gebhart/patrepeval huggingface dataset:
Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal (2022)

Abstract Hundreds of genome-wide loss-of-function screens have been performed, as part of efforts such as The Cancer Dependency Map, to create a catalog of genetic dependencies in a diverse set of cancer contexts. In recent years, large-scale screening efforts have shifted perturbation technology from RNAi to CRISPR-Cas9, due to the superior efficacy and specificity of CRISPR-Cas9-mediated approaches. However, questions remain about the extent to which partial suppression of gene targets could result in selective dependency across cell lines, potentially revealing a larger set of targetable cancer vulnerabilities than can be identified using CRISPR knockout alone. Here, we use CRISPR-Cas9 and RNAi screening data for more than 400 shared cell lines to represent knockout and partial suppression genetic perturbation modalities and evaluate the utility of each for therapeutic target discovery and the inference of gene function. We find that CRISPR screens identify more dependencies, and yield more accurate predictive models and co-dependency relationships overall. However, RNAi outperforms CRISPR in identifying associations (omics, drug, co-dependencies) with genes that are common dependencies for most cell lines (pan-dependencies). As pan-dependencies occur frequently in the CRISPR dataset (~2,000 genes), using results from both RNAi and CRISPR analyses facilitates the discovery of predictive models and associated co-dependencies for a wider range of gene targets than could be detected using either dataset alone. These findings can aid in the interpretation of contrasting results obtained from CRISPR and RNAi screens and reinforce the importance of partial gene suppression methods in building a cancer dependency map.
High-speed write error rate evaluation of a voltage-torque magnetic random access memory cell (2019)

Abstract We developed a system for evaluating the write error rate of a voltage-torque magnetic random access memory cell running at 500 kbps, which is two orders of magnitude faster than the conventional system. This performance enhancement was realized by making the following modifications. First, the bias-tee combining the read and write channels in the conventional system was replaced with a high-speed semiconductor analog switch. Second, a custom amplifier/comparator circuit was built to detect the magnetization state at high-speed. It was confirmed that there was no sign of any thermal influence up to 500 kbps.
High-Performance and Scalable Updates (2016)

Highly performant and scalable techniques such as RCU have been quite successful in read-mostly situations. However, there do come times when updates are necessary. It would be convenient if there was some general update-side counterpart to RCU, but sadly there is not yet any such thing. Nevertheless, there are a number of specialized update-side techniques whose performance and scalability rival that of RCU. This talk will discuss several of them and provide an outlook into the future of low-overhead scalable updates.
Dynamic super-resolution structured illumination imaging in the living brain (2019)

Cells in the brain act as components of extended networks. Therefore, to understand neurobiological processes in a physiological context, it is essential to study them in vivo. Super-resolution microscopy has spatial resolution beyond the diffraction limit, thus promising to provide structural and functional insights that are not accessible with conventional microscopy. However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion. We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy (SIM) in vivo. We imaged the brains of live zebrafish larvae and mice and observed the dynamics of dendrites and dendritic spines at nanoscale resolution.
Increased Gamma Connectivity in the Human Prefrontal Cortex during the Bereitschaftspotential (2017)

The Bereitschaftspotential (BP) is a slow negative cortical potential preceding voluntary movement. Since movement preparation is dependent upon the synchronous activity of a variety of neurons, BP may develop through the exchange of information among motor-related neurons. However, the relationship between BP and information flow is not yet well-known. In the present study, we aimed to investigate how the connectivity in the prefrontal cortex (PFC) changes during the occurrence of BP. Electrocorticography (ECoG) was recorded in five patients with epilepsy. The subjects performed self-paced hand grasping. We compared the intraregional connectivity between PFC and non-PFC regions using partial directed coherence. In the PFC, the connectivity of beta and gamma bands in the BP period increased by an average of 24.4% compared with the baseline connectivity. Conversely, gamma connectivity in non-PFC regions decreased by 31.4%. Moreover, the intraregional connectivity in the PFC increased according to the stage of BP. The increased gamma band connectivity in the PFC implies that the increased communication among neurons in the PFC is associated with development of BP. Intraregional connectivity as one of the factors involved in voluntary movement may reflect the activation of brain networks related to movement preparation in PFC.
Learning Time-Series Data of Industrial Design Optimization using Recurrent Neural Networks (2019)

In automotive digital development, 3D shape morphing techniques are used to create new designs in order to match design targets, such as aerodynamic or stylistic requirements. Control-point based shape morphing alters existing geometries either through human user interactions or through computational optimization algorithms that optimize for product performance targets. Shape morphing is typically continuous and results in potentially large data sets of time-series recordings of control point movements. In the present paper, we utilize recurrent neural networks to model such time-series recordings in order to predict future design steps based on the history of currently performed design modifications. To build a data set sufficiently large for the training of neural networks, we use target shape matching optimization as digital analogy for a human user interactive shape modification and to build data sets of control point movements in an automated fashion. Experiments show the potential of recurrent neural networks to successfully learn time-series data representing design changes and to perform single-and multi-step prediction of potential next design steps. We thus demonstrate the feasibility of recurrent neural networks for learning successful design sequences in order to predict promising next design steps in future design tasks.
Moving Object Detection in Complex Scene Using Spatiotemporal Structured-Sparse RPCA (2018)

Moving object detection is a fundamental step in various computer vision applications. Robust Principal Component Analysis (RPCA) based methods have often been employed for this task. However, the performance of these methods deteriorates in the presence of dynamic background scenes, camera jitter, camouflaged moving objects, and/or variations in illumination. It is because of an underlying assumption that the elements in the sparse component are mutually independent, and thus the spatiotemporal structure of the moving objects is lost. To address this issue, we propose a spatiotemporal structured sparse RPCA algorithm for moving objects detection, where we impose spatial and temporal regularization on the sparse component in the form of graph Laplacians. Each Laplacian corresponds to a multi-feature graph constructed over superpixels in the input matrix. We enforce the sparse component to act as eigenvectors of the spatial and temporal graph Laplacians while minimizing the RPCA objective function. These constraints incorporate a spatiotemporal subspace structure within the sparse component. Thus, we obtain a novel objective function for separating moving objects in the presence of complex backgrounds. The proposed objective function is solved using a linearized alternating direction method of multipliers based batch optimization. Moreover, we also propose an online optimization algorithm for real-time applications. We evaluated both the batch and online solutions using six publicly available datasets that included most of the aforementioned challenges. Our experiments demonstrated the superior performance of the proposed algorithms compared with the current state-of-the-art methods.
Erratum: Visualization of Methanol Concentration Using the Electrochromism of Nickel Oxide [Electrochem. Solid-State Lett., 8, A277 (2005)] (2005)

Erratum: Visualization of Methanol Concentration Using the Electrochromism of Nickel Oxide [Electrochem. Solid-State Lett., 8, A277 (2005)] Hee-Sang Shim, Hyo-Jin Ahn, Tae-Yeon Seong, and Kyung-Won Park Department of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
INVESTIGATION OF THICK BONDLINE ADHESIVE JOINTS. (2001)

In recent years, the use of polymer matrix composite materials as primary structural components has risen, especially in the general aviation (GA) industry. The use of composites not only results in weight savings, but also reduces part counts, joining operations, and results in significant savings in assembly, storage, and inspection. However, joining of some integral parts is still required. GA aircraft industry also uses bonded joints with bondline thicknesses much greater than the 0.01 in. that was standard in aircraft bonded joints. For composites, there are two methods of joining: bonding and mechanical fastening. Of the two, adhesively bonding composite structures is the preferred method for a variety of reasons. There are several adhesive test methods that are used to determine the in situ properties of an adhesive joint for use in design. From these methods, ASTM D 1002, D 3165, and D 5656 were evaluated in this investigation with the substrate materials of 2024-T3 phosphoric anodized aluminum, carbon/epoxy quasi-isotropic laminate, and fiberglass/epoxy quasi-isotropic laminate. Bondline thicknesses from 0.010-0.160 inch were evaluated for three paste adhesive systems using different test methods and substrate materials. The apparent shear strength given by the test methods investigated was found to be highly dependent on adherend bending stiffness, which directly effects the peel stress distributions in the adhesive layer. Thin-adherend specimens, regardless of bondline thickness, yielded lower apparent shear strengths than the thick adherend specimens and gave misleading information when comparing the apparent shear strengths of different adhesive systems. The adhesive shear-stress behavior was characterized over the range of bond thicknesses and environmental conditions and several recommendations and correction factors were offered for the thick-adherend test method.
Safety and Immunogenicity of a Pentavalent Combination Vaccine (Diphtheria, Tetanus, Acellular Pertussis, Polio and Haemophilus Influenzae Type b Conjugate) When Administered as a Fourth Dose at 15 to 18 Months of Age (2005)

A DTaP-IPV//PRP-T combination vaccine (Pentacel) has been universally used in Canada to provide immunization against diphtheria, tetanus, pertussis, polio, and Haemophilus influenzae type b with single injections at 2, 4, 6 and 18 months of age. This randomized, multicenter study was conducted to evaluate administration of a fourth dose of DTaP-IPV//PRP-T at 15 to 18 months of age, similar to the US immunization schedule. Participants who had received three doses of DTaP-IPV//PRP-T by 8 months of age were enrolled at 12 months and randomized to receive a fourth dose at 15, 16, 17 or 18 months. Antibody levels for each vaccine antigen were measured prior to and four weeks following booster vaccination. Overall, 1782 subjects were immunized and monitored for adverse events, and 735 were evaluated for immune responses. Preimmunization antibody levels differed minimally by age, for all antigens. The immune responses elicited by DTaP-IPV//PRP-T were comparable between participants vaccinated at 15 or 16 months and those vaccinated at 17 or 18 months, as demonstrated by specific antibody geometric mean titers, seroprotection/seroresponse rates, and reverse cumulative distribution curves. The fourth dose was well tolerated in all age groups. Toddlers at 15, 16, 17 or 18 months of age are equally suitable recipients for booster immunization with the DTaP-IPV//PRP-T vaccine.
Fast-Degradable Microbeads Encapsulating Human Umbilical Cord Stem Cells in Alginate for Muscle Tissue Engineering (2012)

Human umbilical cord mesenchymal stem cells (hUCMSCs) are inexhaustible and can be obtained without an invasive surgery. To date, there has been no report on seeding hUCMSCs in three-dimensional scaffolds for muscle tissue engineering. The objectives of this study were to (1) investigate hUCMSC seeding in a scaffold for muscle engineering and (2) develop a novel construct consisting of hUCMSC-encapsulating and fast-degradable microbeads inside a hydrogel matrix. The rationale was that the hydrogel matrix would maintain the defect volume, while the microbeads would degrade to release the cells and concomitantly create macropores in the matrix. hUCMSCs were encapsulated in alginate-fibrin microbeads, which were packed in an Arg-Gly-Asp (RGD)-modified alginate matrix (AM). This construct is referred to as hUCMSC-microbead-AM. The control consisted of the usual cell encapsulation in AM without microbeads (referred to as hUCMSC-AM). In the hUCMSC-AM construct, the hUCMSCs showed as round dots with no spreading at 1-14 days. In contrast, cells in the hUCMSC-microbead-AM construct had a healthy spreading and elongated morphology. The microbeads successfully degraded and released the cells at 8 days. Myogenic expressions for hUCMSC-microbead-AM were more than threefold those of hUCMSC-AM (p<0.05). Immunofluorescence for myogenic markers was much stronger for hUCMSC-microbead-AM than hUCMSC-AM. Muscle creatine kinase of hUCMSC-microbead-AM at 14 days was twofold that of hUCMSC-AM (p<0.05). In conclusion, hUCMSC encapsulation in novel fast-degradable microbeads inside a hydrogel matrix was investigated for muscle engineering. Compared to the usual method of seeding cells in a hydrogel matrix, hUCMSC-microbead-AM construct had greatly improved cell viability and myogenic differentiation, and hence, is promising to enhance muscle regeneration.
Synthesis and Characterization of Alumina Microtubes in a Template Process from Short Carbon Fibers (2007)

A novel, two step process for synthesis of Al2O3 microtubes from short carbon fibers as templates is reported. In the first process step, the carbon fibers are coated with a Al-AlN-Al4C3 composite in a microwave plasma fluidized bed CVD process. The coated material is then being treated in a furnace on high temperature in air, resulting finaly with alumina microtubes (hollow fibers).
A CPL-based dual supply 32-bit ALU for sub 180nm CMOS technologies (2004)

In this paper we present the design of a high performance 32-bit ALU for low power applications. We use dual power supply scheme and CPL logic for non-critical units of the ALU. In addition, latches with only n-MOS clocked transistors are used to interface logic operating at different power supplies and achieve static power free operation. Our simulation results indicate that, for the 180nm-65nm CMOS technologies it is possible to reduce the ALU total energy by 18%-24%, with minimal delay degradation. In addition, there is up to 22%-32% reduction in leakage power in the standby mode.
Discriminating Neoantigenic Differences Between Fibrinogen and Fibrin Derivatives (1973)

Discrimination between the physiological cleavage fragments of fibrinogen and fibrin offers an approach to differentiation between fibrinogenolytic processes and fibrinolysis after coagulation. By use of the cleavage-associated neoantigen of fibrinogen (fg-D(neo)) as a molecular marker, characteristic differences between the D regions of fibrinogen derivatives and fibrin derivatives can be demonstrated. The expression of fg-D(neo) by X, Y, D:E complex, and D-fragments of fibrinogen or fibrin is shown to be quantitative and unitary. Characteristic differences between fg-D(neo) sites present on fibrinogen cleavage fragments, as contrasted to fibrin cleavage fragments, are indicated by different competitive inhibition slopes, and appear to reflect differential binding affinity of selected anti-fg-D(neo) antibodies for the specific molecular site. There is a linear relationship between the slope of quantitative competitive inhibition and the relative molar ratio of fibrinogen and fibrin derivatives. Identical immunochemical expressions are observed in vitro and in vivo, and support the thesis that cleavage in vivo is produced by plasmin. The differential immunochemical features of fg-D(neo) expression may be the result of stable conformational and/or subtle structural differences between the D region of fibrinogen and fibrin cleavage fragments and suggest that precise changes in the D region are associated with the fibrin transition. These molecular features not only provide additional insight into the molecular immunology and structure of fibrinogen, but also appear to offer a new molecular approach to discrimination between fibrinogenolytic mechanisms as contrasted to fibrinolysis secondary to coagulation.
ChemInform Abstract: Oligonucleotide Analogues with a Nucleobase‐Including Backbone. Part 5. 2′‐Deoxy‐8‐(hydroxymethyl)adenosine‐ and 2′‐Deoxy‐6‐(hydroxymethyl)uridine‐Derived Phosphoramidites: Synthesis and Incorporation into 14‐Mer DNA Strands. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Crystal Structure of African Swine Fever Virus A179L with the Autophagy Regulator Beclin (2019)

Subversion of programmed cell death-based host defence systems is a prominent feature of infections by large DNA viruses. African swine fever virus (ASFV) is a large DNA virus and sole member of the <i>Asfarviridae</i> family that harbours the B-cell lymphoma 2 or Bcl-2 homolog A179L. A179L has been shown to bind to a range of cell death-inducing host proteins, including pro-apoptotic Bcl-2 proteins as well as the autophagy regulator Beclin. Here we report the crystal structure of A179L bound to the Beclin BH3 motif. A179L engages Beclin using the same canonical ligand-binding groove that is utilized to bind to pro-apoptotic Bcl-2 proteins. The mode of binding of Beclin to A179L mirrors that of Beclin binding to human Bcl-2 and Bcl-x<sub>L</sub> as well as murine γ-herpesvirus 68. The introduction of bulky hydrophobic residues into the A179L ligand-binding groove via site-directed mutagenesis ablates binding of Beclin to A179L, leading to a loss of the ability of A179L to modulate autophagosome formation in Vero cells during starvation. Our findings provide a mechanistic understanding for the potent autophagy inhibitory activity of A179L and serve as a platform for more detailed investigations into the role of autophagy during ASFV infection.
Thermosulfurimonas marina sp. nov., an Autotrophic Sulfur-Disproportionating and Nitrate-Reducing Bacterium Isolated from a Shallow-Sea Hydrothermal Vent (2018)

A thermophilic, anaerobic, chemolithoautotrophic bacterium (strain SU872T) was isolated from a shallow-sea hydrothermal vent at Kunashir Island. The cells were motile, gram-negative, oval or rodshaped 0.5‒0.6 μm thick and 1.5‒2.0 μm long, occurring singly or in pairs. Strain SU872T grew at 50 to 79°C (optimum at 74°C), pH from 5.0 to 8.0 (optimum at 6.7‒7.0), and NaCl concentration of 1.5–4.5%. Strain SU872T was able to grow by disproportionation of elemental sulfur, thiosulfate, or sulfite, with CO2/HCO3− as the sole carbon source. Growth was enhanced in the presence of ferrihydrite (poorly crystalline Fe(III) oxide) as as a sulfide-scavenging agent. Sulfate was not used as an electron acceptor. Growth also occurred with elemental sulfur, thiosulfate, or sulfite (but not sulfide) as electron donors and nitrate as an electron acceptor, with production of sulfate and ammonium. Analysis of the 16S rRNA gene sequence revealed 97.8% similarity between strain SU872T and the type strain Thermosulfurimonas dismutans S95T (phylum Thermodesulfobacteria). According to the results of DNA–DNA hybridization, the similarity of genomic DNA of the strains SU872T and T. dismutans S95T was 48%. Based on its phenotypic characteristics and the results of phylogenetic analysis, it is proposed to assign the isolate to a new species of the genus Thermosulfurimonas,—Thermosulfurimonas marina sp. nov., with the type strain SU872T (=DSM 104922T, =VKM B-3177T, =UNIQEM SU872T).
Protonation Structures of Cys-Sulfinic and Cys-Sulfenic Acids in the Photosensitive Nitrile Hydratase Revealed by Fourier Transform Infrared Spectroscopy (2003)

Nitrile hydratase (NHase) from Rhodococcus N-771, which catalyzes hydration of nitriles to the corresponding amides, exhibits novel photosensitivity; in the dark, it is in the inactive form that binds an endogenous nitric oxide (NO) molecule at the non-heme iron center, and photodissociation of the NO activates the enzyme. NHase is also known to have a unique active site structure. Two cysteine ligands to the iron center, alphaCys112 and alphaCys114, are post-translationally modified to sulfinic acid (Cys-SO(2)H) and sulfenic acid (Cys-SOH), respectively, which are thought to play a crucial role in the catalytic reaction. Here, we have determined the protonation structures of these Cys-SO(2)H and Cys-SOH groups using Fourier transform infrared (FTIR) spectroscopy in combination with density functional theory (DFT) calculations. The light-induced FTIR difference spectrum of NHase between the dark inactive and light active forms exhibited two prominent signals at (1154-1148)/1126 and (1040-1034)/1019 cm(-1), which downshifted to 1141/1114 and 1026/1012 cm(-1), respectively, in the uniformly (34)S-labeled NHase. In addition, a minor signal at 915/908 cm(-1) also showed a considerable downshift upon (34)S labeling. These (34)S-sensitive signals were basically conserved in D(2)O buffer with only slight shifts. Vibrational frequencies of methanesulfenic acid (CH(3)SOH) and methanesulfinic acid (CH(3)SO(2)H), simple model compounds of Cys-SOH and Cys-SO(2)H, respectively, were calculated using the DFT method in both the protonated and deprotonated forms and in metal complexes. Comparison of the calculated frequencies and isotope shifts with the observed ones provided the assignment of the two major signals around 1140 and 1030 cm(-1) to the asymmetric and symmetric SO(2) stretching vibrations, respectively, of the S-bonded Cys-SO(2)(-) complex, and the assignment of the minor signal around 910 cm(-1) most likely to the SO stretch of the S-bonded Cys-SO(-) complex. These assignments and the small frequency shifts upon deuteration are consistent with the view that the deprotonated alphaCys112-SO(2)(-) and alphaCys114-SO(-) are hydrogen-bonded with the protons from betaArg56 and/or betaArg141, forming a reactive cavity at the interface of the alpha and beta subunits. There is further speculation that either of these groups is hydrogen bonded to a reactant water molecule, increasing its basicity to facilitate the nucleophilic attack on the nitrile substrate bound to the iron center.