gebhart/patrepeval huggingface dataset:
Genetic relationship between acylpeptide hydrolase and acylase, two hydrolytic enzymes with similar binding but different catalytic specificities. (1991)

An 87% identity has been found between the reported cDNA sequence that encodes acylpeptide hydrolase (EC 3.4.19.1) [Mitta, M., Asada, K., Uchimura, Y., Kimizuka, F., Kato, I., Sakiyama, F. & Tsunasawa, S. (1989) J. Biochem. 106, 548-551] and a cDNA transcribed from a locus (DNF15S2) on the short arm of human chromosome 3, reported by Naylor et al. [Naylor, S.L., Marshall, A., Hensel, C., Martinez, P.F., Holley, B. & Sakaguchi, A.Y. (1989) Genomics 4, 355-361]; the DNF15S2 locus suffers deletions in small cell lung carcinoma associated with a reduction or loss of acylase activity (EC 3.5.1.14). Acylpeptide hydrolase catalyzes the hydrolysis of the terminal acetylated amino acid preferentially from small acetylated peptides. The acetylamino acid formed by acylpeptide hydrolase is further processed to acetate and a free amino acid by an acylase. The substrates for the acylpeptide hydrolase and the acylase behave in a reciprocal manner since acylpeptide hydrolase binds but does not process acetylamino acids and the acylase binds acetylpeptides but does not hydrolyze them; however, the two enzymes share the same specificity for the acyl group. These findings indicate some common functional features in the protein structures of these two enzymes. Since the gene coding for acylpeptide hydrolase is within the same region of human chromosome 3 (3p21) that codes for the acylase and deletions at this locus are also associated with a decrease in acylase activity, there is a close genetic relationship between the two enzymes. There could also be a relationship between the expression of these two enzymes and acetylated peptide growth factors in some carcinomas.
Cerebrospinal fluid lens-free microscopy: a new tool for the laboratory diagnosis of meningitis (2017)

Cerebrospinal fluid cytology is performed by operator-dependant light microscopy as part of the routine laboratory work-flow diagnosis of meningitis. We evaluated operator-independent lens-free microscopy numeration of erythrocytes and leukocytes for the cytological diagnosis of meningitis. In a first step, prospective optical microscopy counts of leukocytes done by five different operators yielded an overall 16.7% misclassification of 72 cerebrospinal fluid specimens in meningitis/non-meningitis categories using a 10 leukocyte/μL cut-off. In a second step, the lens-free microscopy algorithm adapted for counting cerebrospinal fluid cells and discriminating leukocytes from erythrocytes was modified step-by-step in the prospective analysis of 215 cerebrospinal fluid specimens. The definite algorithm yielded a 100% sensitivity and a 86% specificity compared to confirmed diagnostics. In a third step, a blind lens-free microscopic analysis of 116 cerebrospinal fluid specimens, including six cases of microbiology-confirmed infectious meningitis, yielded a 100% sensitivity and a 79% specificity. Adapted lens-free microscopy is thus emerging as an operator-independent technique for the rapid numeration of leukocytes and erythrocytes in cerebrospinal fluid. In particular, this technique is well suited to the rapid diagnosis of meningitis at point-of-care laboratories.
Recovery of the Hypothalamic-Pituitary-Adrenal Axis in Children and Adolescents after Surgical Cure of Cushing's Disease (2012)

Although this is not a randomized study, we present our standardized tapering regimen for glucocorticoid replacement after TSS that led to recovery of the HPAA in most patients within the first postoperative year. Multiple factors may affect this process, but an early recovery may indicate disease recurrence.
Metabolic Reprogramming by Dual AKT/ERK Inhibition through Imipridones Elicits Unique Vulnerabilities in Glioblastoma (2018)

Abstract Purpose: The goal of this study is to enhance the efficacy of imipridones, a novel class of AKT/ERK inhibitors that displayed limited therapeutic efficacy against glioblastoma (GBM). Experimental Design: Gene set enrichment, LC/MS, and extracellular flux analyses were used to determine the mechanism of action of novel imipridone compounds, ONC206 and ONC212. Orthotopic patient-derived xenografts were utilized to evaluate therapeutic potency. Results: Imipridones reduce the proliferation of patient-derived xenograft and stem-like glioblastoma cell cultures in vitro and in multiple xenograft models in vivo. ONC212 displayed the highest potency. High levels of c-myc predict susceptibility to growth inhibition and apoptosis induction by imipridones and increased host survival in orthotopic patient-derived xenografts. As early as 1 hour, imipridones elicit on-target inhibition, followed by dephosphorylation of GSK3β at serine 9. GSK3β promotes phosphorylation of c-myc at threonine 58 and enhances its proteasomal degradation. Moreover, inhibition of c-myc by BRD4 antagonists sensitizes for imipridone-induced apoptosis in stem-like GBM cells in vitro and in vivo. Imipridones affect energy metabolism by suppressing both glycolysis and oxidative phosphorylation, which is accompanied by a compensatory activation of the serine-one carbon-glycine (SOG) pathway, involving the transcription factor ATF4. Interference with the SOG pathway through novel inhibitors of PHGDH results in synergistic cell death induction in vitro and in vivo. Conclusions: These results suggest that c-myc expression predicts therapeutic responses to imipridones and that imipridones lead to suppression of tumor cell energy metabolism, eliciting unique metabolic vulnerabilities that can be exploited for clinical relevant drug combination therapies. Clin Cancer Res; 24(21); 5392–406. ©2018 AACR.
Hybrid supercapacitors with ionic electrolytes (2006)

We developed a hybrid supercapacitor with N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PYR14TFSI) ionic liquid electrolyte, activated carbon (AC) as the negative electrode and poly(3-methylthiophene) (pMeT) as the positive which provides at 60°C maximum cell voltages higher than 3.4 V as well as long cycling stability over 15,000 cycles. In the present paper we present and discuss the results of our study as well as the strategies for materials and cell design optimization in view of the development of 2 kF-3.9 V AC/PYR14TFSI/pMeT supercapacitors operating at 60°C.
Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology (2015)

Human PIWI-interacting RNAs (piRNAs) are known to be expressed in germline cells, functionally silencing LINEs and SINEs. Their expression patterns in somatic tissues are largely uncharted. We analyzed 6,260 human piRNA transcriptomes derived from non-malignant and tumour tissues from 11 organs. We discovered that only 273 of the 20,831 known piRNAs are expressed in somatic non-malignant tissues. However, expression patterns of these piRNAs were able to distinguish tissue-of-origin. A total of 522 piRNAs are expressed in corresponding tumour tissues, largely distinguishing tumour from non-malignant tissues in a cancer-type specific manner. Most expressed piRNAs mapped to known transcripts, contrary to "piRNA clusters" reported in germline cells. We showed that piRNA expression can delineate clinical features, such as histological subgroups, disease stages, and survival. PiRNAs common to many cancer types might represent a core gene-set that facilitates cancer growth, while piRNAs unique to individual cancer types likely contribute to cancer-specific biology.
Site-specific integration of heterologous genes in yeast via Ty3 retrotransposition (2000)

The Ty3 retrotransposon of Saccharomyces cerevisiae was employed for the site-specific integration of heterologous genes into the yeast genome. A GAL-regulated promoter allowed induction of the retrotransposition process, and a bacterial neo(r) gene inserted in the Ty3 element was used as a selectable model heterologous gene. The frequency of transposition of this neo(r)-marked element was found to be comparable to that of an unmarked element. Three amplification systems were constructed; the systems varied with respect to the location and number of the GAL-regulated helper and neo(r)-marked Ty3 elements. For all three systems, neo(r) integrations were readily selected with a maximum of two insertions obtained per round of amplification. A sequential amplification strategy was effective for further increasing the number of integrated cloned genes, and families of strains varying by only one neo(r) insertion were easily obtained. Resistance to the antibiotic G418 correlated well with the number of integrated neo(r) genes, and Northern blots verified the relationship between cloned gene number (up to four) and neo(r) expression. Structural stability of the integrated genes was also demonstrated. By controlling the number of rounds of amplification and the level of G418 selection, precise numbers of integrated heterologous genes could be obtained. Because the amplification process can be repeated using different cloned genes inserted in the Ty3 element, these results demonstrate the potential of retrotransposition for the regulated integration of a series of different genes at nondeleterious chromosomal locations.
Evaluations of pretensioner activation in rear impacts (2021)

Testing of the effect of retractor pretensioning with out-of-position occupants and additional belt webbing in moderate to high-speed rear sled tests shows no effect on occupant kinematics and biomechanical responses. The displacement of the hips in a rear impact depends on the compliance of the seatback and amount of pocketing, the stiffness of the seat frame limiting rearward rotation, and the dynamic friction between the occupant and the seatback.
Introduction to the OFC 2017 Special Issue (2017)

The OFC 2017 Special Issue is a collection of outstanding optical networking papers based on OFC 2017 invited papers and the most highly ranked OFC contributed papers. The papers in this special issue cover a broad range of topics including elastic optical networks, open systems, machine learning, cross-layer optimization, and access networks.
Resonant nonradiative energy transfer in CdSe/ZnS core/shell nanocrystal solids enhances hybrid white light emitting diodes (2008)

We propose and demonstrate hybrid white light emitting diodes enhanced with resonant nonradiative energy transfer in CdSe/ZnS core/shell nanocrystal solids integrated on near-UV InGaN/GaN LEDs. We observe a relative quantum efficiency enhancement of 13.2 percent for the acceptor nanocrystals in the energy gradient mixed assembly, compared to the monodisperse phase. This enhancement is attributed to the ability to recycle trapped excitons into nanocrystals using nonradiative energy transfer. We present the time-resolved photoluminescence of these nanocrystal solids to reveal the kinetics of their energy transfer and their steady-state photoluminescence to exhibit the resulting quantum efficiency enhancement.
Isoenzyme Polymorphism in Flowering Plants (1972)

Journal Article Isoenzyme Polymorphism in Flowering Plants: VIII. Genetic control and dimeric nature of transaminase hybrid maize isoenzymes Get access TIMOTHY MACDONALD, TIMOTHY MACDONALD geneticist Department of Biological Sciences, Lowell Technical InstituteLowell, Massachusetts 61854 Search for other works by this author on: Oxford Academic PubMed Google Scholar JAMES L. BREWBAKER JAMES L. BREWBAKER professor of horticulture University of HawaiiHonolulu 96822 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 63, Issue 1, January 1972, Pages 11–14, https://doi.org/10.1093/oxfordjournals.jhered.a108209 Published: 01 January 1972
All-optical switching using color centers in an irradiated phosphorus-doped fiber (1996)

We report on all-optical switching of a 900-nm signal in a two-mode silica fiber based upon a resonant nonlinearity introduced by phosphorus color centers in a 22-cm irradiated P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> -SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> fiber. Full switching was observed with only 1 μJ of absorbed 532-nm pump energy, with a projected response time under 10 ns. This switch required a peak power two orders of magnitude lower than for a fiber Kerr effect device operated under identical conditions.
Three‐dimensional in situ sequencing of single cells in intact tissue (2019)

Conventional sequencing methods are unable to measure sequence and spatial information simultaneously, limiting our understanding of the spatial heterogeneity of molecules within cells and intact tissues. To address this issue, multiplexed in situ hybridization and a new generation of sequencing methods termed in situ sequencing have emerged, aiming to spatially resolve RNAs inside cells. Such spatial transcriptomic profiling is critical to resolving cell identity in intact issues, a key question in neuroscience today as the brain consists of a three‐dimensional (3D) tapestry of cell types whose functional diversity arises from the spatial heterogeneity of gene expression. We developed a 3D intact‐tissue RNA sequencing technique in complex organs, termed STARmap, enabling targeted single‐cell gene expression mapping via in situ sequencing within mouse cortex. This new analytical approach has great promises for addressing a series of fundamental questions in neuroscience (e.g. spatial organization of cell types, molecular markers of functional circuits, activity‐triggered gene expression) that are hard to be studied otherwise. Support or Funding Information X.W. is supported by a Life Science Research Foundation fellowship and the Gordon and Betty Moore Foundation. W.E.A. is supported by a Fannie and John Hertz Foundation Fellowship and an NSF Graduate Research Fellowship. K.D. is supported by NIMH (R01MH099647), NIDA (P50DA042012), the DARPA NeuroFAST program W911NF‐14‐2‐0013, the NSF NeuroNex program, the Gatsby Foundation, the AE Foundation, the NOMIS Foundation, the Fresenius Foundation, the Wiegers Family Fund, the James Grosfeld Foundation, the Sam and Betsy Reeves Foundation, and the HL Snyder Foundation. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Structure determination of weak phase objects from interferometric near-field measurements (1994)

Amplitude and phase of diffraction near fields behind two-dimensional weak phase objects (n ≍ 1.02 + iO.0002) are measured with electromagnetic 3-cm waves in TM and TE polarization. Dielectric slabs and strips with a trapezoidal or rectangular cross section are considered (width 1.5λ-36.0λ; thickness 0.6λ-2.4λ; wedge angle 30°-150°). For numerical simulation of the measured fields, a modification of the first Born approximation for weak scatterers is developed, which yields a remarkably better agreement with the measurements but requires no higher numerical efforts than the first Born approximation. Procedures for the determination of width, thickness, and wedge angle of the objects from measured diffraction fields are presented.
Flussabhängigkeit der Lungendeposition nach Inhalation von einem HFA-Dosieraerosol und dem Respimat® Soft Inhaler bei COPD Patienten (2007)

Einleitung: Die Lungendeposition nach Inhalation eines Medikamentes ist nicht nur vom Inhalationsgerät, sondern auch vom Inhalationsmanöver, insbesondere vom Inhalationsfluss abhängig.
Calcium Binding to Leptospira Outer Membrane Antigen LipL32 Is Not Necessary for Its Interaction with Plasma Fibronectin, Collagen Type IV, and Plasminogen (2011)

LipL32 is the most abundant outer membrane protein from pathogenic Leptospira and has been shown to bind extracellular matrix (ECM) proteins as well as Ca(2+). Recent crystal structures have been obtained for the protein in the apo- and Ca(2+)-bound forms. In this work, we produced three LipL32 mutants (D163-168A, Q67A, and S247A) and evaluated their ability to interact with Ca(2+) and with ECM glycoproteins and human plasminogen. The D163-168A mutant modifies aspartate residues involved in Ca(2+) binding, whereas the other two modify residues in a cavity on the other side of the protein structure. Loss of calcium binding in the D163-D168A mutant was confirmed using intrinsic tryptophan fluorescence, circular dichroism, and thermal denaturation whereas the Q67A and S247A mutants presented the same Ca(2+) affinity as the wild-type protein. We then evaluated if Ca(2+) binding to LipL32 would be crucial for its interaction with collagen type IV and plasma proteins fibronectin and plasminogen. Surprisingly, the wild-type protein and all three mutants, including the D163-168A variant, bound to these ECM proteins with very similar affinities, both in the presence and absence of Ca(2+) ions. In conclusion, calcium binding to LipL32 may be important to stabilize the protein, but is not necessary to mediate interaction with host extracellular matrix proteins.
High-Performance Implanted-Channel SiC MESFETs (2011)

We demonstrate for the first time the development of state-of-the-art ion-implanted-channel SiC MESFETs with record dc and RF performance that is comparable to that of epitaxial-channel devices. MESFETs fabricated with this approach show a maximum stable gain exceeding 15.8 dB at 3.1 GHz in class-AB bias condition. An RF power output that is greater than 4 W/mm, with 63% drain efficiency, at 3.5 GHz was also achieved, showing the potential of these devices for high-power operation.
Reaction path in the formation of titanium diboride by a magnesium thermite process (1995)

TiB{sub 2} was formed by a thermite reaction amongst Mg, amorphous B{sub 2}O{sub 3} and TiO{sub 2} powders. Mixtures consisting of 2Mg-TiO{sub 2}, 3Mg-B{sub 2}O{sub 3} and 5Mg-TiO{sub 2}-B{sub 2}O{sub 3} were heat treated using DTA and separately via ignition with a nichrome wire; product phases were identified using XRD. MgO and Ti were products from the first mixture reacted in argon, whereas an incomplete transformation forming Mg{sub 3}TiO{sub 4} occurred in air. For the second mixture, a reaction forming Mg{sub 3}B{sub 2}O{sup 6} occurred in air, but no reaction occurred in argon due to deficiency of oxygen. Minor amounts Of Mg{sub 3}B{sub 2}O{sub 6} and Mg{sub 2}TiO{sub 4} were detected in addition to the predicted product phases of MgO and TiB{sub 2} for the third mixture ignited both in air and argon. Based on available evidence, a path for this reaction was deduced; Mg particles in contact with TiO{sub 2} reacted to form Ti, which in turn reacted with B{sub 2}O{sub 3} to form TiB{sub 2}. TiB{sub 2} product particles from the reaction in argon had a more faceted appearance than those formed during the reaction in air. This was interpreted to be the result of glassy B{sub 2}O{submore » 3} surface layer formation on TiB{sub 2} particles in air.« less
EVANESCENT FIELD ABSORPTION SPECTROSCOPY ON POLY(DIMETHYLSILOXANE) SINGLE-MODE RIB WAVEGUIDE INTEGRATED WITH MICROFLUIDIC SYSTEM (2010)

An integrated poly(dimethylsiloxane) (PDMS) singlemode rib waveguide with microfluidic system is demonstrated for evanescent field absorption spectroscopy. Based on the PDMS singlemode rib waveguide, a photonic circuit is de� signed and fabricated to permit multiple waveguides sensing. The applicability of the integrated photonic and microflui� dic PDMS chip for evanescent field absorption spectroscopy in visible light range (400 - 700 nm) was confirmed by ab� sorbance measurement of Fluorescein and Bromophenol Blue dyes. The lowest detection concentration of 0.1 *M for Bromophenol Blue was obtained. The demonstrations show that the integrated PDMS singlemode waveguide offers dis� posable, multiple sensing and visible light absorption detection.
An Efficient Algorithm for VC-1 to H.264 Video Transcoding in Progressive Compression (2006)

The high definition video adoption has been growing rapidly for the last two years. The two high definition DVD formats HD-DVD and Blueray have mandated MPEG-2, H.264 and VC-1 as video compression formats. The coexistence of these different video coding standards creates a need for transcoding. In this paper, an efficient transcoding algorithm from VC-1 video to H.264 video is discussed. While there has been recent work on MPEG-2 to H.264 transcoding, the published work on VC-1 to H.264 transcoding is non-existent. There is very limited amount of published work on VC-1. This paper gives a brief overview of VC-1 and discusses the opportunities for low-complexity tools for VC-1 to H.264 transcoding. The paper considers I and P frame transcoding from VC-1 to H.264 and proposes two approaches 1) low cost design and 2) high cost design
RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast (2010)

Together, these results provide a global perspective on the relationship between PolII and mRNA production in budding yeast.
Retraction Note to: Partially hydrolysed, prebiotic supplemented whey formula for the prevention of allergic manifestations in high risk infants: a multicentre double-blind randomised controlled trial (2020)

An amendment to this paper has been published and can be accessed via the original article.
Mixed-mode Bytecode Execution (2000)

Modern high-performance virtual machines use dynamic compilation. There is a tension between compilation speed and code quality. We argue that a highly-optimizing compiler is best deployed with both a fast, less-optimizing compiler and an interpreter. We present measurements showing that such a system can achieve the same peak performance as a system with just the optimizing compiler, and startup costs similar to a system with just the interpreter and fast compiler. M/S MTV29-01
RhoA/ROCK inhibition improves the beneficial effects of glucocorticoid treatment in dystrophic muscle: implications for stem cell depletion (2017)

Glucocorticoid treatment represents a standard palliative treatment for Duchenne muscular dystrophy (DMD) patients, but various adverse effects have limited this treatment. In an effort to understand the mechanism(s) by which glucocorticoids impart their effects on the dystrophic muscle, and potentially reduce the adverse effects, we have studied the effect of prednisolone treatment in dystrophin/utrophin double knockout (dKO) mice, which exhibit a severe dystrophic phenotype due to rapid muscle stem cell depletion. Our results indicate that muscle stem cell depletion in dKO muscle is related to upregulation of mTOR, and that prednisolone treatment reduces the expression of mTOR and other pro-inflammatory mediators, consequently slowing down muscle stem cell depletion. However, prednisolone treatment was unable to improve the myogenesis of stem cells and reduce fibrosis in dKO muscle. We then studied whether glucocorticoid treatment can be improved by co-administration of an inhibitor of RhoA/ROCK signaling, which can be activated by glucocorticoids and was found in our previous work to be over-activated in dystrophic muscle. Our results indicate that the combination of RhoA/ROCK inhibition and glucocorticoid treatment in dystrophic muscle have a synergistic effect in alleviating the dystrophic phenotype. Taken together, our study not only shed light on the mechanism by which glucocorticoid imparts its beneficial effect on dystrophic muscle, but also revealed the synergistic effect of RhoA/ROCK inhibition and glucocorticoid treatment, which could lead to the development of more efficient therapeutic approaches for treating DMD patients.