gebhart/patrepeval huggingface dataset:
Tying Down Loose Ends in the <i>Chlamydomonas</i> Genome: Functional Significance of Abundant Upstream Open Reading Frames (2016)

The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence ('uORFs'): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard 'scanning' model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5' untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral.
Zur Konformation geschützter Aminosäuren, IV. NMR‐ und IR‐Untersuchungen von Boc‐ω‐Aminosäuren (1975)

Z,E-Isomerie wird in Boc-ω-Aminosäuren durch temperaturabhängige 1H- und 13C-NMR-sowie IR-Spektroskopie beobachtet. Die bei tiefen Temperaturen in CDCl3 bevorzugte Z-Konformation wird durch Wassertoffbrücken stabilisiert. Boc-Methylamin liegt bevorzugt in der Z-Konformation vor; das Z,E-Gleichgewicht wird durch Zusatz von Lanthanoiden-Verschiebungsreagenz verändert und nachgewiesen. Conformation of Protected Amino Acids, IV. N. M. R. and I. R. Investigations of Boc-ω-Amino Acids Z,E-isomerism of Boc-ω-amino acids is observed by temperature dependent 1H and 13C n.m.r. as well as i.r. spectra. At low temperatures the Z-conformation is stabilized by hydrogen bonds in CDCl3. In Boc-methylamine the Z-conformation dominates, the Z,E-equilibrium is shifted and observed by adding lanthanide shift reagents.
The kinetics of alkylation of isobutane with propylene (1972)

Abstract A 17‐reaction mechanism model was postulated to describe the alkylation of isobutane with propylene using sulfuric acid as the catalyst. The scheme was based on the Schmerling carbonium ion mechanism with modifications introduced to account to iC 9 and iC 10 formation. Solving the steady state rate equations for the rate constants a set of 17 equations of the form k i = f ( rcj , rC k , …)/ g (C i , C k , …) were obtained. Experimental measurements were made in an ideally mixed, continuous‐flow stirred‐tank reactor, and the necessary data were obtained to compute the rate constants from 65°F to 135°F. The reaction model was found to be valid in the range of 81°F to 135°F using a 95% sulfuric acid catalyst since the rate constants obeyed the Arrhenius theory. The results obtained at 65°F and 95% sulfuric acid showed significant departure from the model. This was possibly due to a change in reaction mechanism. There was an apparent change in selectivity of the catalyst when the concentration was lowered to 90% sulfuric acid. This resulted in increased rates of formation of i C 9 's and i C 10 's and decreased rates of formation of i C 5 's, i C 6 's and i C 8 's.
An optical cavity with a strongly focused mode (2013)

Atom-photon interfaces are one of the building blocks of the future quantum information protocols. Accomplishing a strong interaction between the atom and the photons can be successfully done by high finesse and small mode volume cavities. However, this method requires sophisticated dielectric coatings and stabilization of the cavity against even small vibrations and small line width of those cavities impose higher input photon numbers if spontaneously emitted photons are to be used, which make it seem hard to scale up such atom-light interfaces to form quantum networks. An alternative method is to use a nearly concentric cavity, which has a strongly focused optical mode [1].
Cytotoxic Constituents of the Roots of <i>Ekmanianthe </i><i>l</i><i>ongiflora</i> (2000)

Bioactivity-directed fractionation of the CHCl(3) extract of the roots of Ekmanianthe longiflora resulted in the isolation of three new natural products, (2R,3R,4R)-3,4-dihydro-3, 4-dihydroxy-2-(3-methyl-2-butenyl)-1(2H)-naphthalenone (1), (2S,3R, 4R)-3,4-dihydro-3, 4-dihydroxy-2-(3-methyl-2-butenyl)-1(2H)-naphthalenone (2), and (2R, 3aR,9R,9aR)-9-hydroxy-2-(1-hydroxy-1-methylethyl)-2,3,3a,4,9 , 9a-hexahydro-naphtho[2,3-b]furan-4-one (3), together with the known compounds 2-(1-hydroxyethyl)naphtho[2,3-b]furan-4,9-quinone (4), 2-acetylnaphtho[2,3-b]furan-4,9-quinone (5), dehydro-iso-alpha-lapachone (6), alpha-lapachone (7), catalponol, and epi-catalponol. The structures of 1-3 were determined using a combination of NMR spectroscopic techniques, and the absolute configurations of compounds 1 and 2 were obtained using Mosher ester methodology. Compounds 4-6 showed significant cytotoxicity in a panel of human cancer cells. alpha-Lapachone (7) exhibited only marginal activity, and catalponol and epi-catalponol were inactive in this regard. When tested at 72 mg/kg/injection in an in vivo mouse P-388 leukemia system, compound 4 was inactive (110% T/C).
Accelerated coronary MRA by simultaneous acquisition of multiple 3D stacks (2001)

The implementation and first in vivo results of a novel coronary magnetic resonance angiography (MRA) protocol allowing simultaneous acquisition of multiple geometrically independent 3D imaging stacks are presented. Each imaging stack is acquired in a separate cardiac phase using an individual magnetization preparation and navigator-based gating and prospective motion correction. Each stack covers one of the main coronary vessels. Thus, an improvement of scan efficiency was achieved, which was used in this study to reduce total scan time at standard image quality. Experiments performed in healthy volunteers and in patients using a two-stack approach yielded a total scan time reduction of 50% with an image quality equivalent to standard single-stack coronary MRA.
Progress and Setbacks in the Study of CNS Axonal Plasticity and Regeneration (2010)

Understanding of basic mechanisms underlying the refractory state of axonal regeneration in the CNS has advanced remarkably in the last 50 years. Mechanisms that underlie the failure of central regeneration include: 1) an absence of permissive extracellular matrices in lesion sites, 2) insufficient secretion of trophic molecules, 3) the presence of growth‐inhibitory molecules in the CNS, and 4) an intrinsic failure of adult CNS neurons to upregulate extensive sets of growth‐related genes. Addressing several of these mechanisms simultaneously, it is possible to elicit growth of select spinal cord axonal populations into and beyond lesion sites, and to reinnervate normal targets. However, several critical challenges remain in SCI research, including: 1) elicitation of regeneration or corticospinal axonal systems; 2) remyelination of regenerating axons; 3) elicitation of substantial growth at chronic stages after SCI, and 4) translation of these findings to primate systems, given fundamental differences in axonal organization and function between rodent and primate models. This talk will summarize these topics and highlight future directions of research.
[Characteristics of gastric cancer detected after successful eradication of H. pylori]. (2012)

H. pylori infection plays a important role in gastric carcinogenesis. Japanese randomized controlled study has proved that H. pylori eradication has a preventive effect for the development of gastric cancer. However, gastric cancer is sometimes detected after successful eradication of H. pylori. There is a lack of study about gastric cancers detected after H. pylori eradication. These cancers are reported to have the tendency of smaller size and morphologically higher frequency in depressive type. Also there was feature with a lot of complete gastric type or gastric predominant mixed type immunohistologically. The clinicopathological characteristics of gastric cancers detected after H. pylori eradication were different from those of gastric cancers in patients with H. pylori infection. H. pylori eradication is thought to suppress intestinalization during the development of gastric cancer.
Effectiveness of Spatial Coherent Remote Drive Experience with a Telexistence Backhoe for Construction Sites (2015)

In this paper, a spatial coherent remote driving system was designed and implemented to operate a telexistence backhoe over a wireless network. Accordingly, we developed a 6 degrees of Freedom (DOF) slave robot that can mimic the human upper body movement; a cockpit with motion tracking system and a Head Mounted Display (HMD) where the operator was provided with a HD720p ultra low latency video and audio feedback from the remote backhoe, and a controller to manipulate the remote backhoe. Spatial coherent driving could help manipu- lating heavy machinery without any prior training and perform operations as if they were operating the machinery locally. Moreover, construction work could be performed uninterrupted (24/7) by operators remotely log-in from all over the world. This paper describes the design requirements of developing the telexistence backhoe followed by several field experiments carried out to verify the effectiveness of spatial coherent remote driving experience in construction sites.
Kidney transplantation at the University of Illinois at Chicago from 1988-2004. (2004)

The Division of Transplantation at the University of Illinois at Chicago (UIC) was established in 1968 by Dr. Olga M. Jonasson, who performed the first living related kidney transplant in Illinois. The UIC Hospital is a typical inner city hospital serving primarily minorities and under-privileged populations with significant challenge for issues such as compliance, insurance coverage, low income, and degree of education. We analyzed the outcomes of 67 pediatric and 801 adult consecutive renal allotransplantations performed at the University of Illinois at Chicago (UIC) from January 1988-December 2002 and more recent information in relation to newly developed programs (robotic living donation, transplantation in sensitized patients, early steroid discontinuation, ethnicity tailored immunosuppression) until November 2004 (21 pediatric and 172 adults). The one-year graft survival has improved comparing the cases performed between 1988-1998 versus cases after 1998 from 82-88%, with similar patient survival. However, the overall 5-year patient and graft survival has not changed significantly in the 2 different eras and is currently 85% and 65%, respectively. With the use of minimally invasive, robotic-assisted living donor nephrectomy, the use of living donors has increased and these now represent 75% of the kidney donors at UIC. Transplantation in highly sensitized recipients has become more successful with the use of plasmapheresis resulting in 100% patient and graft survival and a 10% acute rejection rate in the first series of 20 patients. Early steroid discontinuation (steroid discontinued at day 6 after transplantation) has allowed for significant improvement of results in pediatric recipients. We have 100% one-year patient and graft survival and no acute rejections in a series of 13 children, compared with a 25% rejection rate in 13 children with steroid-containing immunosuppession. Tailored immunosuppression with early steroid discontinuation now achieves equal early results in African American as in any other ethnic group with 98-99% patient and graft survival and acute rejection rates below 10%. Of interest will be the future evolution of long-term patient and graft survival under the new immunosuppressive protocols with early steroid discontinuation achieving very low acute rejection rates and impressive one-year survival rates. There is reason for optimism that the improved early results will translate into better long-term outcomes.
Modified Flotation Technique for Quantitative Determination of Mite Populations in Feedstuffs (1984)

Modifications are described to a previously published technique for quantitative determination of mite populations in animal feedingstuffs. In the modified method, the oil phase is kerosene instead of a mixture of kerosene and tetralin (1 + 1), and aqueous industrial methylated spirit is substituted for aqueous ethanol in the aqueous phase. Emulsion formation at the interface is considerably reduced by incorporating a pre-extraction stage. Examination of mites on the filter paper is made easier and quicker by staining them with Phloxin B. Trials carried out with known numbers of mites in samples of dairy feed concentrates indicate mean recoveries of 84-96% throughout the range tested. The results show that the accuracy of the technique is not affected by the level of infestation.
Effects of carbohydrate restriction on postprandial glucose metabolism, <b>β</b>-cell function, gut hormone secretion, and satiety in patients with Type 2 diabetes (2020)

Dietary carbohydrate restriction may improve the phenotype of Type 2 diabetes (T2D) patients. We aimed to investigate 6 wk of carbohydrate restriction on postprandial glucose metabolism, pancreatic α- and β-cell function, gut hormone secretion, and satiety in T2D patients. Methods In a crossover design, 28 T2D patients (mean HbA<sub>1c</sub>: 60 mmol/mol) were randomized to 6 wk of carbohydrate-reduced high-protein (CRHP) diet and 6 wk of conventional diabetes (CD) diet (energy-percentage carbohydrate/protein/fat: 30/30/40 vs. 50/17/33). Twenty-four-hour continuous glucose monitoring (CGM) and mixed-meal tests were undertaken and fasting intact proinsulin (IP), 32,33 split proinsulin concentrations (SP), and postprandial insulin secretion rates (ISR), insulinogenic index (IGI), β-cell sensitivity to glucose (<i>B</i><sub>up</sub>), glucagon, and gut hormones were measured. Gastric emptying was evaluated by postprandial paracetamol concentrations and satiety by visual analog scale ratings. A CRHP diet reduced postprandial glucose area under curve (net AUC) by 60% (<i>P</i> < 0.001), 24 h glucose by 13% (<i>P</i> < 0.001), fasting IP and SP concentrations (both absolute and relative to C-peptide, <i>P</i> < 0.05), and postprandial ISR (24%, <i>P</i> = 0.015), while IGI and <i>B</i><sub>up</sub> improved by 31% and 45% (both <i>P</i> < 0.001). The CRHP diet increased postprandial glucagon net AUC by 235% (<i>P</i> < 0.001), subjective satiety by 18% (<i>P</i> = 0.03), delayed gastric emptying by 15 min (<i>P</i> < 0.001), decreased gastric inhibitory polypeptide net AUC by 29% (<i>P</i> < 0.001), but had no significant effect on glucagon-like-peptide-1, total peptide YY, and cholecystokinin responses. A CRHP diet reduced glucose excursions and improved β-cell function, including proinsulin processing, and increased subjective satiety in patients with T2D.
Faculty Opinions recommendation of Diverse Immunomodulatory Effects of Individual IFNα Subtypes on Virus-Specific CD8+ T Cell Responses. (2019)

Clinical administration of Interferon α (IFNα) resulted in limited therapeutic success against some viral infections.Immune modulation of CD8 + T cell responses during IFNα therapy is believed to play a pivotal role in promoting viral clearance.However, these clinical studies primarily focused on IFNα subtype 2. To date, the immunomodulatory roles of the remaining 10-13 IFNα subtypes remains poorly understood, thereby precluding assessments of their potential for more effective treatments.Here, we report that virus-specific CD8 + T cell responses were influenced to various extents by individual IFNα subtypes.IFNα4, 6, and 9 had the strongest effects on CD8 + T cells, including antiproliferative effects, improved cytokine production and cytotoxicity.Interestingly, augmented cytokine responses were dependent on IFNα subtype stimulation of dendritic cells (DCs), while antiproliferative effects and cytotoxicity were mediated by IFNAR signaling in either CD8 + T cells or DCs.Thus, precise modulation of virus-specific CD8 + T cell responses may be feasible for specific antiviral immunotherapies through careful selection and administration of individual IFNα subtypes.
Two approaches to the study of radiocaesium partitioning and mobility in agricultural soils from the Chernobyl area (1995)

Two approaches were followed to study the solid-phase speciation of radiocaesium and predict its mobility and soil-to-plant transfer in agricultural soils from the Chernobyl area. Soils contaminated by Chernobyl fallout or by soluble 137Cs were used. From the application of a sequential extraction scheme and a desorption procedure that uses an ion-exchange technique, the amount of radiocaesium potentially available was determined and the time dynamics of its distribution were predicted, with a significant decrease in the exchangeable fraction over time. However, it was not possible to explain its relative mobility in a number of soils, especially in peaty soils. The ion-exchange technique, with longer desorption times, highlighted the heterogeneity and low reproducibility of fuel-particle deposition. In addition, the calculation of distribution coefficients (KD) allowed the quantification of the partitioning of radiocaesium between specific and regular exchange complex sites (only up to 25% in the latter sites) and, considering K+ and NH4+ levels in soil solution, the calculation of in situKD, which could predict radiocaesium mobility and transfer in the soils studied.
GRN: Gated Relation Network to Enhance Convolutional Neural Network for Named Entity Recognition (2019)

The dominant approaches for named entity recognition (NER) mostly adopt complex recurrent neural networks (RNN), e.g., long-short-term-memory (LSTM). However, RNNs are limited by their recurrent nature in terms of computational efficiency. In contrast, convolutional neural networks (CNN) can fully exploit the GPU parallelism with their feedforward architectures. However, little attention has been paid to performing NER with CNNs, mainly owing to their difficulties in capturing the long-term context information in a sequence. In this paper, we propose a simple but effective CNN-based network for NER, i.e., gated relation network (GRN), which is more capable than common CNNs in capturing long-term context. Specifically, in GRN we firstly employ CNNs to explore the local context features of each word. Then we model the relations between words and use them as gates to fuse local context features into global ones for predicting labels. Without using recurrent layers that process a sentence in a sequential manner, our GRN allows computations to be performed in parallel across the entire sentence. Experiments on two benchmark NER datasets (i.e., CoNLL2003 and Ontonotes 5.0) show that, our proposed GRN can achieve state-of-the-art performance with or without external knowledge. It also enjoys lower time costs to train and test.We have made the code publicly available at https://github.com/HuiChen24/NER-GRN.
Characterization of thin YBaCuO films grown by coevaporation (1989)

Thin films of the Y/sub 1/Ba/sub 2/Cu/sub 3/O/sub x/ superconductor have been grown by coevaporation and postannealing in oxygen on substrates of
IMMUNOLOGIC CROSS-REACTIONS AMONG MAMMALIAN ACUTE PHASE PROTEINS (1960)

Crystalline rabbit Cx-reactive protein has been compared immunologically with the analogous crystalline C-reactive protein of man. Immunologic cross-reactivity has been demonstrated between the acute phase proteins of man, rabbit, and monkey. Double-diffusion reactions in agar and passive cutaneous anaphylaxis reactions in vivo both indicate that these acute phase proteins are antigenically closely similar but not identical. Guinea pigs with delayed hypersensitivity to C-reactive protein exhibit delayed skin reactions when tested with Cx-reactive protein and vice versa.
Multiple-Access Strategies for Frequency-Selective MIMO Channels (2006)

In this paper, we consider frequency-selective coherent multiple-input multiple-output (MIMO) multiple-access fading channels. Assuming that each of the users employs orthogonal frequency-division multiplexing (OFDM), we introduce a multiple-access scheme that gradually varies the amount of user collision in signal space by assigning different subsets of the available OFDM tones to different users. The corresponding multiple-access schemes range from frequency-division multiple access (FDMA) (each OFDM tone is assigned to at most one user) to CDMA (each OFDM tone is assigned to all the users). We quantify the effect of signal space collision between the users by computing the ergodic capacity region for the entire family of multiple-access schemes. It is shown that the ergodic capacity region obtained by a fully collision-based scheme (CDMA) is an outer bound to that corresponding to any other multiple-access strategy. In practice, however, minimizing the amount of user collision in frequency is desirable as this minimizes the receiver complexity incurred by having to separate the interfering (colliding) signals. Our analysis shows that the impact of collision on spectral efficiency depends critically on the channel's spatial fading statistics and the number of antennas
Vortex dynamics of heavy-ion-irradiated<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">YBa</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Cu</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>7</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="normal">δ</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mo>:</mml:mo></mml:math> Experimental evidence for a reduced vortex mobility at the matching field (1998)

Electrical transport measurements in heavy-ion-irradiated ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$ thick films reveal a clear maximum of the critical current when the applied magnetic field is approximately equal to the magnetic field at which all columnar defects are occupied. This result directly indicates that vortex mobility is greatly reduced when no vacant columns are available. We suggest that this result is a vestige of the Mott insulator phase predicted for the vortex system at zero temperatures.