gebhart/patrepeval huggingface dataset:
Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes (2018)

Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following <i>de novo</i> metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.<b>IMPORTANCE</b> The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (<i>Pinus contorta</i>), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.
High Dimensional Quantum Key Distribution with Biphoton Frequency Combs through Energy-Time Entanglement (2019)

Biphoton frequency combs offer a photon-efficient way to achieve a very high-rate quantum key distribution by utilizing both time and frequency-bin encoding, while offering theoretically proven unconditional security.
Teaching tolerance (2012)

Babies born with Pompe disease require life-long treatment with enzyme-replacement therapy (ERT). Despite the human origin of the therapy, recombinant human lysosomal acid α glucosidase (GAA, rhGAA), ERT unfortunately leads to the development of high titers of anti-rhGAA antibody, decreased effectiveness of ERT, and a fatal outcome for a significant number of children who have Pompe disease. The severity of disease, anti-drug antibody (ADA) development, and the consequences thereof are directly related to the degree of the enzyme deficiency. Babies born with a complete deficiency GAA are said to have cross-reactive immunologic material (CRIM)-negative Pompe disease and are highly likely to develop GAA ADA. Less frequently, GAA ADA develop in CRIM-positive individuals. Currently, GAA-ADA sero-positive babies are treated with a combination of immunosuppressive drugs to induce immunological tolerance to ERT, but the long-term effect of these regimens is unknown. Alternative approaches that might redirect the immune response toward antigen-specific tolerance without immunosuppressive agents are needed. Methods leading to the induction of antigen-specific regulatory T cells (Tregs), using peptides such as Tregitopes (T regulatory cell epitopes) are under consideration for the future treatment of CRIM-negative Pompe disease. Tregitopes are natural T cell epitopes derived from immunoglobulin G (IgG) that cause the expansion and activation of regulatory T cells (Treg). Teaching the immune system to tolerate GAA by co-delivering GAA with Tregitope peptides might dramatically improve the lives of CRIM-negative babies and could be applied to other enzyme replacement therapies to which ADA have been induced.
Retinal oximetry technology (2012)

Abstract Purpose Disturbances in retinal oxygenation are believed to be involved in several eye diseases, among them retinal vessel occlusions, diabetic retinopathy and possibly glaucoma and age‐related macular degeneration. The technology to reliably and non‐invasively measure retinal oxygenation is emerging after decades of development. Methods Non‐invasive retinal oximetry utilises the fact that the colour of blood changes as oxygen saturation changes. The most reliable measurements can be obtained from the larger retinal vessels, while measurements of retinal capillaries need further development. Several instruments have been built for non‐invasive oximetry. They measure light absorbance of retinal blood vessels at two or more wavelengths and use the result to calculate retinal vessel oxygen saturation. Results Several research groups have shown that their instruments are sensitive to changes in retinal vessel oxygen saturation and that the measurements are reproducible. Oximetry has successfully been used to detect differences in retinal oxygenation in many diseases as well as responses to treatment or provocation tests. Accurate calibration is, however, difficult. Conclusion The current retinal oximetry technology can reliably be used to measure changes in retinal vessel oxygen saturation in the same eye with time. Oximetry can also easily measure differences in means between groups. Further development is needed to increase the accuracy of single measurements. Commercial interest
Window-Based Image Registration using Variable Window Sizes (2007)

We present an unsupervised image registration algorithm to estimate the background object motion in a real video sequence. The algorithm is based on a Gaussian minimisation technique. It has been shown earlier that initialization of such an approach is very important to achieve the motion parameters of the background object precisely, and that the use of a windowing technique can give better background object motion estimation results, even with large background occlusions. In some cases, however, the fixed window size initializes the gradient descent algorithm in a sub-optimal way. Here, another window size would bring the desired estimation direction. In this paper, we present a technique where variable window sizes are used to prevent these outliers. Experimental results show that the technique works very well with the considered test sequences.
A Study on the Reaction Rate and Cause Analysis of Cyanoacrylate Adhesives According to the Coating Mixtures for Metal Artifacts (2011)

When metal artifacts have to undergo conservation treatment, the person in charge of the treatment selects and uses various coating mixtures based on his judgment regarding their condition, material, or environment. Since the kinds of coating mixtures or solvents make a difference in the set time of cyanoacrylate adhesives, they have something to do with the efficiency of the conservation treatment. This study examines the effects and causes that affect the set time of cyanoacrylate adhesives according to the kinds of coating mixtures and solvents and suggests ways to increase the set time. As a result, it is thought that as the surface roughness gets flatter, the wettability of adhesive is improved further, which increases the set time. Moreover, the C-F binding of V-Flon, C-O-C absorption peak, molecular weight of the coating mixtures, and glass transition temperature (Tg) were the factors that significantly affected the set time. According to the result of measuring the set time based on the result of superficial and chemical analysis, relative difference was shown according to the kind and viscosity of adhesive, but all the adhesives indicated the following order of the set time: V-Flon > Paraloid B-72 (in xylene) > Paraloid NAD-10 > Paraloid B-72 (in acetone).
Size Effects and the Problem with Percolation in Nanostructured Transparent Conductors (2010)

Much research is underway at present to develop nanostructured transparent conductors for use as electrodes. Transparent electrodes typically require high visible transmittances, T > 90%, and so must be very thin. We show that for most nanostructured films thin enough to display T > 90%, the conduction can be described by percolation theory. This means DC conductivities are lower than in bulk, giving correspondingly higher sheet resistances, R(s). To improve our understanding of the consequences of this, we develop a model which relates T to R(s) in the percolation regime. We define a percolative figure of merit, Π, for which high values result in high T and low R(s). High values of Π are achieved for high DC conductivity and low optical conductivity. In addition, the film thickness, t(min), where the DC conductivity first deviates from its bulk value and the percolation exponent, n, must both be as low as possible. We find that this model fits extremely well to much of the data in the literature. We demonstrate that t(min) scales linearly with the smallest dimension of the nanostructure in question (i.e., diameter for wires or thickness for flakes). This clearly confirms that low diameter nanowires or thin platelets are best for transparent conducting applications. We predict the properties of silver nanowire networks to improve as wire diameter is decreased. Networks of wires with D < 20 nm should display properties superior to the best ITO. We demonstrate the deficiencies of standard bulk theory and the importance of understanding percolation by measuring R(s) and T for networks of silver flakes. We measure the bulk ratio of DC to optical conductivity to be ∼35, suggesting R(s) = 100 Ω/◻ and T = 90% are attainable. However, the large flake thickness results in high t(min) and so low Π, resulting in actual values of T = 26% for R(s) = 100 Ω/◻. This makes this material completely unsuitable for transparent conductor applications.
Effective Synchronization of EEG and EMG for Mobile Brain/Body Imaging in Clinical Settings (2018)

Mobile Brain/Body Imaging (MoBI) is rapidly gaining traction as a new imaging modality to study how cognitive processes support locomotion. Electroencephalogram (EEG) and electromyogram (EMG), due to their time resolution, non-invasiveness and portability are the techniques of choice for MoBI, but synchronization requirements among others restrict its use to high-end research facilities. Here we test the effectiveness of a technique that enables us to achieve MoBI-grade synchronization of EEG and EMG, even when other strategies (such as Lab Streaming Layer (LSL)) cannot be used e.g., due to the unavailability of proprietary Application Programming Interfaces (APIs), which is often the case in clinical settings. The proposed strategy is that of aligning several spikes at the beginning and end of the session. We delivered a train of spikes to the EEG amplifier and EMG electrodes every 2 s over a 10-min time period. We selected a variable number of spikes (from 1 to 10) both at the beginning and end of the time series and linearly resampled the data so as to align them. We then compared the misalignment of the "middle" spikes over the whole recording to test for jitter and synchronization drifts, highlighting possible nonlinearities (due to hardware filters) and estimated the maximum length of the recording to achieve a [-5 to 5] ms misalignment range. We demonstrate that MoBI-grade synchronization can be achieved within 10-min recordings with a 1.7 ms jitter and [-5 5] ms misalignment range. We show that repeated spike delivery can be used to test online synchronization options and to troubleshoot synchronization issues over EEG and EMG. We also show that synchronization cannot rely only on the equipment sampling rate advertised by manufacturers. The synchronization strategy described can be used virtually in every clinical environment, and may increase the interest among a broader spectrum of clinicians and researchers in the MoBI framework, ultimately leading to a better understanding of the brain processes underlying locomotion control and the development of more effective rehabilitation approaches.
Discovery of a Metalloenzyme-like Cooperative Catalytic System of Metal Nanoclusters and Catechol Derivatives for the Aerobic Oxidation of Amines (2012)

We have discovered a new class of cooperative catalytic system, consisting of heterogeneous polymer-immobilized bimetallic Pt/Ir alloyed nanoclusters (NCs) and 4-tert-butylcatechol, for the aerobic oxidation of amines to imines under ambient conditions. After optimization, the desired imines were obtained in good to excellent yields with broad substrate scope. The reaction rate was determined to be first-order with respect to the substrate and catechol and zero-order for the alloyed Pt/Ir NC catalyst. Control studies revealed that both the heterogeneous NC catalyst and 4-tert-butylcatechol are essential and act cooperatively to facilitate the aerobic oxidation under mild conditions.
Irinotecan and UFT/leucovorin in patients with advanced cancers. (2000)

The combination of irinotecan and fluorouracil (5-FU) is synergistic when applied to human colon cancer cell lines in vitro and appears to be schedule-dependent: maximal activity occurs when irinotecan is administered prior to 5-FU. In this phase I study, irinotecan is administered in combination with UFT and leucovorin in patients with advanced solid tumors. Irinotecan is given as a 90-minute intravenous infusion on day 1 followed by twice-daily UFT plus oral leucovorin on days 2 through 15. Cycles are repeated every 21 days. Five patients have been treated to date; four are evaluable for toxicity. Starting doses were irinotecan 200 mg/m2/day, UFT 200 mg/m2/day, and leucovorin 60 mg/day. Preliminary results indicate that irinotecan in combination with UFT plus leucovorin is well tolerated at the initial doses (described in this article).
Guest editorial - Equalization techniques for wireless communications theory & applications (2008)

The fifteen articles in this special issue are devoted to new equalization techniques for wireless communications, including new the latest theories and applications.
ChemInform Abstract: Synthesis of α‐Functional Nitro Compounds by Nitration of Activated Carbonyl Derivatives in a Two‐Phase System. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
p53 protein overexpression and allele loss of p53 gene in gastric adenocarcinoma (1994)

Gene alterations of p53 tumor suppressor gene such as point mutations, deletions or insertions occur in various human cancers. p53 protein overexpression was studied immunohistochemically in 80 gastric adenocarcinomas using an anti-human p53 antibody (Pab 1801) and the avidin-biotin-peroxidase technique. We have also analyzed allele loss of the human p53 gene in 54 cases of gastric adenocarcinoma using polymerase chain reaction and restriction fragment length polymorphism. p53 immunostaining was also demonstrated in 48 of 80 carcinomas (60%). Normal mucosa was always negative. No relation could be found between p53 immunostaining and the degree of differentiation. 21 of the 54 patients(39%) were informative for the p53 exon 4. In ten of these informative cases(47.6%), tumor DNAs showed allele loss when compared with nonmetastatic lymph node DNAs. Seven of the ten(70%) showed p53 immunoreactivity. These findings suggest that mutations of the p53 gene may play a role in the development of gastric adenocarcinoma and that allele loss of p53 frequently occurs in p53 immunoreactive gastric adenocarcinoma.
Variability in Genetic Architecture of the Cryptic Species Complex of Acanthocyclops Vernalis (Copepoda). I. Evidence from Karyotypes, Genome Size, and Ribosomal DNA Sequences (2005)

Abstract Populations of the North American cryptic species complex of Acanthocylops vernalis (Fischer 1853) (Copepoda) possess unusually variable karyotypes and levels of reproductive isolation, but are difficult to discern morphologically. We established nine isofemale lines derived from four local and geographically isolated pond populations from Wisconsin and three isofemale lines from a lake in Ohio to explore the variability and relationships of chromosome numbers, genome sizes, and similarity of ribosomal DNA sequences. Five karyotypes (2n = 6, 7, 8, 9 and 10) were observed, although genome sizes were remarkably consistent. A 593 bp region of the 18S ribosomal gene was identical in four Wisconsin and three Ohio lines, but differed among five Wisconsin lines. This variability in 18S rDNA sequences among lines, which is uncharacteristic for well defined cyclopoid species, was used to construct a network of relationships among the isofemale lines. Mapping chromosome number onto this network revealed a cluster of lineages with variable chromosome numbers and a cluster with consistent chromosome number, although the overall pattern was more complex than this. Although 4–5 bivalents were observed in oocytes of the progeny from one isofemale line from Ohio, progeny of the latter had smaller genomes than any of the Wisconsin lines. All Wisconsin and Ohio lines lacked chromatin diminution, a trait previously attributed to some populations of A. vernalis by Standiford (1989, Genetika 79: 207–214) and Akifiev (1974, Priroda (USSR) 9: 49–54). Occurrence of chromosomal aberrations among disjunct populations may account for the unusual genetic variability of this species complex. Such differentiation also may be accelerated in fragmented habitats where genetic isolation seems to be recent and recurrent.
EXAFS Study of Thermal Treatment of Pb-Zr Alkoxide Precursors (1997)

The local environment of Zr atoms in amorphous precursors and intermediate products of the thermal treatment leading to perovskite PbZrO3 ceramic materials is studied by EXAFS. The coordination of Zr depends significantly on the choice of the starting Zr alkoxide. The Zr-O-Zr bond in an amorphous phase persists till the final stage of heating at 800 °C.
Use of the complex between prostate specific antigen and alpha 1-protease inhibitor for screening prostate cancer. (2000)

Serum PSA-alpha 1-protease inhibitor improves the specificity of total and free PSA in a screening population with total PSA 4 to 10 microg./l.
Large effective area optical fibres for lasers and amplifiers (2007)

Built-in mode filtering in a leakage channel fibre enables robust fundamental mode operation with effective mode area much larger than that is possible with conventional approaches. Recently effective area exceeding ~3000 μm2 and PM fibre have been demonstrated. (4 pages)
Operating Concept for a 240-MW Combined Cycle Intermediate Peaking Plant (1971)

This paper describes the design of a combined cycle power plant for intermediate peaking with particular reference to design features resulting in simplified control and operation.
Genetically Engineered Pancreatic β‐Cell Lines for Cell Therapy of Diabetes (1999)

The optimal treatment of insulin-dependent diabetes mellitus (IDDM), which is caused by the autoimmune destruction of pancreatic islet beta cells, would require the regulated delivery of insulin by transplantation of functional beta cells. beta-cell transplantation has so far been restricted by the scarcity of human islet donors. This shortage would be alleviated by the development of differentiated beta-cell lines, which could provide an abundant and well-characterized source of beta cells for transplantation. Using conditional transformation approaches, our laboratory has generated continuous beta-cell lines from transgenic mice. These cells produce insulin amounts comparable to those of normal islets and release insulin in response to physiological stimuli. Cell replication in these beta cells can be tightly controlled both in culture and in vivo, allowing regulation of cell number and cell differentiation. Another challenge to cell therapy of IDDM is the protection of transplanted cells from immunological rejection and recurring autoimmunity. By employing adenovirus genes which downregulate antigen presentation and increase cell resistance to cytokines, beta-cell transplantation across allogeneic barriers was achieved without immunosuppression. In principle, similar beta-cell lines can be derived from isolated human islets using viral vectors to deliver conditionally regulated transforming and immunomodulatory genes into beta cells. The combination of these approaches with immunoisolation devices holds the promise of a widely available cell therapy for treatment of IDDM in the near future.
Generating High-Precision Feedback for Programming Syntax Errors using Large Language Models (2023)

Large language models (LLMs), such as Codex, hold great promise in enhancing programming education by automatically generating feedback for students. We investigate using LLMs to generate feedback for fixing syntax errors in Python programs, a key scenario in introductory programming. More concretely, given a student's buggy program, our goal is to generate feedback comprising a fixed program along with a natural language explanation describing the errors/fixes, inspired by how a human tutor would give feedback. While using LLMs is promising, the critical challenge is to ensure high precision in the generated feedback, which is imperative before deploying such technology in classrooms. The main research question we study is: Can we develop LLMs-based feedback generation techniques with a tunable precision parameter, giving educators quality control over the feedback that students receive? To this end, we introduce PyFiXV, our technique to generate high-precision feedback powered by Codex. The key idea behind PyFiXV is to use a novel run-time validation mechanism to decide whether the generated feedback is suitable for sharing with the student; notably, this validation mechanism also provides a precision knob to educators. We perform an extensive evaluation using two real-world datasets of Python programs with syntax errors and show the efficacy of PyFiXV in generating high-precision feedback.