical energy, irrespective of the time and location. In this research, it was expected that the garment design would play an important role in increasing the efficiency of piezoelectricity scavenged in a garment because the mechanical deformation imposed on the energy harvester could increase through an optimal design configuration for the garment parts supporting a piezoelectricity harvester. With this expectation, this research aimed to analyze the effect of the clothing factors, and that of human factors on the efficiency of piezoelectricity harvesting through clothing in joint movements. These analyses resulted in that the efficiency of the piezoelectricity harvesting was affected from both two clothing factors, tightness level depending upon the property of the textile material and design configuration of the garment part supporting the piezoelectricity harvesting. Among the three proposed designs of the garment part supporting the piezoelectricity harvesting, 'reinforced 3D module design,' which maximized the value of radius in the piezoelectricity harvester, showed the highest efficiency across all areas of the joints in the human body. The two human factors, frequency of movement and body part, affected the efficiency of the piezoelectricity harvesting as well.