gebhart/patrepeval huggingface dataset:
Arabic handwritten text recognition using structural and syntactic pattern attributes (2010)

In this thesis, we have conducted research on off-line automatic recognition of Arabic handwritten text. Automatic recognition of Arabic handwritten text has many applications, like forms processing, postal address and zip code recognition, etc. Recognition performance of Arabic handwritten text lags far behind compared to Latin and Chinese scripts. Cursive nature of Arabic script, overlapping characters and ligatures, presence and variability of dots/diacritics, lack of benchmarking databases are among the reasons that make Arabic handwriting recognition a challenging task.
Research on Arabic handwriting recognition has mainly focused on the recognition of isolated characters, numerals and words. Few works have been reported on the recognition of Arabic handwritten text. Moreover, statistical methods (like Hidden Markov Models (HMM), Neural Networks, etc.) have been more common in the reported results on Arabic handwriting recognition. Structural methods have remained largely unexplored in this regard. In addition, some recent multi–classifier based systems have tried to integrate both statistical and structural techniques. 
We present several novel techniques for different phases of Arabic handwriting recognition using a structural approach. We present three segmentation algorithms: segmentation of a page into lines, a line into words/sub–words and a word into characters/graphemes. In addition, we introduce polygonal approximation based representation and modeling of Arabic text. The recognition system is based on a proposed dissimilarity measure. Polygon–based modeling of text, prototype selection using set–medians, lexicon reduction using dot–descriptors etc. are some of the techniques that are applied to Arabic handwriting recognition for the first time. These techniques are applied to Arabic handwritten isolated–characters, digits, words and text recognition. Hence, this thesis addresses the lack of research in structural methods for Arabic handwriting recognition. In addition, the presented techniques may provide alternate sources of information to be utilized in multi–classifiers systems.
The proposed techniques are applied to different databases. We have obtained competitive results compared to the state of the art performance in statistical approaches and have surpassed the results based on structural techniques. In addition, the proposed techniques can be further extended. Moreover, we believe that several avenues of research in Arabic handwriting recognition have been initiated in this thesis.
Genome-Based Characterization of Two Prenylation Steps in the Assembly of the Stephacidin and Notoamide Anticancer Agents in a Marine-Derived <i>Aspergillus</i> sp. (2010)

Stephacidin and notoamide natural products belong to a group of prenylated indole alkaloids containing a core bicyclo[2.2.2]diazaoctane ring system. These bioactive fungal secondary metabolites have a range of unusual structural and stereochemical features but their biosynthesis has remained uncharacterized. Herein, we report the first biosynthetic gene cluster for this class of fungal alkaloids based on whole genome sequencing of a marine-derived Aspergillus sp. Two central pathway enzymes catalyzing both normal and reverse prenyltransfer reactions were characterized in detail. Our results establish the early steps for creation of the prenylated indole alkaloid structure and suggest a scheme for the biosynthesis of stephacidin and notoamide metabolites. The work provides the first genetic and biochemical insights for understanding the structural diversity of this important family of fungal alkaloids.
Total Synthesis of a Densely Functionalized <i>Plesiomonas shigelloides</i> Serotype 51 Aminoglycoside Trisaccharide Antigen (2018)

Plesiomonas shigelloides, a pathogen responsible for frequent outbreaks of severe travelers' diarrhea, causes grave extraintestinal infections. Sepsis and meningitis due to P. shigelloides are associated with a high mortality rate as antibiotic resistance increases and vaccines are not available. Carbohydrate antigens expressed by pathogens are often structurally unique and are targets for developing vaccines and diagnostics. Here, we report a total synthesis of the highly functionalized trisaccharide repeating unit 2 from P. shigelloides serotype 51 from three monosaccharides. A judicious choice of building blocks and reaction conditions allowed for the four amino groups adorning the sugar rings to be installed with two N-acetyl (Ac) groups, rare acetamidino (Am), and d-3-hydroxybutyryl (Hb) groups. The strategy for the differentiation of amino groups in trisaccharide 2 will serve well for the syntheses of other complex glycans.
Induction of virus-induced gene silencing and <i>in planta</i> validation in cucurbits using the CFMMV-Cm vector (2021)

Abstract Virus-induced gene silencing (VIGS) has been employed for the high-throughput analysis of endogenous gene function. We developed a CaMV 35S promoter-driven cucumber fruit mottle mosaic virus-Cm vector (pCF93) for the efficient generation of viral transcripts in plants. Using the novel pCF93 vector, we identified genes related to male sterility in watermelon ( Citrullus lanatus ), which is recalcitrant to genetic transformation. We previously reported reference-based and de novo transcriptomic profiling for the detection of differentially expressed genes between a male fertile line (DAH3615) and its near isogenic male sterile line (DAH3615-MS). Based on the RNA-seq results, we identified 38 de novo -exclusive differentially expressed genes (DEDEGs) that are potentially responsible for male sterility. Partial genes of 200∼300bp were cloned into pCF93 which was then inoculated into DAH, a small type of watermelon that enables high-throughput screening with a small cultivation area. In this manner, we simultaneously characterized phenotypes associated with the 38 candidate genes in a common-sized greenhouse. Eight out of the 38 gene-silenced plants produced male sterile flowers with abnormal stamens and no pollens. Gene expression levels in flowers were validated via RT-qPCR. Stamen histological sections from male sterile floral buds and mature flowers showed developmental disruption and shrunken pollen sacs. Based on the current findings, we believe that the novel pCF93 vector and our VIGS system facilitate high-throughput analysis for the study of gene function in watermelons. One sentence summary The CaMV 35S promoter-driven cucumber fruit mottle mosaic virus-Cm vector (pCF93) facilitates large-scale validation of male sterility-related gene functions in watermelon.
Structural and functional insights into a novel pre-clinical-stage antibody targeting IL-17A for treatment of autoimmune diseases (2022)

The pro-inflammatory cytokine interleukin-17A (IL-17A) is a key driver of multiple inflammatory and immune disorders. Therapeutic antibodies targeting IL-17A have been proven effective in treating patients with these diseases; however, large variations in clinical outcomes have been observed with different antibodies. In this study, we developed HB0017, a novel monoclonal antibody that targets human IL-17A. HB0017 specifically and strongly bound to human, cynomolgus monkey, and mouse IL-17A at the physiological interface with the IL-17A receptor. In human and monkey cells, HB0017 potently antagonized the functions of IL-17A through competitive binding. HB0017 functioned equivalently to that of clinically approved antibodies in terms of therapeutic efficacy for inflammatory disorders and psoriasis in a mouse model. The results indicate that HB0017 may be an alternative biological therapy for treating patients with inflammation and autoimmune diseases.
A 300-Kilometer Optical Fiber Time Transfer Using Bidirectional TDM Dissemination (2014)

We propose a long-distance high precise time transfer scheme over single optical fiber employing the same wavelengths in both directions. It can suppress the impact of the Rayleigh backscattering and the dispersion-induced symmetric deviation over fiber links at the same time by using bidirectional time division multiplexing (BTDM) mechanism. A single-fiber bidirectional amplifier (SFBA) is also optimized for the proposed scheme. A 300km time transfer over single optical fiber with identical optical wavelengths in both directions is demonstrated. The results show that the bidirectional propagation delay asymmetry is less than 25 ps with fiber link up to 300km without any calibration, which is closed to the floor of the used time interval counters, and almost keep unchanged as the fiber length increases. The measured stabilities in term of TDEV are less than 40ps/s and 11ps/d, respectively.
Optical multipass matrix systems (1991)

Large relative aperture three- and four-objective multipass matrix systems ensuring the longest optical path length in an absorbing medium have been developed for high resolution laser spectroscopy. In these systems the images are formed on the field mirrors as compact rectangular matrices with a controlled amount of lines and columns. The number of passes may reach 500 for mirrors with high reflectivity layers. Having a simple construction, the matrix systems provide high optical and operational features. In view of their capacities the matrix systems are new generation multipass systems.
A New Method for Nonlinear and Nonstationary Time Series Analysis: The Empirical Mode Decomposition Method (2001)

A new method for analyzing nonlinear and nonstationary data has been developed. The key part of the method is the Empirical Mode Decomposition method with which any complicated data set can be decomposed into a finite and often small number of Intrinsic Mode Functions (IMF). An IMF is defined as any function having the same numbers of zero-crossing and extrema, and also having symmetric envelopes defined by the local maxima and minima respectively. The IMF also admits well-behaved Hilbert transform. This decomposition method is adaptive, and, therefore, highly efficient. Since the decomposition is based on the local characteristic time scale of the data, it is applicable to nonlinear and nonstationary processes. With the Hilbert transform, the Intrinsic Mode Functions yield instantaneous frequencies as functions of time that give sharp identifications of imbedded structures. The final presentation of the results is an energy-frequency-time distribution, designated as the Hilbert Spectrum. Classical nonlinear system models are used to illustrate the roles played by the nonlinear and nonstationary effects in the energy-frequency-time distribution.
Improved Solar Cell Efficiency Through the Use of an Additive Nanostructure-Based Optical Downshifter: Final Subcontract Report, January 28, 2010 -- February 28, 2011 (2011)

This final report summarizes all SpectraWatt's progress in achieving a boost in solar cell efficiency using an optical downshifter. Spectrawatt's downshifting technology is based on a nanostructured material system which absorbs high energy (short wavelength) light and reemits it at a lower energy (long wavelength) with high efficiency. This system has shown unprecedented performance parametersincluding near unity quantum yield and high thermal stability.
Tumor autoantibodies as biomarkers for predicting ovarian cancer recurrence (2012)

Ovarian cancer (OVCA) has a high incidence of recurrence and a high rate of mortality. We performed a pilot study to evaluate the usefulness of tumor autoantibodies to tumor associated antigens (TAA) to predict OVCA recurrence. A validation study with 56 antigens, previously identified in the initial phase of the study, along with 13 known tumor antigens on protein arrays was performed on an independent cohort of recurrent and non-recurrent OVCA patients. Statistical analyses revealed that a panel of 3 antigens predicted recurrence at a median time of 9.07 months prior to clinical recurrence in a study population, where majority of patients had CA125 values less than 35 U/ml, with an average sensitivity, specificity and accuracy of 94.7%, 86.7% and 93.3% respectively. One of the top 3 antigens has been associated with the development of polymyositis (PM) which has been shown in some cases to precede the occurrence of ovarian carcinoma. Our results indicate that these 3 antigens have potential for predicting recurrence at an early time and may have better prognostic utility than CA125 alone for early therapeutic intervention. These biomarkers could guide us to identify those patients that could benefit most from maintenance or consolidation therapy.
Comparison of Plaster Casting with Three-Dimensional Cranial Imaging (2005)

In this investigation, the 3D models created by the new imaging system were found to be within 1.0 mm RMS of the models created by the plaster casting technique. Two-dimensional cranial contours demonstrated excellent agreement between the two methods. The results of this investigation confirmed that the new cranial imaging system and the traditional plaster casting technique yield equivalent models.
Mitosis: Transparently Self-Replicating Page-Tables for Large-Memory Machines (2020)

Multi-socket machines with 1-100 TBs of physical memory are becoming prevalent. Applications running on such multi-socket machines suffer non-uniform bandwidth and latency when accessing physical memory. Decades of research have focused on data allocation and placement policies in NUMA settings, but there have been no studies on the question of how to place page-tables amongst sockets. We make the case for explicit page-table allocation policies and show that page-table placement is becoming crucial to overall performance. We propose Mitosis to mitigate NUMA effects on page-table walks by transparently replicating and migrating page-tables across sockets without application changes. This reduces the frequency of accesses to remote NUMA nodes when performing page-table walks. Mitosis uses two components: (i) a mechanism to efficiently enable and (ii) policies to effectively control -- page-table replication and migration. We implement Mitosis in Linux and evaluate its benefits on real hardware. Mitosis improves performance for large-scale multi-socket workloads by up to 1.34x by replicating page-tables across sockets. Moreover, it improves performance by up to 3.24x in cases when the OS migrates a process across sockets by enabling cross-socket page-table migration.
A new sequence distance measure for phylogenetic tree construction (2003)

Available on request from the authors.
Anionic polymerization to high vinyl polybutadiene (1981)

Abstract 1,3‐Butadiene was polymerized anionically to polybutadiene which contained up to 100% 1,2‐addition product. The atactic 100% 1,2‐polybutadiene was prepared with n ‐butyllithium modified with bis piperidino ethane. The polymerization was done in hexane solvent at −5 to +20°C polymerization temperature.
Bioactive glass-mesoporous silica coatings on Ti6Al4V through enameling and triblock-copolymer-templated sol-gel processing (2001)

The combination of thick glass coatings that can protect Ti6Al4V from corrosion in the body fluids, and mesoporous silica films able to readily induce the formation of apatite when immersed in a simulated body fluid (SBF), has been investigated in this work as a possible route towards more resistant and long-lasting implants. Glasses in the system Si-Ca-Mg-Na-K-P-O with thermal expansion coefficients close to that of Ti6Al4V were prepared and used to coat this alloy by an enameling technique. However, the glasses apt to coat Ti6Al4V exhibited a very limited capacity to induce apatite formation in SBF. In order to enhance their bioactivity, a thin film of mesoporous silica was applied on the exterior of the specimens by spin coating a sol-gel solution. When tested in SBF, these coatings induced apatite formation after 7 days. The mesoporosity of the silica film was created through a triblock-copolymer-templating process. The diameters of the mesochannels could be adjusted by changing the size of the directing agent. A preferred alignment of the mesostructure was observed. The removal of the organic templates could be achieved through a photocalcination treatment, which, compared to conventional thermocalcination, offered several advantages.
Patterns of CD8 T-Cell Epitopes within the Human Papillomavirus Type 16 (HPV 16) E6 Protein among Young Women Whose HPV 16 Infection Has Become Undetectable (2005)

The patterns of CD8 T-cell epitopes recognized within the E6 protein in women who had cleared their human papillomavirus 16 infection were examined. T-cell lines were established using autologous dendritic cells infected with a recombinant vaccinia virus. Evidence of potential antigenic epitopes was shown in 8 of 23 (34.8%) women.
Development of screen printed electrochemical sensors for selective detection of heavy metals (2015)

A flexible electrochemical sensor for selective detection of heavy metals was successfully fabricated using screen printing technique. The sensor consists of three electrodes: counter, working and reference electrodes printed using silver (Ag), carbon and silver/silver chloride (Ag/AgCl) inks, respectively. 1,10-phenanthroline and its derivative naphtha [2,3-a] dipyrido [3,2-h:2',3'-f'] phenazine-5,18-dione (QDPPZ) was synthesized and drop casted on the working electrode of the printed device as sensitive layers for mercury ions (Hg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> ) and lead ions (Pb <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> ), respectively. Cyclic voltammetry response (CV) of the electrochemical sensor towards Hg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> and Pb <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> demonstrated a very low detection level of 50 μΜ with reduction peaks at 0.2 eV and −0.6 eV, respectively. An 87 % and 9 % change in the average peak currents were observed for the 50 μΜ concentration of Pb <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> and Hg <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> , respectively, against a reference signal established for deionized water (DI). The response of the electrochemical sensor is analyzed and presented in this paper.
Packaged high-speed electro-optic polymer modulators (2006)

Electro-optic (EO) polymer modulators have demonstrated high speed external modulation of optical signals. Additionally, EO polymers have closely matched refractive indices at optical and microwave wavelengths, which enables high bandwidth operation. An EO polymer includes a polymer matrix and an organic "push-pull" chromophore that can be modified to give poled polymers with high EO activity. This high EO activity and optical-microwave velocity match offer the promise of accomplishing broadband, high speed optical modulation with low drive voltage. Such optical signal modulation is critical for applications in phased array radar and RF photonics. Practical issues such as electrode design, optical fiber coupling, and hermetic packaging are critical in final device performance. Herein, we report on high-speed electrode parameters as well as electro-optic performance versus frequency of packaged modulators fabricated with novel, highly photostable chromophores.
A complexity reducing transformation in algebraic list decoding of Reed-Solomon codes (2004)

The main computational steps in algebraic soft decoding, as well as Sudan-type list decoding, of Reed-Solomon codes are interpolation and factorization. A series of transformations is given for the interpolation problem that arises in these decoding algorithms. These transformations reduce the space and time complexity to a small fraction of the complexity of the original interpolation problem. A factorization procedure that applies directly to the reduced interpolation problem is also presented.
An open source based network as a service (NaaS) platform for cloud provisioning (2015)

Cloud provisioning is an emerging area and highly embraced by Enterprises. There are several commercial and open source solutions available in the market. We discuss the problem areas in NaaS with respect to the available solutions and our approach to address the concerns by means of an open source middle layer single umbrella platform called “TCS Network as a Service (TNaaS)”. This platform is modular in nature and provides a vendor agnostic NaaS for cloud provisioning. We also provide a lab based evaluation comprising of OpenStack cloud software, TNaaS, open vSwitches and Floodlight Software Defined Network (SDN) controller.
Exploring Immersive Interpersonal Communication via AR (2022)

A central challenge of social computing research is to enable people to communicate expressively with each other remotely. Augmented reality has great promise for expressive communication since it enables communication beyond texts and photos and towards immersive experiences rendered in recipients' physical environments. Little research, however, has explored AR's potential for everyday interpersonal communication. In this work, we prototype an AR messaging system, ARwand, to understand people's behaviors and perceptions around communicating with friends via AR messaging. We present our findings under four themes observed from a user study with 24 participants, including the types of immersive messages people choose to send to each other, which factors contribute to a sense of immersiveness, and what concerns arise over this new form of messaging. We discuss important implications of our findings on the design of future immersive communication systems.
Patterning of Epitaxial Organic Films by Selective Epitaxial Growth (1996)

A new method of patterning crystalline organic molecular films is proposed and demonstrated. It utilizes a selective growth, or the difference in the sticking coefficient of an organic material on various inorganic substrates in a certain temperature range. The object structure is first patterned on a single-crystalline substrate with an epitaxial film of a different material grown by molecular beam epitaxy (MBE) through a mask, and then a beam of the organic molecule is irradiated uniformly after removing the mask.
A Fully Integrated Architecture for Fast Programming of Floating Gates (2007)

We present an on-chip system that enables programming floating gate arrays at a high speed. The main component allowing this speedup is a floating point current measuring ADC operating over 4 decades at 10bit accuracy or 7decades at 7 bit accuracy. The conversion time is around 200 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> s till around 30 pA of current. The gate and drain voltages are set by on-chip DACs. The digital words for the DAC are sent by an FPGA through an SPI interface. The controller for sequencing the operations as well as the look-up-table with characterization data are on the FPGA. Algorithms using either pulse-width modulation or drain voltage modulation can be implemented.