gebhart/patrepeval huggingface dataset:
DNA ligases ensure fidelity by interrogating minor groove contacts (2004)

DNA ligases, found in both prokaryotes and eukaryotes, covalently link the 3'-hydroxyl and 5'-phosphate ends of duplex DNA segments. This reaction represents a completion step for DNA replication, repair and recombination. It is well established that ligases are sensitive to mispairs present on the 3' side of the ligase junction, but tolerant of mispairs on the 5' side. While such discrimination would increase the overall accuracy of DNA replication and repair, the mechanisms by which this fidelity is accomplished are as yet unknown. In this paper, we present the results of experiments with Tth ligase from Thermus thermophilus HB8 and a series of nucleoside analogs in which the mechanism of discrimination has been probed. Using a series of purine analogs substituted in the 2 and 6 positions, we establish that the apparent base pair geometry is much more important than relative base pair stability and that major groove contacts are of little importance. This result is further confirmed using 5-fluorouracil (FU) mispaired with guanine. At neutral pH, the FU:G mispair on the 3' side of a ligase junction is predominantly in a neutral wobble configuration and is poorly ligated. Increasing the solution pH increases the proportion of an ionized base pair approximating Watson-Crick geometry, substantially increasing the relative ligation efficiency. These results suggest that the ligase could distinguish Watson-Crick from mispaired geometry by probing the hydrogen bond acceptors present in the minor groove as has been proposed for DNA polymerases. The significance of minor groove hydrogen bonding interactions is confirmed with both Tth and T4 DNA ligases upon examination of base pairs containing the pyrimidine shape analog, difluorotoluene (DFT). Although DFT paired with adenine approximates Watson-Crick geometry, a minor groove hydrogen bond acceptor is lost. Consistent with this hypothesis, we observe that DFT-containing base pairs inhibit ligation when on the 3' side of the ligase junction. The NAD+-dependent ligase, Tth, is more sensitive to the DFT analog on the unligated strand whereas the ATP-dependent T4 ligase is more sensitive to substitutions in the template strand. Electrophoretic gel mobility-shift assays demonstrate that the Tth ligase binds poorly to oligonucleotide substrates containing analogs with altered minor groove contacts.
Analysis of candidate genes has proposed the role of y chromosome in human prostate cancer. (2014)

Correct inference of master genes, which mediate molecular, has changed during cancer progression would be one of the major challenges in cancer genomics. In this paper, we have shown the role of Y chromosome genes in finding of the prostate cancer susceptibility genes. Application of our approach to the prostate cancer has led to the establishment of the previous knowledge about this cancer as well as prediction of other new genes.
Charity deserts and social justice: exploring variations in the distribution of charitable organisations and their resources in England (2015)

Eleven Charity deserts and social justice: exploring variations in the distribution of charitable organisations and their resources in England was published in New Philanthropy and Social Justice on page 191.
Modélisation CEM de type boîte noire d'un onduleur triphasé (2018)

International audience
Adenosine magnetic resonance imaging versus dobutamine stress echocardiography in patients with low probability for coronary artery disease (2009)

Accurate assessment of patients with chest pain without electrocardiographic changes or elevation of serum cardiac enzymes is challenging. There is increased interest in the role of dobutamine stress echocardiography (DSE) and adenosine magnetic resonance imaging (AMRI) performed in the chest pain unit as a diagnostic method to rule out Coronary Artery Disease (CAD) as the cause of the chest pain in this population.
An Industrial Perspective on Counter Anions in Gold Catalysis: On Alternative Counter Anions (2018)

Abstract A comparison of versatile counter anions was investigated by means of a variety of well‐known test reactions representing the key reactivity patterns of homogeneous gold catalysis, the catalytic activity was monitored by GC and 1 H NMR. As previously reported, the counter anion influence is usually more pronounced than the corresponding ligand effect. Due to this, the study is focused on the investigation of counter anions so far not included from investigation of homogeneous gold‐catalyzed reactions. The examinations using so far neglected counter anions (BAr F 4 ) − , [B(C 6 F 5 ) 4 ] − , [Al(OC(CF 3 ) 3 ) 4 ] − and [B(C 6 F 5 ) 3 (OAc F )] − showed surpassing or at least similar catalytic activities as the commonly used counter anions. The expanded use of counter anions can occupy an important role in future concerning catalyst optimization in gold catalysis. magnified image
A Hybrid-Driven Elevator System With Energy Regeneration and Safety Enhancement (2019)

Elevator has been the most critical equipment for vertical transportation and one of the largest energy consumption sources in buildings. The main cause of energy waste in elevator is the dissipation of the energy regenerated by the motor. To achieve energy saving, this article proposes an electro-hydraulic hybrid driving elevator system. With an auxiliary hydraulic system, the energy generated by the motor can be stored in the form of hydraulic accumulator pressure, which can be reused to assist motor start in the form of supporting torque. In addition, due to the additional torque provided by the hydraulic system, elevator safety can be enhanced. Simulation results have been obtained, demonstrating that large amount of energy can be saved with the proposed system. Field test results with elevator in a real building environment are also presented to verify the efficacy of the proposed idea.
Colloidal preparation and electrocatalytic hydrogen production of MoS2and WS2nanosheets with controllable lateral sizes and layer numbers (2016)

Although layered transition metal dichalcogenide (TMD) nanosheets have attracted great attention due to their unique properties, it still remains challenge to develop a facile strategy for the precise control of the lateral sizes and layer numbers of TMD nanosheets. In this study, we demonstrate a solution-phase synthetic protocol to prepare colloidal MS2 (M = Mo, W) nanosheets which possess extremely small lateral dimensions from 15 to 40 nm and well-controlled odd numbers of layers, such as 1, 3, and 5 layers, as characterized by transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy. The size- and layer-dependence of the optical properties of colloidal MS2 (M = Mo, W) nanosheets are revealed by Raman and absorption spectra for the first time. These colloidal nanosheets, especially the single-layer ones, possess a large number of edge sites that serve as active sites for the hydrogen evolution reaction (HER). The catalysts exhibit a small HER overpotential and low Tafel slope of approximately 100 mV and 52 mV per decade for MoS2, and 80 mV and 46 mV per decade for WS2, respectively. Importantly, these products show enhanced stability after 500 potential cycles, and the current density remains almost unchanged during the test.
Synthesis of Carp Proinsulin in Xenopus Ocytes (1978)

Total poly(A)‐containing RNA from Brockmann bodies of carp (Cyprinus carpio) directs the synthesis of authentic carp proinsulin in Xenopus oocytes . Neither preproinsulin nor further processing of pronisulin to insulin can be detected in the oocytes.
Learning based compression of surface light fields for real-time rendering of global illumination scenes (2013)

We present an algorithm for compression and real-time rendering of surface light fields (SLF) encoding the visual appearance of objects in static scenes with high frequency variations. We apply a non-local clustering in order to exploit spatial coherence in the SLF data. To efficiently encode the data in each cluster, we introduce a learning based approach, Clustered Exemplar Orthogonal Bases (CEOB), which trains a compact dictionary of orthogonal basis pairs, enabling efficient sparse projection of the SLF data. In addition, we discuss the application of the traditional Clustered Principal Component Analysis (CPCA) on SLF data, and show that in most cases, CEOB outperforms CPCA, K-SVD and spherical harmonics in terms of memory footprint, rendering performance and reconstruction quality. Our method enables efficient reconstruction and real-time rendering of scenes with complex materials and light sources, not possible to render in real-time using previous methods.
A simple self-mode-locked atmospheric pressure CO2laser (1972)

The construction and operation of a particularly simple atmospheric pressure CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> laser that uses a fast voltage doubling is described.
Focusing on the Silver Lining: How COVID-19 Pandemic is Influencing the Pedagogy of Mechatronic Course Delivery to Support the Industrial Role of a Mechanical Engineering Technologist (2024)

He has developed and taught several engineering courses primarily in first-year engineering, civil and environmental engineering, and general engineering
Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation (2020)

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator–prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.
Intraparenchymal Cyst Development after Deep Brain Stimulator Placement (2013)

Following deep brain stimulation (DBS) surgery, a variety of potential mechanical or functional complications ranging from perioperative events to hardware malfunction may occur. We present 2 patients who developed a unique complication of cyst formation at the tip of the DBS electrode in the absence of infection. One patient had a unilateral ventral intermediate lead placement for essential tremor, and the other had bilateral subthalamic nucleus (STN) placement for Parkinson's disease. After a period of symptom control, at 3 and 8 months after surgery, respectively, both patients developed new neurological deficits and were found to have a cyst at the left DBS lead tip. The right lead in the patient with the bilateral STN implant was without issue. Both affected leads were removed and the problematic symptoms regressed quickly over several days, though the lesion effect on the patients' initial tremor symptoms lasted for months. Bacteriological cultures of the removed electrodes and wounds were negative. We report a rare complication of DBS and show that simply removing the involved lead results in cyst resolution.
A Simple and Efficient Selective Repeat Scheme for High Throughput WLAN, IEEE802.11n (2007)

The standardization of IEEE802.11n aims to achieve 100 Mbps at MAC-SAP (medium access control - service access point). The frame aggregation scheme in which MAC (medium access control) frames are aggregated into one PHY (physical) frame is proposed as the main MAC technique of IEEE802.11n, because it decreases MAC overhead. The block ack mechanism of IEEE802.11e is applied as a selective repeat method of the frame aggregation. In this paper, we propose the extended block ack mechanism as a selective repeat mechanism to be adapted to the frame aggregation scheme. We present the performance evaluation to compare the throughput of the extended block ack mechanism and the legacy block ack of IEEE802.11e and show that the average improvement is expected to be around 10% and the maximum improvement is about 39% compared with the conventional method.
Isolation and Screening of Thermophilic Bacilli from Compost for Electrotransformation and Fermentation: Characterization of Bacillus smithii ET 138 as a New Biocatalyst (2015)

Thermophilic bacteria are regarded as attractive production organisms for cost-efficient conversion of renewable resources to green chemicals, but their genetic accessibility is a major bottleneck in developing them into versatile platform organisms. In this study, we aimed to isolate thermophilic, facultatively anaerobic bacilli that are genetically accessible and have potential as platform organisms. From compost, we isolated 267 strains that produced acids from C5 and C6 sugars at temperatures of 55°C or 65°C. Subsequently, 44 strains that showed the highest production of acids were screened for genetic accessibility by electroporation. Two Geobacillus thermodenitrificans isolates and one Bacillus smithii isolate were found to be transformable with plasmid pNW33n. Of these, B. smithii ET 138 was the best-performing strain in laboratory-scale fermentations and was capable of producing organic acids from glucose as well as from xylose. It is an acidotolerant strain able to produce organic acids until a lower limit of approximately pH 4.5. As genetic accessibility of B. smithii had not been described previously, six other B. smithii strains from the DSMZ culture collection were tested for electroporation efficiencies, and we found the type strain DSM 4216(T) and strain DSM 460 to be transformable. The transformation protocol for B. smithii isolate ET 138 was optimized to obtain approximately 5 × 10(3) colonies per μg plasmid pNW33n. Genetic accessibility combined with robust acid production capacities on C5 and C6 sugars at a relatively broad pH range make B. smithii ET 138 an attractive biocatalyst for the production of lactic acid and potentially other green chemicals.
A Fast and Efficient Conditional Learning for Tunable Trade-Off between Accuracy and Robustness (2022)

Existing models that achieve state-of-the-art (SOTA) performance on both clean and adversarially-perturbed images rely on convolution operations conditioned with feature-wise linear modulation (FiLM) layers. These layers require many new parameters and are hyperparameter sensitive. They significantly increase training time, memory cost, and potential latency which can prove costly for resource-limited or real-time applications. In this paper, we present a fast learnable once-for-all adversarial training (FLOAT) algorithm, which instead of the existing FiLM-based conditioning, presents a unique weight conditioned learning that requires no additional layer, thereby incurring no significant increase in parameter count, training time, or network latency compared to standard adversarial training. In particular, we add configurable scaled noise to the weight tensors that enables a trade-off between clean and adversarial performance. Extensive experiments show that FLOAT can yield SOTA performance improving both clean and perturbed image classification by up to ~6% and ~10%, respectively. Moreover, real hardware measurement shows that FLOAT can reduce the training time by up to 1.43x with fewer model parameters of up to 1.47x on iso-hyperparameter settings compared to the FiLM-based alternatives. Additionally, to further improve memory efficiency we introduce FLOAT sparse (FLOATS), a form of non-iterative model pruning and provide detailed empirical analysis to provide a three way accuracy-robustness-complexity trade-off for these new class of pruned conditionally trained models.
Philosophies for Assessing Durability of Commercial and Infrastructure Composite Systems (2002)

A key need for the commercial acceptance and viability of composite structural material systems is a methodology for reliability and lifetime predictions. In this paper, we present a philosophy in which the residual strength of the composite material is calculated as a function of applied loading conditions, environment, and resulting failure mode. Two specific example applications are considered: the assessed and verified performance of fiber wound composite tubes and pultruded shapes. We attempt to demonstrate the understanding of the controlling damage mechanisms and the degradation processes that contribute to the loss in stiffness and strength under simulated service conditions.
Inhibition of the calcium paradox in isolated rat hearts by high perfusate sucrose concentrations (1994)

If a colloid osmotic (oncotic) pressure gradient develops across the myocyte membrane during the calcium paradox, adding an oncotic agent to the perfusate should be inhibitory. After 10-min perfusion with Ca(2+)-free Krebs-Henseleit (KH) buffer under constant flow at 34 degrees C, myoglobin release was measured from Langendorff hearts reperfused with Ca(2+)-containing KH buffer. When the Ca(2+)-free medium contained 200 mM sucrose, myoglobin release was reduced to 5% of that observed in the absence of sucrose, a change that was not seen when 200 mosM NaCl, choline chloride, LiCl, or glycerol was added. Replacement of 75 mM NaCl in the perfusate with 150 mM sucrose resulted in myoglobin release values that were 4% of the control. Plots of myoglobin release against sucrose concentration under these hypertonic and isotonic conditions yielded similar though separate curves. Sucrose also inhibited increases in wet weight-to-dry weight ratio and decreases in ATP and phosphocreatine contents. These results support the hypothesis that an oncotic pressure gradient arises during the calcium paradox at the moment of increased membrane permeability and plays a major role in its development.
Performance study of conditional and unconditional direction-of-arrival estimation (1990)

A numerical and analytical study of conditional and unconditional direction-of-arrival (DOA) estimation is presented. Explicit expressions for the unconditional Cramer-Rao bounds on the DOA estimation accuracy and the covariance matrix of the conditional maximum likelihood method are given. It is shown that many DOA estimation methods have the same asymptotic statistical properties under conditional and unconditional models. The situation of two narrowband plane signals impinging on a uniformly spaced linear array is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Towards connectivity management adaptability (2004)

An infrastructure based on multiple heterogeneous access networks is one of the leading enablers for the emerging pervasive and ubiquitous computing paradigm, in which the optimal management of diverse networking resources is a challenging problem. This paper presents a context-aware policy mechanism and related end-to-end evaluation algorithm for adaptive connectivity management of multi-access wireless networks. A policy is used to express the criteria for adaptive selection of the best local and remote network interfaces. The best connection can then be used for the establishment of a channel as well as the maintenance of on-going data transmission. Rich context information is considered in the policy representation with respect to user profile and preference, application characteristics, device capability, and network QoS condition. The decision of the best access networks to be used is made on the basis of an end-to-end evaluation process. The decision can be made in both Master-Slave and Peer-to-Peer modes. The paper focuses on the methods for policy representation and connection evaluation algorithm. A case study is presented to show the usability of the proposed policy mechanism and decision-making algorithm in the adaptive management of heterogeneous networking resources.
Retinal Ganglion Cells with Distinct Directional Preferences Differ in Molecular Identity, Structure, and Central Projections (2011)

The retina contains ganglion cells (RGCs) that respond selectively to objects moving in particular directions. Individual members of a group of ON-OFF direction-selective RGCs (ooDSGCs) detect stimuli moving in one of four directions: ventral, dorsal, nasal, or temporal. Despite this physiological diversity, little is known about subtype-specific differences in structure, molecular identity, and projections. To seek such differences, we characterized mouse transgenic lines that selectively mark ooDSGCs preferring ventral or nasal motion as well as a line that marks both ventral- and dorsal-preferring subsets. We then used the lines to identify cell surface molecules, including Cadherin 6, CollagenXXVα1, and Matrix metalloprotease 17, that are selectively expressed by distinct subsets of ooDSGCs. We also identify a neuropeptide, CART (cocaine- and amphetamine-regulated transcript), that distinguishes all ooDSGCs from other RGCs. Together, this panel of endogenous and transgenic markers distinguishes the four ooDSGC subsets. Patterns of molecular diversification occur before eye opening and are therefore experience independent. They may help to explain how the four subsets obtain distinct inputs. We also demonstrate differences among subsets in their dendritic patterns within the retina and their axonal projections to the brain. Differences in projections indicate that information about motion in different directions is sent to different destinations.
Multilevel three-phase rectifier with sinusoidal input currents (2002)

A multilevel three-phase PWM rectifier absorbing sinusoidal and in phase mains currents is proposed in this paper. The article deals with this new structure, its control and the way to balance the voltage of the output capacitors in order to optimize its characteristics without disturbing the current waveform.
Some Probiotic Properties of Vaginal Lactobacilli Isolated from Healthy Women (2006)

Lactobacilli have long been considered to be protective flora in the vagina. In this study, samples were taken from the lateral vaginal wall of 19 healthy women, and 58 strains of Lactobacillus spp. were isolated from 10 of these women. The identification results revealed that Lactobacillus gasseri was the predominant lactobacilli in healthy women. The amounts of lactic acid and hydrogen peroxide (H(2)O(2)) produced by Lactobacillus spp. were determined. The vaginal pH levels induced by Lactobacillus spp. strains ranged from 1.00 to 2.15. The titratable acidity of the strains ranged from 0.27 to 1.33%. The H(2)O(2) concentration produced in the lactobacilli strains ranged between 1.01 microg/ml and 15.50 microg/ml. The antimicrobial effects of the lactobacilli against the pathogenic bacteria Escherichia coli ATCC 11230, Staphylococcus aureus ATCC 2392, Pseudomonas aeruginosa ATCC 29212 and Salmonella enterica serovar Enteritidis RSKK 171 were also determined by the agar diffusion methods.