gebhart/patrepeval huggingface dataset:
Structure and functional mapping of the KRAB‐KAP1 repressor complex (2022)

Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
Anharmonic vibrational modes of chemisorbed H on the Rh(001) surface (1988)

The potential for H atoms in the vicinity of the fourfold hollow chemisorption site on the Rh(001) surface at monolayer coverage is calculated using local-density-functional theory, and the linear-augmented-plane-wave method. The potential is found to contain important anharmonic components, one that couples parallel and perpendicular motion, and another producing azimuthal anisotropy. Variational solutions are found for the ground and low-lying excited states of H and D in this potential. The fundamental asymmetric- and symmetric-stretch H vibrational excitations are found to have energies of 67 and 92 meV. The latter agrees with recent experimental results, and higher-lying experimental modes are interpreted as mixed excitations. Comparisons are made with spring-constant models, calculated potentials for H on Ni and Pd(001), and theories of Bloch states for H on Ni(001).
DDIS-37. SMALL MOLECULE AUTOPHAGY ACTIVATORS IN GROWTH INHIBITION OF GLIOBLASTOMA (2019)

Abstract Glioblastoma (GBM) is one of the most lethal human tumors, and despite considerable advances in multimodality treatments consisting of surgical removal, radiation and chemotherapy, overall survival is 14 to 16 months after diagnosis. Therefore, there is a need to target non-apoptotic death pathways and inhibit pro-survival signaling mechanisms that contribute to both tumorigenesis and treatment resistance. Depending on tumor type and environment, autophagy modulation plays an important role in tumor cell survival and inhibition pathways. Increasing evidence supports that chemical modulation of autophagy inhibition and activation holds a therapeutic potential and these studies have led to the initiation of multiple clinical trials combining chemotherapeutic agents and autophagy inhibitors and activators for various cancer types. However, recent studies have also demonstrated a therapeutic potential for enhancers of autophagy in GBM. This clearly demonstrates the need for further investigation into the autophagy induced mechanism of GBM, and the development of better treatments. We have identified a new chemical entity VMY-BC-1 that showed promising effects in both serum and patient-derived glioma cell lines. Drug target engagement studies identified an autophagy induction protein, UNC-51 like kinase 1 (ULK1), as the main target of VMY-BC-1, in which VMY-BC-1 covalently bound to the protein’s active pocket and increased ULK1 phosphorylation.ULK1 is a component of the ULK1 complex (ULK1-ATG13-FIP200) that is essential for inducing autophagy, a lysosome-dependent mechanism of intracellular degradation for maintaining cellular homeostasis. Additionally, our molecule cross talks to the apoptotic and DNA damage pathways, which could potentially overcome treatment resistance.VMY-BC-1 is orally bioavailable, brain penetrant, and inhibits cell invasion and tumor growth in GBM flank models, making this small molecule an ideal candidate for further development. We hypothesize that activating ULK1-modulated autophagy will be a therapeutic strategy for GBM growth inhibition
Increased frequency of co-existingJAK2exon-12 orMPLexon-10 mutations in patients with lowJAK2V617Fallelic burden (2015)

The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.
ChemInform Abstract: Asymmetric Hydrogenation of β‐Keto Carboxylic Esters. A Practical, Purely Chemical Access to β‐Hydroxy Esters in High Enantiomeric Purity. (1988)

Abstract Hydrogenation reactions of β‐keto esters (I), (III), (V) catalyzed by the Ru(II) complexes shown in the scheme under an initial H 2 pressure of 50‐100 atm provide the β‐hydroxy esters (II), (IV), or (VI) in high enantiomeric purity.
Steigerung der Enantioselektivität chemischer Reaktionen in Gegenwart chiraler Lewis‐Säuren durch hohen Druck (1993)

Von 4.5 auf 20.4% ee steigt die Enantioselektivität bezüglich des ()‐Enantiomers bei der intramolekularen Hetero‐Diels‐Alder‐Reaktion von 1 zu 2 und 3 bei der Erhöhung des Drucks von 1 auf 5000 bar. Bei der Reaktion wurde eine chirale Lewis‐Säure eingesetzt. magnified image
Hierarchical Spatio-Temporal Graph Neural Networks for Pandemic Forecasting (2022)

The spread of COVID-19 throughout the world has led to cataclysmic consequences on the global community, which poses an urgent need to accurately understand and predict the trajectories of the pandemic. Existing research has relied on graph-structured human mobility data for the task of pandemic forecasting. To perform pandemic forecasting of COVID-19 in the United States, we curate Large-MG, a large-scale mobility dataset that contains 66 dynamic mobility graphs, with each graph having over 3k nodes and an average of 540k edges. One drawback with existing Graph Neural Networks (GNNs) for pandemic forecasting is that they generally perform information propagation in a flat way and thus ignore the inherent community structure in a mobility graph. To bridge this gap, we propose a Hierarchical Spatio-Temporal Graph Neural Network (HiSTGNN) to perform pandemic forecasting, which learns both spatial and temporal information from a sequence of dynamic mobility graphs. HiSTGNN consists of two network architectures. One is a hierarchical graph neural network (HiGNN) that constructs a two-level neural architecture: county-level and region-level, and performs information propagation in a hierarchical way. The other network architecture is a Transformer-based model that captures the temporal dynamics among the sequence of learned node representations from HiGNN. Additionally, we introduce a joint learning objective to further optimize HiSTGNN. Extensive experiments have demonstrated HiSTGNN's superior predictive power of COVID-19 new case/death counts compared with state-of-the-art baselines.
METAMORPHIC III-V MATERIALS, SUBLATTICE DISORDER, AND MULTIJUNCTION SOLAR CELL APPROACHES WITH OVER 37% EFFICIENCY (2004)

Studies of the material properties of lattice-mismatched and lattice-matched GaInAs and GaInP, and control of their bandgap by varying composition and sublattice disorder, have allowed terrestrial concentrator solar cells to reach new heights of efficiency. The bandgaps of both GaInP and GaInAs are controlled by varying indium content, up to 35% indium in the GaInAs middle cell, or 2.4% lattice mismatch. The bandgap of lattice-mismatched GaInP is additionally controlled through ordering of Ga and In atoms on the group-III sublattice. Minority-carrier lifetime measurements are made in GaInAs, and in GaInP with different ordering states, as a function of lattice mismatch to the Ge substrate. The lifetimes are observed to be much longer than previously attainable, due to graded buffer growth conditions that inhibit propagation of threading dislocation segments into the active cell regions. In other approaches to high-efficiency multijunction solar cell design, the first 6-junction solar cells have been built and measured. These cells designed for use in space employ an active GaInNAs subcell 5 in a (Al)GaInP/ GaInP/ AlGaInAs/ GaInAs/ GaInNAs/ Ge 6-junction structure, with measured open-circuit voltage over 5.1 V. Terrestrial 3- junction concentrator cells with lattice-matched and metamorphic GaInP/GaInAs/Ge structures have been produced at Spectrolab with 37.3% efficiency measured at NREL, the highest independently verified solar conversion efficiency measured to date for a photovoltaic device (AM1.5 Direct, low-AOD spectrum, 175 suns, 25±1°C).
On the accuracy of self-normalized log-linear models (2015)

Calculation of the log-normalizer is a major computational obstacle in applications of log-linear models with large output spaces. The problem of fast normalizer computation has therefore attracted significant attention in the theoretical and applied machine learning literature. In this paper, we analyze a recently proposed technique known as "self-normalization", which introduces a regularization term in training to penalize log normalizers for deviating from zero. This makes it possible to use unnormalized model scores as approximate probabilities. Empirical evidence suggests that self-normalization is extremely effective, but a theoretical understanding of why it should work, and how generally it can be applied, is largely lacking. We prove generalization bounds on the estimated variance of normalizers and upper bounds on the loss in accuracy due to self-normalization, describe classes of input distributions that self-normalize easily, and construct explicit examples of high-variance input distributions. Our theoretical results make predictions about the difficulty of fitting self-normalized models to several classes of distributions, and we conclude with empirical validation of these predictions.
Development of Multianvil Techniques for Studies in Deep Earth Mineralogy (2009)

Aspects of development of experimental techniques at Geodynamics Research Center (GRC), Ehime University, using Kawai-type multianvil apparatus (KMA) for various studies in deep Earth mineralogy, have been reviewed in conjunction with the author’s scientific achievements in this field. Precise measurements of some physical properties of minerals at the pressure and temperature conditions corresponding to certain depths of the lower mantle are now possible, by combinations of synchrotron radiation, advanced anvil materials, new cell designs, and ultrasonic and other techniques using KMA. KMA has also been used to synthesize ultrahard nano-polycrystalline diamond (NPD) by direct conversion from graphite. NPD has potential as new hard material for generation of higher pressures, and challenges in producing large (∼1 cm) NPD and its application to various apparatus have just started at GRC and other related laboratories.
Design and analysis of transmit-beamforming based on limited-rate feedback (2006)

This paper deals with design and performance analysis of transmit beamformers for multiple-input multiple-output (MIMO) systems based on bandwidth-limited information that is fed back from the receiver to the transmitter. By casting the design of transmit beamforming based on limited-rate feedback as an equivalent sphere vector quantization (SVQ) problem, multiantenna beamformed transmissions through independent and identically distributed (i.i.d.) Rayleigh fading channels are first considered. The rate-distortion function of the vector source is upper-bounded, and the operational rate-distortion performance achieved by the generalized Lloyd's algorithm is lower-bounded. Although different in nature, the two bounds yield asymptotically equivalent performance analysis results. The average signal-to-noise ratio (SNR) performance is also quantified. Finally, beamformer codebook designs are studied for correlated Rayleigh fading channels, and a low-complexity codebook design that achieves near-optimal performance is derived.
Quality of Gastric Ulcer Healing (1991)

Assessment of gastric ulcer healing is usually based on a visual examination (by endoscopy in patients, or the evaluation of ulcer size in experimental studies), and not on histologic and ultrastructural assessment of subepithelial mucosal healing. This approach has led to the assumption that the mucosa of grossly "healed" gastric and/or duodenal ulcers returns to normal, either spontaneously or following treatment. However, the re-epithelialized mucosa of grossly "healed" experimental gastric ulcer has recently been found to have prominent histologic and ultrastructural abnormalities, including reduced height, marked dilation of gastric glands, poor differentiation and/or degenerative changes in glandular cells, increased connective tissue, and disorganized microvascular network. It has been postulated that these residual abnormalities might interfere with mucosal defense and may be the basis of ulcer recurrence. In the present article, the ulcer healing process and the role of luminal factors, transitional zone at the ulcer margin, and granulation tissue are discussed. The healing of an ulcer is accomplished by filling of the mucosal defect with epithelial cells and connective tissue to reconstruct mucosal architecture. Under influence of growth factors [predominantly epidermal growth factor (EGF) and transforming growth factor (TGF alpha)], the epithelial cells at the ulcer margin dedifferentiate and proliferate, supplying cells for re-epithelialization of the mucosal scar surface and reconstruction of glandular structures. Granulation tissue at the ulcer base supplies connective tissue cells to restore the lamina propria and endothelial cells and microvessels for mucosal microvasculature reconstruction. The final outcome of healing reflects a dynamic interaction between an "epithelial" component from the ulcer margin and a connective tissue component including microvessels originating from granulation tissue.(ABSTRACT TRUNCATED AT 250 WORDS)
Endoprothetische Versorgung nach distalen Humerusfrakturen (2012)

Trümmerfrakturen des distalen Humerus, insbesondere bei Patienten mit einer Osteoporose, stellen eine große Herausforderung an den behandelnden Unfallchirurgen dar. Ist eine Gelenkrekonstruktion und osteosynthetische Versorgung nicht möglich, kann der primäre endoprothetische Ersatz des Ellenbogens eine mögliche Behandlungsalternative darstellen. Auch Patienten mit einer Vorschädigung des Ellenbogens, z. B. im Rahmen einer rheumatischen Erkrankung oder einer vorbestehenden posttraumatischen Arthrose, können von einer Prothese profitieren. Gerade bei geriatrischen Patienten ist die Narkosefähigkeit infolge von Begleiterkrankungen häufig eingeschränkt. Durch die im Schnitt deutlich kürzeren OP-Zeiten und das Vermeiden der, für eine Osteosynthese meist notwendigen, Bauchlage kann auch in diesen Fällen eine operative Therapie möglich sein und eine konservative Therapie und deren häufig schlechte Ergebnisse vermieden werden. Im Rahmen von klinischen Untersuchungen zeigt sich ein meist gutes bis sehr gutes funktionelles Outcome bei gleichzeitig guten Prothesenstandzeiten und einem moderaten Komplikationsrisiko, insbesondere im Vergleich zu einer herkömmlichen Gelenkrekonstruktion.
Virtualizing Virtual Channels for Increased Network-on-Chip Robustness and Upgradeability (2012)

The Network-on-Chip (NoC) router buffers are instrumental in the overall operation of Chip Multi-Processors (CMP), because they facilitate the creation of Virtual Channels (VC). Both the NoC routing algorithm and the CMP's cache coherence protocol rely on the presence of VCs within the NoC for correct functionality. In this article, we introduce a novel concept that completely decouples the number of supported VCs from the number of VC buffers physically present in the design. Virtual Channel Renaming enables the virtualization of existing virtual channels, in order to support an arbitrarily large number of VCs. Hence, the CMP can (a) withstand the presence of faulty VCs, and (b) accommodate routing algorithms and/or coherence protocols with disparate VC requirements. The proposed VC Renamer architecture incurs minimal hardware overhead to existing NoC designs and is shown to exhibit excellent performance without affecting the router's critical path.
Mathematical modelling of expanded bed adsorption – a perspective on in silico process design (2018)

Expanded bed adsorption (EBA) emerged in the early 1990s in an attempt to integrate the clarification, capture and initial product concentration/purification process. Several mathematical models have been put forward to describe its operation. However, none of the models developed specifically for EBA allows simultaneous prediction of bed hydrodynamics, mass transfer/adsorption and (unwanted) interactions and fouling. This currently limits the development and early optimization of EBA-based separation processes. In multiphase reactor engineering, the use of multiphase computational fluid dynamics has been shown to improve fundamental understanding of fluidized beds. To advance EBA technology, a combination of particle, equipment and process scale models should be used. By employing a cascade of multiscale simulations, the various challenges EBA currently faces can be addressed. This allows for optimal design and selection of equipment, materials and process conditions, and reduces risks and development times of downstream processes involving EBA. © 2018 The Authors. <i>Journal of Chemical Technology & Biotechnology</i> published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Kalman filter estimation with edge detection-based hybrid sensing (2016)

A novel sensing and estimation scheme is introduced as an integrated part of a micro-stage based calibration method for a MEMS gyroscope. The proposed sensing scheme combines a periodically updating analog sensor with an event-based threshold sensor. A first derivative of Gaussian filter is applied to the threshold sensor signal to detect threshold crossings. A Kalman filter with the proposed sensing scheme is used to estimate the micro-stage's states. In the measurement update steps, analog sensor measurement is used when a threshold crossings event is not triggered, and the threshold sensor measurement is used when the crossing event is triggered. The impact of detection error of the proposed threshold detection technique on the estimation performance is evaluated with estimation error covariance analysis and simulations.
Low Complexity Multiply-Accumulate Units for Convolutional Neural Networks with Weight-Sharing (2018)

Convolutional neural networks (CNNs) are one of the most successful machine-learning techniques for image, voice, and video processing. CNNs require large amounts of processing capacity and memory bandwidth. Hardware accelerators have been proposed for CNNs that typically contain large numbers of multiply-accumulate (MAC) units, the multipliers of which are large in integrated circuit (IC) gate count and power consumption. “Weight-sharing” accelerators have been proposed where the full range of weight values in a trained CNN are compressed and put into bins, and the bin index is used to access the weight-shared value. We reduce power and area of the CNN by implementing parallel accumulate shared MAC (PASM) in a weight-shared CNN. PASM re-architects the MAC to instead count the frequency of each weight and place it in a bin. The accumulated value is computed in a subsequent multiply phase, significantly reducing gate count and power consumption of the CNN. In this article, we implement PASM in a weight-shared CNN convolution hardware accelerator and analyze its effectiveness. Experiments show that for a clock speed 1GHz implemented on a 45nm ASIC process our approach results in fewer gates, smaller logic, and reduced power with only a slight increase in latency. We also show that the same weight-shared-with-PASM CNN accelerator can be implemented in resource-constrained FPGAs, where the FPGA has limited numbers of digital signal processor (DSP) units to accelerate the MAC operations.
Fiberoptic-aided Endobronchial Intubation (1994)

Although bronchial blockers can be used to isolate the lungs, Robert-shaw double-lumen tubes are the most popular method for establishing one-lung ventilation. Blind placement of these tubes is the most commonly used technique in adults [1]. Unsatisfactory positioning of left-sided Robertshaw double-lumen tubes occurs in 25 to 50% of cases in which the tubes are passed blindly [2, 3]. Blind positioning of right-sided double-lumen tubes has an even greater failure rate [4]. Difficulties encountered with blind placement include intubation of the wrong bronchus; advancing the tube too far down the main stem bronchus thus occluding the upper lobe bronchus (Fig IB, C) or placing the tracheal lumen within the main stem bronchus (Fig 1C); not advancing the tube far enough (leading to incomplete lung separation) (Fig 1A); or herniation of the bronchial cuff across the carina with obstruction of the contralateral main stem bronchus (Fig 1D). The fiberoptic endoscope facilitates positioning of the double lumen tube and significantly decreases the incidence of unsuccessful tube placement. The following paragraphs describe tracheobronchial anatomy and techniques for fiberoptic-guided double-lumen tube and bronchial-blocker placement. For additional details the reader is referred to a recent review [5].
Simultaneous Transmitting and Reflecting Reconfigurable Array (STAR-RA) With Independent Beams (2023)

A simultaneous transmitting and reflecting reconfigurable array (STAR-RA) with independent beams is proposed in this communication. This STAR-RA can realize bidirectional beams simultaneously and the forward and backward beam directions can be controlled independently. To realize this function, a novel element consisting of the forward and backward phase-controlling patches is proposed. With the help of two pairs of p-i-n diodes, it divides the incident wave into a 1 bit reconfigurable reflecting part and a 1 bit reconfigurable transmitting part. Further, a STAR-RA prototype with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$16\times16$ </tex-math></inline-formula> elements is designed, fabricated, and measured. The measured results show a good beam-scanning capability of ±60° with a maximum gain fluctuation of 5.5 dB in E- and H-planes for both the transmitting and reflecting beams. The 1 dB gain bandwidth of the STAR-RA is 8.4% from 5.7 to 6.2 GHz. The distinctive advantage of the proposed design is the independently controlled bidirectional beams that work simultaneously, which is suitable for bidirectional wireless communication applications.