gebhart/patrepeval huggingface dataset:
Knowledge harvesting from text and Web sources (2013)

The proliferation of knowledge-sharing communities such as Wikipedia and the progress in scalable information extraction from Web and text sources has enabled the automatic construction of very large knowledge bases. Recent endeavors of this kind include academic research projects such as DBpedia, KnowItAll, Probase, ReadTheWeb, and YAGO, as well as industrial ones such as Freebase and Trueknowledge. These projects provide automatically constructed knowledge bases of facts about named entities, their semantic classes, and their mutual relationships. Such world knowledge in turn enables cognitive applications and knowledge-centric services like disambiguating natural-language text, deep question answering, and semantic search for entities and relations in Web and enterprise data. Prominent examples of how knowledge bases can be harnessed include the Google Knowledge Graph and the IBM Watson question answering system. This tutorial presents state-of-the-art methods, recent advances, research opportunities, and open challenges along this avenue of knowledge harvesting and its applications.
Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity (2017)

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.
Parametric resonance for vibration energy harvesting with design techniques to passively reduce the initiation threshold amplitude (2014)

A vibration energy harvester designed to access parametric resonance can potentially outperform the conventional direct resonant approach in terms of power output achievable given the same drive acceleration. Although linear damping does not limit the resonant growth of parametric resonance, a damping dependent initiation threshold amplitude exists and limits its onset. Design approaches have been explored in this paper to passively overcome this limitation in order to practically realize and exploit the potential advantages. Two distinct design routes have been explored, namely an intrinsically lower threshold through a pendulum-lever configuration and amplification of base excitation fed into the parametric resonator through a cantilever-initial-spring configuration. Experimental results of the parametric resonant harvesters with these additional enabling designs demonstrated an initiation threshold up to an order of magnitude lower than otherwise, while attaining a much higher power peak than direct resonance.
A semi-preemptive garbage collector for solid state drives (2011)

NAND flash memory is a preferred storage media for various platforms ranging from embedded systems to enterprise-scale systems. Flash devices do not have any mechanical moving parts and provide low-latency access. They also require less power compared to rotating media. Unlike hard disks, flash devices use out-of-update operations and they require a garbage collection (GC) process to reclaim invalid pages to create free blocks. This GC process is a major cause of performance degradation when running concurrently with other I/O operations as internal bandwidth is consumed to reclaim these invalid pages. The invocation of the GC process is generally governed by a low watermark on free blocks and other internal device metrics that different workloads meet at different intervals. This results in I/O performance that is highly dependent on workload characteristics. In this paper, we examine the GC process and propose a semi-preemptive GC scheme that can preempt on-going GC processing and service pending I/O requests in the queue. Moreover, we further enhance flash performance by pipelining internal GC operations and merge them with pending I/O requests whenever possible. Our experimental evaluation of this semi-preemptive GC sheme with realistic workloads demonstrate both improved performance and reduced performance variability. Write-dominant workloads show up to a 66.56% improvement in average response time with a 83.30% reduced variance in response time compared to the non-preemptive GC scheme.
Northwest Atlantic ecosystem-based management for fisheries (2011)

The northwest Atlantic has had a rich history of living marine resource exploitation. As stocks have undergone sequential depletion with some dramatic instances of stock declines in this region, there have been calls for evaluating and improving approaches to managing our use of these resources. As part of these calls and along with recognition that there are broader issues to consider when managing a fishery, the need for more holistic ecosystem-based approaches to manage living marine resources (LMRs) have been increasingly recognized. Here we present a history of LMR management for both Canadian and US waters. We also provide contextual information for the major ecosystems in this region, with synopses and descriptions of major biophysical features in the northwest Atlantic. After noting the main data sets in this region, we discuss some of the major ecosystem models produced by our institutions. Finally, we discuss current efforts to implement ecosystem-based marine fisheries management in the northwest Atlantic.
Development of New Building Blocks for Constructing Novel Polymer Semiconductors for Organic Thin Film Transistors (2013)

Organic semiconductors are envisioned to have widespread applications in flexible displays, radio-frequency identification (RFID) tags, bio- and chem-sensors, as well as organic solar cells. Polymer semiconductors are particularly suitable for the low-cost manufacture of organic electronics using printing techniques due to their excellent solution processability and mechanical properties. This work focuses on the development of two novel building blocks, IBDF and DTA, which can be used for the construction of high performance organic thin film transistors (OTFTs) and organic photovoltaics (OPVs). Two copolymers, P6-IBDF-T and P5-IBDF-T, and a homopolymer P6-IBDF were prepared using the IBDF building block. Copolymer P6-IBDF-T has been prepared via the Stille-coupling polymerization. This polymer exhibits a small band gap of 1.36 eV with HOMO/LUMO energy level of -5.69 eV/-4.43 eV. P6-IBDF-T showed stable electron transport performance in encapsulated thin film transistors and ambipolar transport performance in non-encapsulated TFTs. Balanced hole/electron mobilities of up to 8.2 ×10-3/1.0 ×10-2 cm2V-1s-1 was achieved in bottom-contact, bottom-gate organic thin film transistors. In addition, the broad absorption of the polymer over the UV-Vis range suggested that this polymer is suitable for applications in solar cells. The effect of conjugation on mobility and UV-vis spectra of the polymer was studied by comparing P5-IBDF-T with P6-IBDF-T. The ideal of indirect electron transition was proposed to explain the difference between UV-Vis light absorption spectra for these two polymers. \nDTA building block was used to construct four D-A copolymers, namely PDTA-T, PDTA-BT, PDAT-BTV, and PDTA-TT. These polymers were characterized by UV-Vis, CV, DSC, TGA, AFM and XRD. Device performance was also investigated on OTFTs. The device performance of DTA based polymer increased as the area of electron donor increase from T in PDTA-T to BTV in PDTA-BTV. PDTA-BTV exhibits hole mobility of 1.3×10-3 cm2 V-1 s-1 with Ion/Ioff value of ~103-4 in bottom-contact, bottom-gate organic thin film transistors. All DTA based copolymers exhibited small optical bandgaps (1.18 – 1.27 eV) and required none or moderate thermal treatment during fabrication process. These make them promising candidates for cost-effective OPV applications.
A user profile-based personalization system for digital multimedia content (2008)

With the steadily increasing amount of digital multimedia content, the user will be more and more overstrained. This applies to content being permanently available like videos of online video services as well as broadcast content like in the TV or radio domain. A promising solution for this problem is personalization. In the context of this paper, we refer to the selection and recommendation of content with respect to user's interests and preferences as personalization. These recommendations can either be presented to the user herself or be further used by services like a personalized electronic program guide (EPG) in the TV domain or for automated and personalized selection of content of online video services.
Decision-Theoretic Diagnosis-Repair Planning Using Bayesian Networks (1998)

: Common diagnosis systems view the accurate identication of components responsible for the faulty behavior of the system as the ultimate goal of the diagnostic activity. Restoring the system to its functioning state is a secondary concern that is not explicitly addressed during the fault identication process. In this article, we take the restoration of the system to be our ultimate objective and ,thus, the diagnosis is important only to the extend that it contributes to derive a repair plan with minimal expected cost. Both in case of a single fault and multiple-independent faults, we build on existing approaches for repair planning to construct an algorithm for scheduling repair actions. Encoding our knowledge about the system in a Bayesian network, we, then, account for the possibility of sensing using an approximation algorithm based on limited look-ahead evaluation of pending sources of information based on their degree of informativeness and associated costs. 1 Introduction Alt...
Importance sampling of many lights with adaptive tree splitting (2017)

We present a technique to importance sample large collections of lights. A bounding volume hierarchy over all lights is traversed at each shading point using a single random number in a way that importance samples their predicted contribution. We further improve the performance of the algorithm by forcing splitting until the importance of a cluster is sufficiently representative of its contents.
Numerical Simulation and Experimental Study on Profile-Rolling Process for Micro-Teeth Components (2013)

This paper presents a numerical simulation and experimental study on profile-rolling process for micro-teeth components. The target component was made of AISI 304 stainless steel with 6.0 mm outer diameter, and its number of teeth was 25. Three raw material rods with different diameters 5.6 mm, 6.0 mm, and 6.4 mm were investigated in the finite-element simulation. The spindle speed of the rolls was 60 rpm, and the material forward speed was 1.8 mm/s, which were reasonably compatible with the practical profile-rolling conditions. The simulation results showed that the different numbers of teeth were produced by employing different diameters of raw materials. Only the rod with the 6.0 mm diameter could be rolled into the near desired shape. Experimental verification was also undertaken. The numerical simulation was found to be in good agreement with the measured profile of the actual rolled component. The microstructure of the material after rolling was improved also as the hardness of the teeth was 40% higher than that of the core.
Interpretation of the Coherence Function When Using Pseudorandom Inputs to Identify Nonlinear Systems (1986)

Use of certain types of pseudorandom input stimuli to identify linear transfer function models of biological or physiological systems can lead to bias errors if the system is nonlinear. Moreover, use of the coherence function to assess the linearity of the system may yield misleading results. Results from a computer simulation are presented, along with example experimental data.
Abstract 135: Pim-1 Modification Reverses Senescent Phenotype Of Hcpcs From Patients With Heart Disease (2013)

Rationale: Adoptive transfer of human cardiac progenitor cells (hCPCs) can repair damaged myocardium and improve function in a pathologically challenged heart. hCPC’s isolated from multiple patients exhibit differences in growth kinetics, expression of cell cycle regulators and telomere length suggesting hCPCs with slow growth kinetics may compromise effective regeneration of damaged or aged myocardium. There is a dire need to reverse the senescent phenotype of hCPCs exhibiting slow growth kinetics to improve the outcome of regenerative therapy. Objective: Demonstrate that Pim-1 engineering reverses the senescent phenotype of human cardiac progenitor cells (hCPCs) with slow growth kinetics by increasing their telomere length and decreasing population doubling time and cell cycle inhibitors. Methods and Results: hCPCs positive for stem cell marker c-kit were isolated from heart biopsy samples from patients undergoing Left Ventricular Assist Device (LVAD) implantation. hCPCs isolated from multiple patients were characterized for growth kinetics, telomere length, expression of cell cycling regulators. hCPCs with slow growth kinetics exhibit decreased telomere length concomitant with increased population doubling time and upregulation of senescent markers compared to hCPCs with fast growth kinetics. hCPCs were engineered to express Pim-1-GFP (hCPCeP), a fused GFP version of the kinase by using a lentivirus expression system. Cell cycling measured by population doubling time was decreased in hCPCeP. Similarly, telomere lengths in hCPCeP were significantly increased relative to control hCPCs expressing GFP (hCPCe). Similarly, the expression cell cycling inhibitors including p16 and p53 is down regulated indicative of reversal of senescent characteristics. Conclusion: Ex vivo gene delivery of Pim-1 in hCPCS enhances telomere length and decreases population-doubling time and senescent phenotype. These changes are more significant and distinct in hCPCs with slow growth kinetics. Pim-1 modification of hCPCs with slow growth kinetics from patients with heart failure can augments their ability to regenerate damaged myocardium and address current limitations associated with senescent phenotype of aged hCPCs.
Windows in ellipsometry measurements (1999)

The effect of windows or lenses placed between the polarization-state generator and the polarization-state detector in a general ellipsometry measurement is examined. It is found that three parameters are required for describing the effects of the window retardation on the ellipsometry measurements. Two of these window parameters can be measured at the same time as the sample parameters if the sample is isotropic, but the third window parameter cannot be determined independently and must be measured separately. If the sample is anisotropic, then none of the windows parameters can be measured independently at the same time as the sample parameters. An example is given in which the strain-induced retardation in fused-silica focusing lenses is measured with a two-modulator generalized ellipsometer and the results are used to correct the sample data.
Interaction of Human Plasma Membrane Proteins and Oligodeoxynucleotides (1998)

Two oligodeoxynucleotide (oligodN) binding proteins of 100–110 kDa on plasma membranes of human cell lines were recently identified by us. These two proteins seemed to play a role in oligodN uptake. In this study, the impact of the chain length and the sequence of the oligodN on the interaction with those two proteins was investigated. Chain length of oligodN was an important determinant, but not the sole determinant for the interaction. Binding affinity of oligodNs was determined predominantly by base composition, where pyrimidine bases but not purine bases were required in the sequence to retain high affinity. The binding kinetics of the homopolymers of deoxycytidine (dC21) and deoxythymidine (dT21) suggests that the proteins may have different binding sites, with one site preferring thymine bases and the other cytosine bases. Moreover, some additional plasma membrane proteins were identified, with an apparent molecular mass ranging from 40 to 58 kDa, which could bind thymine bases but not cytosine bases.
Using Semantic Relations with World Knowledge for Question Answering. (2006)

Two research directions are to be explored in realizing our group’s TREC QA system in 2006. The first one is to investigate the possibilities of applying linguistically sophisticated grammatical framework in tackling the realworld natural language processing task such as question answering. The other is to exploit the possible world’s entities and relations as described in online encyclopedia in adding redundancy and hidden relations as those contained in the TREC corpus where the entities and relations are only implicitly mentioned and related. Our focus is on the factoid and list question as these two types of questions benefit
Central role of lactic acidosis in cancer cell resistance to glucose deprivation‐induced cell death (2011)

Solid tumours are dependent on glucose, but are generally glucose-deprived due to poor vascularization. Nevertheless, cancer cells can generally survive glucose deprivation better than their normal counterparts. Thus, to render cancer cells sensitive to glucose depletion may potentially provide an effective strategy for cancer intervention. We propose that lactic acidosis, a tumour microenvironment factor, may allow cancer cells to develop resistance to glucose deprivation-induced death, and that disruption of lactic acidosis may resume cancer cells' sensitivity to glucose depletion. Lactic acidosis, lactosis, or acidosis was generated by adding pure lactic acid, sodium lactate, or HCl to the culture medium. Cell death, cell cycle, autophagy, apoptosis, and gene expression profiling of the surviving cancer cells under glucose deprivation with lactic acidosis were determined. Under glucose deprivation without lactic acidosis, 90% of 4T1 cancer cells died within a single day; in a sharp contrast, under lactic acidosis, 90% of 4T1 cells died in a period of 10 days, with viable cells identified even 65 days after glucose was depleted. Upon glucose restoration, surviving cells resumed proliferation. Lactic acidosis also significantly extended survival of other cancer cells under glucose deprivation. G1/G0 arrest, autophagy induction, and apoptosis inhibition were tightly associated with lactic acidosis-mediated resistance to glucose deprivation. Lactosis alone had no effect on cell survival under glucose deprivation; acidosis alone can prolong cell survival time but is not as potent as lactic acidosis. Thus, the ability of cancer cells to resist glucose deprivation-induced cell death is conferred, at least in part, by lactic acidosis, and we envision that disrupting the lactic acidosis may resume the sensitivity of cancer cells to glucose deprivation.
Quality control material containing hemoglobin for blood gas and pH measurement: Preparation of stroma-free hemoglobin solution (1987)

A method for the preparation of stroma-free hemoglobin solution suitable for quality control of blood gas and pH measurements as well as hemoglobinometry, is described. Several methods were compared for purification and lysis of red blood cells. For separation of stroma from hemoglobin solution tangential cross-flow filtration has been used. Diluted hemoglobin solutions were concentrated using various forms of ultrafiltration as well as other methods. A precipitate removing procedure is introduced in which the pH is increased temporarily to 8.0 and the ionic strength is enhanced by adding 130 mmol NaCl per litre stroma-free hemoglobin solution, to remove a precipitate that was observed during tonometry at 37 degrees C in the pH-range 7.4-8.0 and when electrolytes were added to create a plasma-like composition of stroma-free hemoglobin solution. Tests were designed to quickly detect turbidity and precipitate. During storage at 4 degrees C no methemoglobin was formed in contrast with two other types of stroma-free hemoglobin solution, which formed appreciable amounts of methemoglobin within 40 days.
Characterization of operating parameters for <scp>XMuLV</scp> inactivation by low p <scp>H</scp> treatment (2015)

To ensure the viral safety of protein therapeutics made in mammalian cells, purification processes include dedicated viral clearance steps to remove or inactivate adventitious and endogenous viruses. One such dedicated step is low pH treatment, a robust and effective method commonly used in monoclonal antibody production to inactivate enveloped viruses. To characterize the operating space for low pH viral inactivation, we performed a statistically designed experiment evaluating the effect of pH, temperature, hold duration, acid type, and buffer concentration on inactivation of the retrovirus model, XMuLV. An additional single factor experiment was performed to study the effect of protein concentration. These data were used to generate predictive models of inactivation at each time point studied, which can be used to identify conditions for robust and effective XMuLV inactivation. At pH 3.6, XMuLV inactivation was rapid, robust, and relatively unaffected by the other factors studied, providing support for this as a generic viral inactivation condition for products that can tolerate this low pH. At pH 3.7 and 3.8, other factors besides pH affected XMuLV inactivation. By understanding the impact of each factor on inactivation, the factors can be manipulated within the operating space to ensure effective inactivation while achieving desired product quality goals.
The beneficiation of lunar regolith for space resource utilisation: A review (2020)

Space Resource Utilisation (SRU) technology will enable further exploration and habitation of space by humankind. The production of oxygen on the Moon is one of the first objectives for SRU; this can be achieved through the thermo-chemical reduction of the lunar regolith. Several techniques, such as hydrogen reduction and molten salt electrolysis, have been proposed. All reduction techniques require a consistent feedstock from the regolith to reliably and consistently produce oxygen. The preparation of this feedstock, known as beneficiation, is a critical intermediate stage of the SRU flowsheet, however it has received little consideration relative to the preceding excavation, and the subsequent oxygen production stage. This review describes the physics of the main beneficiation methods suitable for SRU. Further, we collate and review all of the previous studies on the beneficiation of lunar regolith.
Codewebs (2014)

Massive open online courses (MOOCs), one of the latest internet revolutions have engendered hope that constant iterative improvement and economies of scale may cure the ``cost disease" of higher education. While scalable in many ways, providing feedback for homework submissions (particularly open-ended ones) remains a challenge in the online classroom. In courses where the student-teacher ratio can be ten thousand to one or worse, it is impossible for instructors to personally give feedback to students or to understand the multitude of student approaches and pitfalls. Organizing and making sense of massive collections of homework solutions is thus a critical web problem. Despite the challenges, the dense solution space sampling in highly structured homeworks for some MOOCs suggests an elegant solution to providing quality feedback to students on a massive scale.