gebhart/patrepeval huggingface dataset:
Widespread recognition of 5′ splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides (2012)

An established paradigm in pre-mRNA splicing is the recognition of the 5' splice site (5'ss) by canonical base-pairing to the 5' end of U1 small nuclear RNA (snRNA). We recently reported that a small subset of 5'ss base-pair to U1 in an alternate register that is shifted by 1 nucleotide. Using genetic suppression experiments in human cells, we now demonstrate that many other 5'ss are recognized via noncanonical base-pairing registers involving bulged nucleotides on either the 5'ss or U1 RNA strand, which we term "bulge registers." By combining experimental evidence with transcriptome-wide free-energy calculations of 5'ss/U1 base-pairing, we estimate that 10,248 5'ss (∼5% of human 5'ss) in 6577 genes use bulge registers. Several of these 5'ss occur in genes with mutations causing genetic diseases and are often associated with alternative splicing. These results call for a redefinition of an essential element for gene expression that incorporates these registers, with important implications for the molecular classification of splicing mutations and for alternative splicing.
Tuning the Peri Effect for Enantioselectivity: Asymmetric Hydrogenation of Unfunctionalized Olefins with the BIPI Ligands (2013)

Abstract The modular nature of the BIPI ligands allows for systematic optimization of each ligand region. The development of ligands optimized for asymmetric hydrogenation of the challenging unfunctionalized olefin substrate class is described. The naphthyl peri position, C‐8, has been identified as a critical stereocontrol element in the design of these ligands. Highly enantioselective ligands suitable for hydrogenation of tri‐ and tetrasubstituted olefins are detailed.
Taste, Chemical Biology of (2008)

Abstract The mammalian sense of taste is crucial for evaluating food palatability and nutritional quality. To achieve the detection of relevant chemicals, evolution has shaped a set of receptor molecules that allow the detection of five basic taste qualities: sweet, umami, bitter, salty, and sour. Each taste modality has unique characteristics and serves a distinct function for an animal's nutrition. Therefore, we address the characteristics, the recent advances, the persisting difficulties, and the future perspectives of the basic taste qualities in separate paragraphs. Enormous progress has been made in the identification and the characterization of taste receptor molecules, and in the growing number of animal genomes accessible from databases, which has inspired us to devote a section of this review to discuss a series of sophisticated evolutionary studies on taste receptor molecules. Finally, evidence is accumulating to show that taste receptor and signal transduction molecules have nongustatory functions as well. The extragustatory expression of such genes and the resulting implications are summarized in the final section.
Neutron Radiography of Irradiated Nuclear Fuel at Idaho National Laboratory (2015)

Neutron radiography of irradiated nuclear fuel provides more comprehensive information about the internal condition of irradiated nuclear fuel than any other non-destructive technique to date. Idaho National Laboratory (INL) has multiple nuclear fuels research and development programs that routinely evaluate irradiated fuels using neutron radiography. The Neutron Radiography reactor (NRAD) sits beneath a shielded hot cell facility where neutron radiography and other evaluation techniques are performed on these highly radioactive objects. The NRAD currently uses the foil-film transfer technique for imaging fuel that is time consuming but provides high spatial resolution. This paper describes the NRAD and hot cell facilities, the current neutron radiography capabilities available at INL, planned upgrades to the neutron imaging systems, and new facilities being brought online at INL related to neutron imaging.
Commercial potato protein concentrate as a novel source for thermoformed bio-based plastic films with unusual polymerisation and tensile properties (2015)

Films thermoformed from commercial potato protein concentrate exhibited a constant Young's modulus and increasing strain at break with increasing processing temperature, in contrast to the usually observed behaviour for protein-based materials.
Efficient Generation of Fusion Flames Using PW-ps Laser Pulses for Ultrahigh Acceleration of Plasma Blocks by Nonlinear (Ponderomotive) Forces (2014)

Changing the high intensity interaction time of lasers with plasma from nanosecond duration to picoseconds results in a categorically different regime. With high intensity picoseconds laser pulses, the optical energy is converted directly into kinetic energy of plasma blocks without thermal losses, without delays by collisions, and with exclusion of most of the instabilities. Following the long known theory by the nonlinear (ponderomotive) force, the plasma receives a predicted ultrahigh acceleration in agreement with measurements by Sauerbrey. Interaction of the generated plasma blocks with solid state fusion fuel should produce a side-on ignition of a Chu-Bobin fusion flame. Using hydrodynamics with separate electron and ion fluids, detailed properties can be studied about shock generation, including the varying velocity of the flame fronts far . Results from recent computations confirm how the collective nonthermal nonlinear force driven plasma interactions are causing only marginal electron heating.
Fusiform Correlates of Facial Memory in Autism (2013)

Prior studies have shown that performance on standardized measures of memory in children with autism spectrum disorder (ASD) is substantially reduced in comparison to matched typically developing controls (TDC). Given reported deficits in face processing in autism, the current study compared performance on an immediate and delayed facial memory task for individuals with ASD and TDC. In addition, we examined volumetric differences in classic facial memory regions of interest (ROI) between the two groups, including the fusiform, amygdala, and hippocampus. We then explored the relationship between ROI volume and facial memory performance. We found larger volumes in the autism group in the left amygdala and left hippocampus compared to TDC. In contrast, TDC had larger left fusiform gyrus volumes when compared with ASD. Interestingly, we also found significant negative correlations between delayed facial memory performance and volume of the left and right fusiform and the left hippocampus for the ASD group but not for TDC. The possibility of larger fusiform volume as a marker of abnormal connectivity and decreased facial memory is discussed.
Separation of Water and Organic Solvnts by Use of a Microreactor with Plural Partition Walls in the Center of the Channel. (2004)

double Y型マイクロリアクタによる水と有機溶媒の分離について検討した. 粘性率がほぼ等しい水とシクロヘキサンを汎用のリアクタに等しい流速で供給すると, 目視的には層流が観察されたが, 排出液は両者の混合物となった. これは, ガラスチャンネル内壁が親水性であるためと考えられる. そこで,チャンネル中央に等間隔で不連続な仕切壁を設けた破線状ガイドライン構造としたところ, 分離能は飛躍的に向上した.
Design of Heterogeneous Catalysts via Multiple Active Site Positioning in Organic−Inorganic Hybrid Materials (2003)

Catalytic materials bearing multiple sulfonic acid functional groups and positioned at varying distances from one another on the surface of mesoporous solids are prepared to explore the effects that the spatial arrangement of active sites have on catalytic activity and selectivity. A series of organosiloxane precursors containing either disulfide or sulfonate ester functionalities (synthons of the eventual sulfonic acid groups) are synthesized. From these molecular precursors, a variety of organic-inorganic hybrid, mesostructured SBA-15 silica materials are prepared using a postsynthetic grafting procedure that leads to disulfide and sulfonate ester modified silicas: [Si]CH(2)CH(2)CH(2)SS-pyridyl, 2.SBA, [Si]CH(2)CH(2)CH(2)SSCH(2)CH(2)CH(2)[Si], 3.SBA, [Si]CH(2)CH(2)(C(6)H(4))(SO(2))OCH(2)CH(3), 4.SBA, and [Si]CH(2)CH(2)(C(6)H(4))(SO(2))OC(6)H(4)O(SO(2))(C(6)H(4))CH(2)CH(2)[Si], 6.SBA ([Si] = (tbd1;SiO)(x)()(RO)(3)(-)(x)()Si, where x = 1, 2). By subsequent chemical derivatization of the grafted species, thiol and sulfonic acid modified silicas are obtained. The materials are characterized by a variety of spectroscopic ((13)C and (29)Si CP MAS NMR, X-ray diffraction) and quantitative (TGA/DTA, elemental analysis, acid capacity titration) techniques. In all cases, the organic fragment of the precursor molecule is grafted onto the solid without measurable decomposition, and the precursors are, in general, attached to the surface of the mesoporous oxide by multiple siloxane bridges. The disulfide species 2.SBA and 3.SBA are reduced to the corresponding thiols 7.SBA and 8.SBA, respectively, and 4.SBA and 6.SBA are transformed to the aryl sulfonic acids 11.SBA and 12.SBA, respectively. 7.SBA and 8.SBA differ only in terms of the level of control of the spatial arrangement of the thiol groups. Both 7.SBA and 8.SBA are further modified by oxidation with hydrogen peroxide to produce the alkyl sulfonic acid modified materials 9.SBA and 10.SBA, respectively. The performances of the sulfonic acid containing SBA-15 silica materials (with the exception of 12.SBA) are tested as catalysts for the condensation reaction of phenol and acetone to bisphenol A. The alkyl sulfonic acid modified material 10.SBA derived from the cleavage and oxidation of the dipropyl disulfide modified material 3.SBA is more active than not only its monosite analogue 9.SBA, but also the presumably stronger acid aryl sulfonic acid material 11.SBA. It appears that a cooperative effect between two proximal functional groups may be operating in this reaction.
Diversity in the Acute CD8 T Cell Response to Vaccinia Virus in Humans (2005)

Orthopoxviruses have complex proteomes. Infection provokes a brisk CD8 response, which is required in some systems for recovery from primary infection. Little is known concerning the Ags and epitopes recognized by CD8 T cells. We examined the fine specificity of cloned and bulk human vaccinia-specific CD8 CTL by expressing polypeptide fragments from a library of vaccinia genomic DNA. This epitope discovery method emphasizes virus-specific biological activity, as the responder cells are all reactive with whole vaccinia virus. Sixteen novel epitopes, restricted by several HLA A and B alleles, were defined to the nomamer peptide level in diverse vaccinia open reading frames. An additional seven epitope were mapped to short regions of vaccinia proteins. Targets of the CD8 response included proteins assigned to structural, enzymatic, transcription factor, and immune evasion functions, and included members of all viral kinetic classes. Most epitopes were conserved in other orthopoxviruses. Responses to at least 18 epitopes were detected within a single blood sample, revealing a surprising degree of diversity. These epitopes will be useful in natural history studies of CD8 responses to vaccinia, a nonpersisting virus with long-term memory, and in the design and evaluation of attenuated and replication-incompetent vaccinia strains being tested for variola and monkeypox prevention and for the delivery of heterologous Ags.
On the finite-SNR Diversity-Multiplexing Tradeoff in large Rayleigh product channels (2015)

The Diversity-Multiplexing Tradeoff (DMT) is studied for the large Rayleigh product channel at non-asymptotic SNRs. The first result is that, as matrix dimensions growing to infinity, the channel capacity converges to a Gaussian random variable. Based on this, we derive a compact expression for the finite-SNR DMT. From the analytical and numerical results, we gain useful insight into the fundamental tradeoff of the considered channel model in the realistic SNR regime.
Dipole Crosstalk in an Inverse Cardiac Generator (1978)

Previous work has demonstrated that dipole crosstalk occurs in an inverse cardiac generator consisting of multiple fixed dipoles when only the summed-square error of the potentials is minimized. This paper provides evidence that when cardiac electrical activity can be approximated by a single locatable dipole, crosstalk can be decreased by adding an additional term to the function that is minimized.
Short laser pulse compression in air (2004)

A negatively chirped laser pulse propagating in air compresses and focuses resulting in intensity increase and ionization near focal region. Using femtosecond laser we observe pulse compression and focusing that is controlled by induced chirp.
Charge order transitions in manganese oxides (2001)

The reflectance of a La0.85Sr0.15MnO3 crystal and the transmittance of LiMn2O4 powders have been measured for different temperatures ranging from 330 K down to 10 K. Synchrotron radiation was used in the far infrared range, while laboratory sources were used above 600 cm-1. These oxides exhibit major changes of the phonon spectrum as T becomes lower than T* (T* = 180 K for La0.85Sr0.15MnO3 and T* = 290 K, with a hysteresis of about 15 K for LiMn2O4). For both of these manganese oxides, the increasing number of phonon structures observed for T<T* is ascribed to a rupture of the cubic crystal symmetry. The deformation of the high temperature cubic crystal follows die development into a charge ordered phase at T*, as recently observed by neutron scattering studies.
Specializing FGPU for Persistent Deep Learning (2021)

Overlay architectures are a good way to enable fast development and debug on FPGAs at the expense of potentially limited performance compared to fully customized FPGA designs. When used in concert with hand-tuned FPGA solutions, performant overlay architectures can improve time-to-solution and thus overall productivity of FPGA solutions. This work tunes and specializes FGPU, an open source OpenCL-programmable GPU overlay for FPGAs. We demonstrate that our persistent deep learning (PDL )-FGPU architecture maintains the ease-of-programming and generality of GPU programming while achieving high performance from specialization for the persistent deep learning domain. We also propose an easy method to specialize for other domains. PDL-FGPU includes new instructions, along with micro-architecture and compiler enhancements. We evaluate both the FGPU baseline and the proposed PDL-FGPU on a modern high-end Intel Stratix 10 2800 FPGA in simulation running persistent DL applications (RNN, GRU, LSTM), and non-DL applications to demonstrate generality. PDL-FGPU requires 1.4–3× more ALMs, 4.4–6.4× more M20ks, and 1–9.5× more DSPs than baseline, but improves performance by 56–693× for PDL applications with an average 23.1% degradation on non-PDL applications. We integrated the PDL-FGPU overlay into Intel OPAE to measure real-world performance/power and demonstrate that PDL-FGPU is only 4.0–10.4× slower than the Nvidia V100.
Milk Exosomes Prevent Intestinal Inflammation in a Genetic Mouse Model of Ulcerative Colitis: A Pilot Experiment (2020)

Milk exosomes have cytoprotective/anti-inflammatory activity in a genetic mouse model of ulcerative colitis. The mechanisms behind this need to be elucidated. This pilot study needs verification before a therapeutic strategy is developed.
Sequential magnetic switching in Fe/MgO(001) superlattices (2018)

Polarized neutron reflectometry is used to determine the sequence of magnetic switching in interlayer exchange coupled Fe/MgO(001) superlattices in an applied magnetic field. For 19.6 \AA{} thick MgO layers we obtain a ${90}^{\ensuremath{\circ}}$ periodic magnetic alignment between adjacent Fe layers at remanence. In an increasing applied field the top layer switches first followed by its second-nearest neighbor. For 16.4 \AA{} MgO layers, a ${180}^{\ensuremath{\circ}}$ periodic alignment is obtained at remanence and with increasing applied field the layer switching starts from the two outermost layers and proceeds inwards. This sequential tuneable switching opens up the possibility of designing three-dimensional magnetic structures with a predefined discrete switching sequence.
Graph Pooling with Representativeness (2020)

Graph Neural Networks (GNNs), which extend deep neural networks to graph-structured data, have attracted increasing attention. They have been proven to be powerful for numerous graph related tasks such as graph classification, link prediction, and node classification. To adapt GNNs to graph classification, recent works aim to learn graph-level representation through a hierarchical pooling procedure. One major direction is to select important nodes to hierarchically coarsen the input graph and gradually reduce the information into the graph representation. However, most of the existing methods only select important nodes, which can be redundant and cannot represent the original graph well. Meanwhile, the information of non-selected nodes is often overlooked when generating a new coarser graph, which may lead to the tremendous loss of important structural and node feature information. In this paper, we propose a novel pooling operator RepPool to learn hierarchical graph representations. Specifically, we introduce the concept of representativeness that is combined with the importance for node selection and we provide a learnable way to integrate non-selected nodes. By combining the RepPool operator with conventional GCN convolutional layers, a hierarchical graph classification architecture is developed. Extensive experiments on various public benchmarks have demonstrated the effectiveness of the proposed method. The implementation of the proposed framework is available.
Benchmarking at the Frontier of Hardware Security: Lessons from Logic Locking (2020)

Integrated circuits (ICs) are the foundation of all computing systems. They comprise high-value hardware intellectual property (IP) that are at risk of piracy, reverse-engineering, and modifications while making their way through the geographically-distributed IC supply chain. On the frontier of hardware security are various design-for-trust techniques that claim to protect designs from untrusted entities across the design flow. Logic locking is one technique that promises protection from the gamut of threats in IC manufacturing. In this work, we perform a critical review of logic locking techniques in the literature, and expose several shortcomings. Taking inspiration from other cybersecurity competitions, we devise a community-led benchmarking exercise to address the evaluation deficiencies. In reflecting on this process, we shed new light on deficiencies in evaluation of logic locking and reveal important future directions. The lessons learned can guide future endeavors in other areas of hardware security.
Microwave Ovens—Out of the Kitchen (2001)

We are all aware of the advantages cooking or heating meals in a microwave oven can offer, but we may be less familiar with what this technology brings to the field of chemistry. This paper reviews the applications of microwaves in the chemical laboratory, including their use in undergraduate laboratory classes. We show that microwave ovens have successfully made the transition from kitchens to laboratories and the story continues. Perhaps the greatest impact of microwaves in the laboratory over the past 20 years has been in analytical chemistry, where rapid and efficient heating of samples in closed vessels or flow-through systems has revolutionized sample preparation methodology. The use of microwaves in extraction procedures before chromatographic analysis has sharply reduced the total analysis time and has allowed larger numbers of samples to be analyzed. More recently microwave technology has expanded into other branches of chemistry and is now being used in the relatively new field of combinatorial chemistry for fast preparation of large numbers of similar compounds.
Cerebrospinal Fluid Proteomic Profiling of HIV-1-Infected Patients with Cognitive Impairment (2007)

Advanced HIV-1 infection is commonly associated with progressive immune suppression and the development of cognitive, motor, and behavior disturbances. In its most severe form, it is diagnosed as HIV-1 associated dementia (HAD) and can progress to profound functional disability and death. Despite prodigious efforts to uncover biomarkers of HAD, none can adequately reflect disease onset or progression. Thus, we developed a proteomics platform for HAD biomarker discovery and used it to perform a pilot study on cerebrospinal fluid (CSF) from HIV-1-infected people with or without HAD. A 2-dimensional electrophoresis (2-DE) map of a HAD CSF proteome was focused on differentially expressed proteins. 2-DE difference gel electrophoresis (2-D DIGE) analysis showed >90 differences in protein spots of which 20 proteins were identified. Differential expression of 6 proteins was validated by Western blot tests and included vitamin D binding protein, clusterin, gelsolin, complement C3, procollagen C-endopeptidase enhancer 1, and cystatin C. We posit that these proteins, alone or together, are potential HAD biomarkers.
Stool DNA testing for the detection of colorectal neoplasia in patients with inflammatory bowel disease (2013)

These findings demonstrate the feasibility of stool DNA testing for non-invasive detection of colorectal neoplasia associated with inflammatory bowel disease.
DeepCABAC: A Universal Compression Algorithm for Deep Neural Networks (2020)

In the past decade deep neural networks (DNNs) have shown state-of-the-art performance on a wide range of complex machine learning tasks. Many of these results have been achieved while growing the size of DNNs, creating a demand for efficient compression and transmission of them. In this work we present DeepCABAC, a universal compression algorithm for DNNs that is based on applying Context-based Adaptive Binary Arithmetic Coder (CABAC) to the DNN parameters. CABAC was originally designed for the H.264/AVC video coding standard and became the state-of-the-art for the lossless compression part of video compression. DeepCABAC applies a novel quantization scheme that minimizes a rate-distortion function while simultaneously taking the impact of quantization to the DNN performance into account. Experimental results show that DeepCABAC consistently attains higher compression rates than previously proposed coding techniques for DNN compression. For instance, it is able to compress the VGG16 ImageNet model by x63.6 with no loss of accuracy, thus being able to represent the entire network with merely 9 MB. The source code for encoding and decoding can be found at https://github.com/fraunhoferhhi/DeepCABAC.
Fabrication and testing of a PZT thin film high-pressure sensor (2001)

Abstract A thin film pressure sensor was fabricated and tested to a high pressure of 40,000 psi. The MEMS fabrication process utilized a 0.5 μm film of sol-gel deposited PZT (PbZr0.52Ti0.48O3) and platinum metallization for the top and bottom electrodes. The sensor was mounted on a customized stainless steel housing and placed into a high-pressure vessel for both calibration and testing. The sensor responded non-linearly to the applied pressure and generated a charge of 202 pico coulombs at the maximum tested pressure of 40,000 psi. The shape and configuration of the Pt/PZT/Pt structure has been redesigned to correct for the non-linear response and to increase the charge output of the device. Key Words: sensorpressurePZTsol-gelpiezoelectricMEMS