gebhart/patrepeval huggingface dataset:
Improving Backup and Restore Performance for Deduplication-based Cloud Backup Services (2012)

The benefits provided by cloud computing and the space savings offered by data deduplication make it attractive to host data storage services like backup in the cloud. Data deduplication relies on comparing fingerprints of data chunks, and store them in the chunk index, to identify and remove redundant data, with an ultimate goal of saving storage space and network bandwidth. However, the chunk index presents a bottleneck to the throughput of the backup operation. While several solutions to address deduplication throughput have been proposed, the chunk index is still a centralized resource and limits the scalability of both storage capacity and backup throughput in public cloud environments. In addressing this challenge, we propose the Scalable Hybrid Hash Cluster (SHHC) that hosts a low-latency distributed hash table for storing fingerprints. SHHC is a cluster of nodes designed to scale and handle numerous concurrent backup requests while maintaining high fingerprint lookup throughput. Each node in the cluster features hybrid memory consisting of DRAM and Solid State Drives (SSDs) to present a large usable memory for storing the chunk index. Our evaluation with real-world workloads shows that SHHC is consistently scalable as the number of nodes increases. The throughput increases almost linearly with the number of nodes. The restore performance over the relatively low bandwidth wide area network (WAN) links is another drawback in the use of cloud backup services. High speed network connectivity is either too expensive for most organizations or reserved for special applications. Removing redundant data before transmitting over the WAN offers a viable option to improve network throughput during the restore operation. To that end, we propose Application-Aware Phased Restore (AAPR), a simple restore solution for deduplication-based cloud backup clients. AAPR improves restore time by removing redundant data before transmitting over the WAN. Furthermore, we exploit application awareness to restore critical data first and thus improve the recovery time. Our evaluations show that, for workloads with high redundancy, AAPR reduces restore time by over 85%. Advisor: Hong Jiang
DeepDive: A Data Management System for Automatic Knowledge Base Construction (2015)

iACKNOWLEDGMENTS I owe Christopher Re ́ my career as a researcher, the greatest dream of my life. Since the day I first met Chris and told him about my dream, he has done everything he could, as a scientist, an educator, and a friend, to help me. I am forever indebted to him for his completely honest criticisms and feedback, the most valuable gifts an advisor can give. His training equipped me with confidence and pride that I will carry for the rest of my career. He is the role model that I will follow. If my whole future career achieves an approximation of what he has done so far in his, I will be proud and happy. I am also indebted to Jude Shavlik and Miron Livny, who, after Chris left for Stanford, kindly helped me through all the paperwork and payments at Wisconsin. If it were not for their help, I would not have been able to continue my PhD studies. I am also profoundly grateful to Jude for being the chair of my committee. I am also likewise grateful to Jeffrey Naughton, David Page, and Shanan Peters for serving on my committee; and Thomas Reps for his feedback during defense. DeepDive would have not been possible without all its users. Shanan Peters was the first user, working with it before it even got its name. He spent three years going through a painful process with us before we understood the current abstraction of DeepDive. I am grateful to him for sticking with
Single mammalian cell gene expression analysis using microfluidics (2006)

Single cell gene expression studies hold great promise for deciphering the ubiquitous heterogeneity present in biological organisms. Although much progress has been made in the field, tools to study gene expression (specific and global) in single cells are generally lacking. This thesis describes the development of novel microfluidic technologies and processes capable of processing single cells to first strand cDNA in a parallel fashion, thereby filling a void in the single cell biology field. The author then utilizes the technology to probe for transcriptional noise in ubiquitous genes present in single mammalian cells. The noise measured far exceeds any measurement reported to this date, and was shown to be attenuated during the G2 stage of the cell cycle. The work presented here is first hand proof that technological innovation is a key component in undertaking novel science.
Effect of Controlled Ice Nucleation on Primary Drying Stage and Protein Recovery in Vials Cooled in a Modified Freeze-Dryer (2009)

The freezing step influences lyophilization efficiency and protein stability. The main objective of this work was to investigate the impact on the primary drying stage of an ultrasound controlled ice nucleation technology, compared with usual freezing protocols. Lyophilization cycles involving different freezing protocols (applying a constant shelf cooling rate of 1 degrees C/min or 0.2 degrees C/min, putting vials on a precooled shelf, and controlling nucleation by ultrasounds or by addition of a nucleating agent) were performed in a prototype freeze-dryer. Three protective media including sucrose or maltodextrin and differing by their thermal properties and their ability to preserve a model protein (catalase) were used. The visual aspect of the lyophilized cake, residual water content, and enzymatic activity recovery of catalase were assessed after each lyophilization cycle and after 1 month of storage of the lyophilized product at 4 degrees C and 25 degrees C. The freezing protocols allowing increasing nucleation temperature (precooled shelf and controlled nucleation by using ultrasounds or a nucleating agent) induced a faster sublimation step and higher sublimation rate homogeneity. Whatever the composition of the protective medium, applying the ultrasound technology made it possible to decrease the sublimation time by 14%, compared with the freezing method involving a constant shelf cooling rate of 1 degrees C/min. Concerning the enzyme activity recovery, the impact of the freezing protocol was observed only for the protective medium involving maltodextrin, a less effective protective agent than sucrose. Higher activity recovery results were obtained after storage when the ultrasound technology or the precooled shelf method was applied. Controlling ice nucleation during the freezing step of the lyophilization process improved the homogeneity of the sublimation rates, which will, in turn, reduce the intervial heterogeneity. The freeze-dryer prototype including the system of controlled nucleation by ultrasounds appears to be a promising tool in accelerating sublimation and improving intrabatch homogeneity.
A Pilot Design Technique for Single-Carrier Transmission over Fast Fading Relay Channels (2008)

Relay-assisted space-time block code (STBC) and space-frequency block code (SFBC) for single carrier frequency-domain equalization (SC-FDE) were presented. They achieve spatial diversity over fading relay channels under the assumption of perfect channel state information (CSI). In this paper, we propose a pilot position selection/detection technique for channel estimation of those systems. Unlike the conventional block-type channel estimation techniques, the proposed scheme superimposes pilots on data-carrying tones whose positions are selected to minimize the distortion of original signals. Without additional pilot overhead, the proposed technique can track the CSI even when the mobile equipment speed is high. The corresponding destination structure and frequency domain equalization are also presented, where the pilot positions are blindly detected and the distorted data symbols are iteratively reconstructed. Simulation results show that the proposed method gives better BER performance than the block-type channel estimation for the distributed SFBC (D-SFBC) SC-FDE over fast fading relay channels, without the loss of spectral efficiency.
An architecture for a next-generation holistic e-recruiting system (2007)

Online recruiting has revolutionized the way businesses worldwide hire employees. The next step is to seamlessly integrate existing systems to create a comprehensive---and complex---corporate career center.
Design of Automatic Equalizer Including a Decoder of Error-Correcting Code (1985)

A new proposed automatic equalizer including a decoder of error-correcting code (AEDEC) is obtained by the joint adaptive operation of an automatic equalizer and a decoder. This AEDEC can reduce misadjustment of tap values and error propagation owing to decision errors, and stabilize convergence even without a known training signal in noisy channels.
Production and Characterization of Bifunctional Enzymes. Domain Swapping To Produce New Bifunctional Enzymes in the Aspartate Pathway (2002)

The bifunctional enzyme aspartokinase-homoserine dehydrogenase I from Escherichia coli catalyzes non-consecutive reactions in the aspartate pathway of amino acid biosynthesis. Both catalytic activities are subject to allosteric regulation by the end product amino acid L-threonine. To examine the kinetics and regulation of the enzymes in this pathway, each of these catalytic domains were separately expressed and purified. The separated catalytic domains remain active, with each of their catalytic activities enhanced in comparison to the native enzyme. The allosteric regulation of the kinase activity is lost, and regulation of the dehydrogenase activity is dramatically decreased in these separate domains. To create a new bifunctional enzyme that can catalyze consecutive metabolic reactions, the aspartokinase I domain was fused to the enzyme that catalyzes the intervening reaction in the pathway, aspartate semialdehyde dehydrogenase. A hybrid bifunctional enzyme was also created between the native monofunctional aspartokinase III, an allosteric enzyme regulated by lysine, and the catalytic domain of homoserine dehydrogenase I with its regulatory interface domain still attached. In this hybrid the kinase activity remains sensitive to lysine, while the dehydrogenase activity is now regulated by both threonine and lysine. The dehydrogenase domain is less thermally stable than the kinase domain and becomes further destabilized upon removal of the regulatory domain. The more stable aspartokinase III is further stabilized against thermal denaturation in the hybrid bifunctional enzyme and was found to retain some catalytic activity even at temperatures approaching 100 degrees C.
Candidate Genes Colocalized to Linkage Regions in Inflammatory Bowel Disease (2002)

Regardless of the disease phenotype, the associations between the polymorphisms and inflammatory bowel disease investigated herein are modest, even after stratification for the disease phenotypes. Hence, these polymorphisms are unlikely to confer the reported linkage between inflammatory bowel disease and chromosomes 6, 7 and 12.
Eros en Platón (2006)

La nocion platonica de Eros ha tenido una repercusion tan amplia en la historia del pensamiento occidental, que ha penetrado hasta en el habla cotidiana de todas las lenguas europeas, el famoso platonico. Es un lugar comun tambien en todas las exposiciones acerca del tema hacer referencia a la poca relacion existente entre el fenomeno que expresa este giro y el verdadero significado de la concepcion platonica del amor. No es mi intencion considerar aqui hasta que punto el giro moderno refleja o no la concepcion platonica, pero si puede subrayarse, sin lugar a dudas, que ese mismo hecho manifiesta las dificultades hermeneuticas que presenta el tema propuesto. TH. GOULD ha analizado en un ya clasico libro 1 las semejanzas y diferencias existentes entre lo que el denomina las cuatro teorias mas importantes del amor en la historia: la platonica, la cristiana, la romantica y la freudiana. Es evidente, tal como el mismo GOULD senala, que estas comparaciones tienden a determinar nuestra comprension del amor y pueden ser tanto una ayuda como un impedimento para poder comprender mejor lo que Platon sostenia. Me propongo avanzar por un camino diferente y, en cierto sentido, opuesto. Platon da al concepto de eros una dimension ontologica primordial, pero su concepcion del amor nace en un contexto historico y pretende diferenciarse de lo que su epoca concebia como el amor. Para comprender mejor el fenomeno, me propongo partir precisamente de lo que los griegos entendian por amor, para luego tratar de interpretar la dimension ontologica y antropologica de la doctrina platonica del eros. Un panorama previo de las costumbres griegas, en especial atenienses, en lo que hace al amor mostrara como la reflexion platonica surge en un contexto historico y social determinado y hasta que punto se diferencia su sexualidad de la nuestra. 1. La sexualidad en la Grecia clasica A. El amor y el sexo
JobSense: A Data-Driven Career Knowledge Exploration Framework and System (2018)

Today's job market sees rapid changes due to technology and business model disruptions. To fully tap on one's potential in career development, one has to acquire job and skill knowledge through working on different jobs. Another approach is to seek consultation with career coaches who are trained to offer career advice in various industry sectors. The above two approaches, nevertheless, suffer from several shortcomings. The on-the-job career development approach is highly inefficient for today's fast changing job market. The latter career coach assisted approach could help to speed up knowledge acquisition but it relies on expertise of career coaches but experienced career coaches are scarce, and they too require update of jobs and skills knowledge. Meanwhile, with wide adoption of Online Professional Net-works (OPNs) such as LinkedIn, Xing and others, publicly shared user profiles have become a treasure trove of job and skill related data. Job and skill related information is also hidden in the sea of online job posts and ads. Manually exploring and acquiring knowledge from these varieties of information are daunting and time-consuming. On the other hand, one needs substantial effort to personalize the acquired knowledge to his/her career interests. There is a dire need for a self-help tool to ease this knowledge acquisition and exploration problems. Before that, there is also a need to create and maintain a large knowledge base of these jobs, skills and careers. Our data-driven, automated knowledge acquisition and interactive exploration system, JobSense, would help users meet the above challenges. JobSense enables users at several stages of career, to explore this knowledge at ease via interactive search, easy navigation, bookmarking of information entities and personalized suggestions. Also we have introduced a career path generation module, to return relevant career paths to the users.
Australian film industry profile: Bob Weis (1984)

Bob Weis is Melbourne's most prolific film maker. He is also something of a maverick. In the commercial and sometimes cynical world of film and television production, Weis has the knack for taking up projects other producers treat as too risky because of the controversial nature of the subject matter. And brining them off with a suprising degree of success. Weis's first major television production was the award winning, Women of the Sun, (1981), a four part mini series chronicling the lives of Aboriginal women at different times in history. Women of the Sun was followed by The Clinic (1982), a contemporary feature film set in a Melbourne VD clinic, which was directed by David Stevens and co-produced with Robert Le Tet. In 1983 Weis produced Waterfront, a three part TV series directed by Chris Thompson from screenplays by Mac Gudgeon. It deals with the bitter strikes of Melbourne's wharfs in the late 1920s. Weis is currently involved in five film and television projects. Earlier this year, he produced a feature film in Hollywood, Heart breakers, which will be released in the United States later this year. There is also a feature length television documentary, The Red Pimpernel, directed by Karyn Altmann, that was shot in a number of countries including America, Portugal, Israel and Australia, which is nearing completion. It is about Raoul Wallenberg, the Swedish diplomat credited with saving thousands of Jews from Nazi concentration camps, who disappeared in mysterious circumstances in 1945. Most of Weis's attention at the moment though, is focused on The Dunera Boys, a four part series directed by Ben Lewinfor Network 10, which starts production later this year. It is based on that extraordinary story of a boatload of refugees sent from Britain to Australia as prisoners of war. Weis is also the executive producer on Chris Thompson's The Empty Beach, an adaption of a Peter Corris novel, that is being made in Sydney. And during the next year, he plans to direct a feature film about Burke and Wills.
Underwater Computer Vision - Fish Recognition (2017)

The Underwater Computer Vision – Fish Recognition project includes the design and implementation of a device that can withstand staying underwater for a duration of time, take pictures of underwater creatures, such as fish, and be able to identify certain fish. The system is meant to be cheap to create, yet still able to process the images it takes and identify the objects in the pictures with some accuracy. The device can output its results to another device or an end user.
BayesHammer: Bayesian clustering for error correction in single-cell sequencing (2013)

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.
An Efficient Cyclic Prefix Reconstruction Technique for MIMO Single-Carrier Frequency-Domain Equalization (2007)

In this letter, an efficient cyclic prefix reconstruction (CPR) technique with turbo equalization is developed for a multi-input multi-output (MIMO) single-carrier frequency-domain equalization (SC-FDE) system. The proposed method consists of pre-processing estimation (PPE) and residual inter-carrier interference suppression (RICIS). The PPE is employed to compute initial values of MIMO turbo equalization, and the RICIS is used to mitigate residual intercarrier interference (ICI) after each iteration of the CPR. By applying the proposed method to MIMO SC-FDE system with insufficient cyclic prefix (CP), we can significantly improve its error performance, obtaining both the benefits of multiplexing gain and spectral efficiency gain
A Novel Gαq/11-selective Inhibitor (2004)

YM-254890, which was isolated from the culture broth of Chromobacterium sp., inhibits ADP-induced platelet aggregation and has antithrombotic and thrombolytic effects. YM-254890 blocks Galpha(q/11)-coupled ADP receptor P2Y1-mediated Ca(2+) mobilization. Here we report that YM-254890 is a selective Galpha(q/11) inhibitor. YM-254890 blocked Ca(2+) mobilization mediated by several Galpha(q/11)-coupled receptors but not by Galpha(i)- or Galpha(15)-coupled receptor, indicating that phospholipase Cbeta activation and subsequent signaling molecules are not the target of YM-254890. YM-254890 completely prevented the serum response factor (SRF)-mediated gene transcription induced by Galpha(q)R183C, which is constitutively active in a receptor-dependent manner because of its reduced k(cat) of GTP hydrolysis. Conversely, YM-254890 had only a modest effect on the SRF-mediated gene transcription by Galpha(q)Q209L, which is GTPase-deficient (activated) Galpha(q). These suggested that the acting point of YM-254890 is receptor-Galpha(q) interaction or the subsequent guanine nucleotide exchange step. The fact that YM-254890 (i) inhibited the SRF-mediated gene transcription by Galpha(qi5), which interacts with Galpha(i)-coupled receptor and possesses the effector function of Galpha(q), and (ii) had no effect on the K(d) value of high affinity [(3)H]2MeSADP binding to P2Y1, which reflects the agonist-receptor-Galpha ternary complex, suggested that receptor-Galpha(q/11) interaction is not the target of YM-254890. On the other hand, specific [(35)S]GTPgammaS binding to Galpha(q/11) stimulated by the M1 muscarinic acetylcholine receptor and P2Y1 were inhibited by YM-254890. These data indicate that YM-254890 blocks the exchange of GDP for GTP in Galpha(q/11) activation. This novel Galpha(q/11)-selective inhibitor is a promising and powerful tool for studying Galpha(q/11) protein activation, Galpha(q/11) -coupled receptor signaling, and Galpha(q/11)-mediated biological events.
Use of image analysis to estimate anthocyanin and UV-excited fluorescent phenolic compound levels in strawberry fruit (2013)

Strawberry is rich in anthocyanins, which are responsible for the red color, and contains several colorless phenolic compounds. Among the colorless phenolic compounds, some, such as hydroxycinammic acid derivatives, emit blue-green fluorescence when excited with ultraviolet (UV) light. Here, we investigated the effectiveness of image analyses for estimating the levels of anthocyanins and UV-excited fluorescent phenolic compounds in fruit. The fruit skin and cut surface of 12 cultivars were photographed under visible and UV light conditions; colors were evaluated based on the color components of images. The levels of anthocyanins and UV-excited fluorescent compounds in each fruit were also evaluated by spectrophotometric and high performance liquid chromatography (HPLC) analyses, respectively and relationships between these levels and the image data were investigated. Red depth of the fruits differed greatly among the cultivars and anthocyanin content was well estimated based on the color values of the cut surface images. Strong UV-excited fluorescence was observed on the cut surfaces of several cultivars, and the grayscale values of the UV-excited fluorescence images were markedly correlated with the levels of those fluorescent compounds as evaluated by HPLC analysis. These results indicate that image analyses can select promising genotypes rich in anthocyanins and fluorescent phenolic compounds.
A Cross-Layer Rate Control Mechanism for Link-Adaptive Satellite Integrated Services (2007)

This paper presents a mechanism for dynamic rate control of satellite integrated services, based on a cross-layer approach, utilising link quality feedback from the satellite terminals. The mechanism, namely, satellite resource management system (SRMS) relies on the adaptive coding and modulation (ACM) capabilities of DVB-S2 in order to perform real-time adjustments on the physical, network and services layer and optimise the usage of satellite spectrum. The functionality of the SRMS is discussed along with its implementation in the frame of the IST IMOSAN Project. Simulation results are presented, involving modelled rain fading and prioritised heterogeneous services, which illustrate the efficiency of the proposed solution against current static transmission schemes.