gebhart/patrepeval huggingface dataset:
Post-translational Modification of Bone Morphogenetic Protein-1 Is Required for Secretion and Stability of the Protein (2002)

Bone morphogenetic protein (BMP)-1 is a glycosylated metalloproteinase that is fundamental to the synthesis of a normal extracellular matrix because it cleaves type I procollagen, as well as other precursor proteins. Sequence analysis suggests that BMP-1 has six potential N-linked glycosylation sites (i.e. NXS/T) namely: Asn(91) (prodomain), Asn(142) (metalloproteinase domain), Asn(332) and Asn(363) (CUB1 domain), Asn(599) (CUB3 domain), and Asn(726) in the C-terminal-specific domain. In this study we showed that all these sites are N-glycosylated with complex-type oligosaccharides containing sialic acid, except Asn(726) presumably because proline occurs immediately C-terminal of threonine in the consensus sequence. Recombinant BMP-1 molecules lacking all glycosylation sites or the three CUB-specific sites were not secreted. BMP-1 lacking CUB glycosylation was translocated to the proteasome for degradation. BMP-1 molecules lacking individual glycosylation sites were efficiently secreted and exhibited full procollagen C-proteinase activity, but N332Q and N599Q exhibited a slower rate of cleavage. BMP-1 molecules lacking any one of the CUB-specific glycosylation sites were sensitive to thermal denaturation. The study showed that the glycosylation sites in the CUB domains of BMP-1 are important for secretion and stability of the molecule.
Comprehensive Audiometric Analysis of Hearing Impairment and Tinnitus After Cisplatin-Based Chemotherapy in Survivors of Adult-Onset Cancer (2016)

Follow-up of adult-onset cancer survivors given cisplatin should include routine inquiry for hearing status and tinnitus, referral to audiologists as clinically indicated, and hypertension control. Patients should be urged to avoid noise exposure, ototoxic drugs, and other factors that further damage hearing.
Stoichiometry and Specificity of In Vitro Phosphopantetheinylation and Aminoacylation of the Valine-Activating Module of Surfactin Synthetase (1998)

Surfactin synthetase is the enzyme responsible for biosynthesis of the lipoheptapeptide antibiotic surfactin by Bacillus subtilis. Fragments of SrfB1, the L-valine-activating module of the second subunit of surfactin synthetase, were overproduced in Escherichia coli. In addition to a 143-kDa SrfB1 fragment that contains four domains putatively involved in activation (adenylation domain), autoaminoacylation (peptidyl carrier protein (PCP) domain), and peptide bond formation (two condensation domains), subfragments comprising two domains (104-kDa condensation-adenylation and 73-kDa adenylation-PCP), and one domain (18-kDa PCP) were also overproduced in and purified from E. coli as N-terminal hexahistidine fusion proteins. Incubation of these domains with pure Sfp, a phosphopantetheinyl transferase (PPTase) from B. subtilis, and CoA allowed quantitation of posttranslational phosphopantetheinylation of Ser999 by mass spectrometry for the 18-kDa PCP fragment and by radioassay using cosubstrate [3H] pantetheinyl-coenzyme A for all PCP-containing constructs. The phosphopantetheine stoichiometry correlated with the subsequent mole fractions of [14C] valyl groups that could be covalently transferred to these holo-PCP domains. In turn, the catalytic efficiency of intramolecular aminoacylation of the 143-kDa fragment could be compared with the reaction "in trans" between adenylation and PCP fragments of SrfB1. The corresponding holo-PCP domain of the next module, SrfB2, was not detectably aminoacylated by SrfB1, indicative of protein-protein recognition between adenylation and cognate PCP domains. These results should permit future exploration of the timing and specificity of peptide bond formation by this class of biosynthetic enzymes.
Linearizing nonlinear dynamics using deep learning (2022)

The majority of systems of practical interest are characterized by nonlinear dynamics. This renders the control and optimization of such systems a complex task owing to their nonlinear behaviour. Standard methods of dealing with nonlinear systems such as linearizing around a fixed point may not be an effective strategy for many systems, thus requiring an alternative approach. For this reason, we propose a novel deep learning framework to discover a transformation of a nonlinear dynamical system to an equivalent higher dimensional linear system using data generated from identification experiments. We demonstrate that the resulting learned linear representation accurately captures the dynamics of the original system for a wide range of conditions defined by the training dataset used. As a result of this, we show that the learned linear model can subsequently be used for the successful control of the original system. We demonstrate this by applying the proposed framework to three examples; a benchmark example from the literature, and two practical, complex nonlinear dynamical systems from the chemical engineering domain: the Continuous Stirred Tank Reactor (CSTR) system and finally the four-tank system.
Continuous passive motion after primary total knee arthroplasty: Does it offer any benefits? (1997)

We report a prospective randomly controlled trial to examine the effectiveness of continuous passive motion (CPM) in improving postoperative function and range of movement after total knee arthroplasty (TKA). We allocated 53 patients (57 knees) to one of three postoperative regimes: no CPM (n = 19); CPM at 0 to 40 degrees (0 to 40 CPM; n = 18); and CPM at 0 to 70 degrees (0 to 70 CPM; n = 20). Those in the CPM groups had CPM for 48 hours and all patients had an identical regime of physiotherapy. There was an even distribution of various cemented and cementless TKAs in each group. Patients were assessed preoperatively and at one week and at one year postoperatively. At one week, there was a statistically significant increase in the range of flexion and total range of movement in the 0 to 70 CPM group compared with the no-CPM group. At one year we found no significant differences in mean flexion, overall range of movement, fixed flexion deformity or functional results in the three groups. Those who had CPM had a significant increase in analgesic requirement (p = 0.04). There was an increased mean blood drainage postoperatively in those who had 0 to 70 CPM (1558 ml) compared with those with no CPM (956 ml) (t = 2.96, p = 0.005) and with 0 to 40 CPM (1017 ml) (t = 2.62, p = 0.01). Our findings show that CPM had no significant advantage in terms of improving function or range of movement, and that its use increased blood loss and analgesic requirements.
A general approach to iridoids by applying a new Julia olefination and a tandem anion-radical-carbocation crossover reaction (2016)

A unified, asymmetric approach to the total synthesis of naturally occurring iridoids is presented. The synthesis features a recently discovered ortho → α transmetalation of alkyl aryl sulfone carbanions, thus enabling Julia reactions, by which so far hardly accessible disilylated olefins have been obtained. A subsequent tandem alkoxycarbonylation/oxidative radical cyclization afforded substituted cyclopentane building blocks with high diastereoselectivity. These compounds serve as unique central intermediates for short access to dihydronepetalactone, dolicholactone and potentially other iridoids.
Supplementary Figure Legend from Tumor Suppressor Functions of miR-133a in Colorectal Cancer (2023)

&lt;p&gt;PDF file - 56K&lt;/p&gt;
Africa Is Poised to Become the Next Energy Superpower (2003)

Abstract In early 2002 Washington DC policy-makers suggested, that within a generation, Africa might supplant the Middle East as the United States most critically strategic energy supplier. This is a significant departure from the situation, which permeated the previous three decades when the Middle East was perceived as the singularly most important source of world energy. Such potential of Africa, if realized, would have a decided influence on future energy economics and geopolitics. Grandiose statements notwithstanding, is Africa (and in this context this implies the Sub-Saharan regions) at the brink of becoming an energy superpower? Does Africa have the potential reserves, production capability and capacity for such a role? This is not just an issue of geology but also one that touches on the rest of the development of the continent, its economic and political future. This paper presents an in-depth investigation of the true energy potential of Africa. One obvious focus is the potential of deep- and ultra-deep-water production, spanning almost the entire Western Coast of Africa. Areas of interest involve the deep waters off the Gulf of Guinea and the continental shelves and include the inland basins of Benin, Nigeria, Cameroon, Sao Tome and Principe, Equatorial Guinea, Gabon, Congo and Angola. We are proposing here a number of mechanisms of potential production and couplets of exploitation, i.e., optimum and likely ways to link producers with consumers, taking into account distances and hydrocarbon volumes and incorporating regional integration and co-operation. Finally, we are offering conclusions and recommendations that will enhance sustainable energy development in Africa, and continuous availability of uninterrupted global supply of oil and gas, which indeed will usher the era of Africa as an energy superpower.
Shared Sensemaking: Enhancing the Value of Collaborative Web Search Tools (2008)

Current Web search tools, such as browsers and search engine sites, are designed for a single user, working alone. However, users frequently need to collaborate on information-finding tasks; for example, students often work together in groups on homework assignments. To address this need, we have prototyped and evaluated several collaborative web search tools (S 3, SearchTogether, and CoSearch) that enable synchronous, asynchronous, colocated, and remote collaboration on Web search tasks. Such tools could be further enhanced by enabling collaborators to transition from shared Web searching to joint sensemaking activities; the products of this sensemaking could in turn be offered to others in response to their queries, enabling a community-level search/sensemaking cycle.
Guidance on home blood pressure monitoring: A statement of the HOPE Asia Network (2018)

Hypertension is an important modifiable cardiovascular risk factor and a leading cause of death throughout Asia. Effective prevention and control of hypertension in the region remain a significant challenge despite the availability of several regional and international guidelines. Out-of-office measurement of blood pressure (BP), including home BP monitoring (HBPM), is an important hypertension management tool. Home BP is better than office BP for predicting cardiovascular risk and HBPM should be considered for all patients with office BP ≥ 130/85 mm Hg. It is important that HBPM is undertaken using a validated device and patients are educated about how to perform HBPM correctly. During antihypertensive therapy, monitoring of home BP control and variability is essential, especially in the morning. This is because HBPM can facilitate the choice of individualized optimal therapy. The evidence and practice points in this document are based on the Hypertension Cardiovascular Outcome Prevention and Evidence (HOPE) Asia Network expert panel consensus recommendations for HBPM in Asia.
Donor–acceptor interface modification by zwitterionic conjugated polyelectrolytes in polymer photovoltaics (2013)

We report that we can enhance the performance of polymer photovoltaics by introducing materials with dipoles at the donor–acceptor interface of the polymer solar cells. We use a zwitterionic conjugated polyelectrolyte (ZCPE) as an interfacial layer in a model bi-layer system consisting of donor and acceptor polymers. We find an increase in short-circuit current and fill factor when a 2 nm thin layer of ZCPE is introduced between donor and acceptor polymers. Absorption of light in the ZCPE interlayer contributes to the photocurrent, and, as revealed by time-resolved pump–push optical spectroscopy, the interlayer reduces the probability of electron–hole recombination at the donor–acceptor interface.
Restoration of noisy images blurred by a random point spread function (2002)

An estimation method based on the constrained least-squares principle is presented for the restoration of images distorted by a random point spread function and additive measurement noise. The proposed filter modifies the conventional constrained least-squares filter by incorporating additional statistical characteristics about the randomness of the point spread function. Simulation results show that the proposed method outperforms the conventional constrained least-squares method, which neglects the randomness of the point spread function. For space-invariant systems, the modified constrained least-squares filter can be constructed in the discrete frequency domain and its overall computation can be carried out using the fast Fourier transform.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figure S1 from Misannotated Multi-Nucleotide Variants in Public Cancer Genomics Datasets Lead to Inaccurate Mutation Calls with Significant Implications (2023)

&lt;p&gt;Example knitr report based on CBio export for 26 TCGA melanoma samples&lt;/p&gt;
A Multilingual Embodied Conversational Agent (2005)

In our paper last year, we described our language-training program, which utilizes Baldi as a tutor, who guides students through a variety of exercises designed to teach vocabulary and grammar, to improve speech articulation, and to develop linguistic and phonological awareness. In this paper, we describe the technology of Baldi in more detail, and how it has been enhanced along a number of dimensions. First, Baldi is now multilingual and is capable of acquiring new languages fairly easily. Second, Baldi has grown a body to allow the communication of communicative gesture.
Water‐Based Paintable LiCoO2 Microelectrodes: A High‐Rate Li‐Ion Battery Free of Conductive and Binder Additives (2019)

Abstract A simple, low‐cost, and environmentally friendly water‐based colloidal spray‐painting process is developed to obtain mechanically stable microelectrodes of pure LiCoO 2 on stainless steel disks, which display reversible high‐rate discharge capacity and good cyclability. By using a simple nanostructuring process with commercially available LiCoO 2 , the use of dispersant, conductive, and binder additives during the electrode preparation is completely avoided. The nanostructuring approach is based on: i) planetary ball milling and annealing of LiCoO 2 microparticles and ii) LiCoO 2 surface modification through dissociative H 2 O adsorption during contact with air‐ and water‐based colloid preparation. The coating technique involves: i) water‐based colloid preparation, ii) spray‐coating, and iii) post‐treatment (drying and calcination) processes. The effects of particle size distribution, shape, crystallinity, specific surface area, and LiCoO 2 surface modification on the electrode architecture (roughness, thickness, packing density, and porosity) are studied, together with their impact on the final electrochemical performances of batteries assembled with such a LiCoO 2 electrode.
The Determination of Microamounts of Cadmium, Copper, Nickel and Manganese in Fats and Oils by Atomic Absorption Spectrophotometry (1975)

A rapid and precise method for the determination of microamounts of cadmium, copper, nickel and manganese in fats and oils has been studied. The samples were decomposed by wet-digestion procedure using sulfuric acid and hydrogen peroxide (30%), then, cadmium and other metals in the decomposed solution were extracted into methyl isobutyl ketone as the complexes with sodium diethyldithiocarbamate. The extracts were directly atomized into the air-acetylene flame, and the absorbances were measured at 228.8nm for cadmium, 324.7nm for copper, 232.0nm for nickel and 279.5nm for manganese. The most suitable pH for the extraction of these metals was about 7, and these metals were quantitatively extracted into methyl isobuthyl ketone by once extraction.The proposed method was evaluted with respect to recovery and reproducibility by carring out collaborative studies on the samples which were prepared by adding known amounts of cadmium and other metals to soybean oil. The results thus obtained showed good agreement with the theoretical values and satisfactory reproducibility.
The noise from turbulence convected at high speed (1963)

Abstract The theory initiated by Lighthill (1952) for the purpose of estimating the sound radiated from a turbulent fluid flow is extended to deal with both the transonic and supersonic ranges of eddy convection speed. The sound is that which would be produced by a distribution of convected acoustic quadrupoles whose instantaneous strength per unit volume is given by a turbulence stress tensor, T{j. At low subsonic speeds the radiated intensity increases with the eighth power of velocity although quadrupole convection augments this basic dependence by a factor 11 — cos | ~5, where M is the eddy convection Mach number and Q the angular position of an observation point measured from the direction of eddy motion. At supersonic speeds the augmentation factor becomes singular whenever the eddy approaches the observation point at sonic velocity, Mcos At that condition a quadrupole degenerates into its constituent simple sources, for each quadrupole element moves with the acoustic wave front it generates and cancelling contributions from opposing sources, so essential in determining quadrupole behaviour, cannot combine but are heard independently. This simple-source radiation is likened to a type of eddy Mach wave whose strength increases with the cube of a typical flow velocity. When quadrupoles approach the observer with supersonic speed sound is heard in reverse time, but is once again of a quadrupole nature and the general low-speed result is again applicable. The limiting high-speed form of the convection augmentation factor is | Mcos 6|-5 which combines with the basic eighth power velocity law to yield the result that radiation intensity increases only as the cube of velocity at high supersonic speed. The mathematical theory is developed in some detail and supported by more physical arguments, and the paper is concluded by a section where some relevant experimental evidence is discussed.
Flow Cytometric Analysis of Canine Umbilical Cord Blood Lymphocytes (2008)

Lymphocyte subsets in canine umbilical cord blood were flow cytometrically analyzed and compared with those of the dams' peripheral blood. The proportion of CD3+ T lymphocytes, CD21+CD3- B lymphocytes, and CD3-CD21- non-T non-B lymphocytes in umbilical cord blood was 52.9%, 30.4%, and 16.7%, respectively. T lymphocyte/B lymphocyte ratio was significantly lower in the umbilical cord blood than in the dams' peripheral blood (2.1 +/- 1.4 versus 11.0 +/- 8.1, P < 0.001). In contrast, CD4+ lymphocyte/CD8+ lymphocyte ratio was significantly higher in the umbilical cord blood than in the dams' peripheral blood (7.6 +/- 2.2 versus 1.8 +/- 0.6, P<0.001). These findings clarified the phenotypic characters of canine umbilical cord blood lymphocytes.
Purealidin S and Purpuramine J, Bromotyrosine Alkaloids from the Fijian Marine Sponge Druinella sp. (2002)

Two bromotyrosine alkaloids, purealidin S (2) and purpuramine J (5), were isolated from the Fijian marine sponge Druinella sp. Eight known bromotyrosine compounds were also isolated. This is the first report of a bromotyrosine N-oxide containing alkaloid. These two compounds were found to have moderate cytotoxic activity. In addition, bioassay data for the eight known bromotyrosine metabolites are reported.
Where Is The Fake? Patch-Wise Supervised Gans For Texture Inpainting (2020)

We tackle the problem of texture inpainting where the input images are textures with missing values along with masks that indicate the zones that should be generated. Many works have been done in image inpainting with the aim to achieve global and local consistency. But these works still suffer from limitations when dealing with textures. In fact, the local information in the image to be completed needs to be used in order to achieve local continuities and visually realistic texture inpainting. For this, we propose a new segmentor discriminator that performs a patch-wise real/fake classification and is supervised by input masks. During training, it aims to locate the generated parts (which we will call fake parts in consistency with the GAN framework), thus making the difference between real and fake patches given one image. We tested our approach on the publicly available DTD dataset, as well as Electo-Magnetic borehole images dataset and showed that it achieves state-of-the-art performances and better deals with local consistency than existing methods.
Experience-based learning support system to enhance child learning in a museum (2015)

This paper presents a support system to assist learning within museums. Museums represent important places of scientific learning for children. However, because the main learning method in museums is the study of displayed specimens and their corresponding explanations, the motivation of a child to learn is low. Hence, we are developing an experience-based learning support system such as entertainment that will enable learners to enhance their motivation to learn in any museum. We develop two systems to realize experience-based entertainment. One is "Live Biblia," which is a digital installed book system that uses real fossil. Another is the immersive learning system we called "Body Experience and Sense of Immersion in Digital paleontological Environment" or "BESIDE," which enables learners to explore a virtual paleontological environment. In this paper, we present a summary of the current system of Live Biblia and BESIDE.
Foldable Graphene Electronic Circuits Based on Paper Substrates (2013)

Graphene electronic circuits are prepared on paper substrates by using graphene nanoplates and applied to foldable paper-based electronics. The graphene circuits show a small change in conductance under various folding angles and maintain an electronic path on paper substrates after repetition of folding and unfolding. Foldable paper-based applications with graphene circuits exhibit excellent folding stability.
Personalizable and Interactive Sequence Recommender System (2018)

Sequence recommender systems assist people in making decisions, such as which product to purchase and what places to visit on vacation. Despite their ubiquity, most sequence recommender systems are black boxes and do not offer justifications for their recommendations or provide user controls for steering the algorithm. In this paper, we design and develop an interactive sequence recommender system (SeRIES) prototype that uses visualizations to explain and justify the recommendations and provides controls so that users may personalize the recommendations. We conducted a user study comparing SeRIES to a black-box system with 12 participants using real visitor trajectory data in Melbourne and show that SeRIES users are more informed about how the recommendations are generated, more confident in following the recommendations, and more engaged in the decision process.