gebhart/patrepeval huggingface dataset:
Enzymatic syntheses of glucobioses by a condensation reaction with .ALPHA.-glucosidase, .BETA.-glucosidases and glucoamylase. (1988)

Various glucobioses were synthesized enzymatically by two procedures, an incubation of a highly concentrated solution of D-glucose in the presence of glycosidases (batch method reaction), and the other is circulation of highly concentrated D-glucose solution through an immobilized glycosidase column and an activated carbon column connected in series (column method reaction). The composition of disaccharides differed with the difference of reaction methods and with the kind of glycosidases. A similar reaction was also done with glucoamylase and the factors controlling the regioselectivity of the reaction with the differences of enzyme or with the differences of the procedures are discussed.
Science review: Mechanisms of impaired adrenal function in sepsis and molecular actions of glucocorticoids (2004)

This review describes current knowledge on the mechanisms that underlie glucocorticoid insufficiency in sepsis and the molecular action of glucocorticoids. In patients with severe sepsis, numerous factors predispose to glucocorticoid insufficiency, including drugs, coagulation disorders and inflammatory mediators. These factors may compromise the hypothalamic-pituitary axis (i.e. secondary adrenal insufficiency) or the adrenal glands (i.e. primary adrenal failure), or may impair glucocorticoid access to target cells (i.e. peripheral tissue resistance). Irreversible anatomical damages to the hypothalamus, pituitary, or adrenal glands rarely occur. Conversely, transient functional impairment in hormone synthesis may be a common complication of severe sepsis. Glucocorticoids interact with a specific cytosolic glucocorticoid receptor, which undergoes conformational changes, sheds heat shock proteins and translocates to the nucleus. Glucocorticoids may also interact with membrane binding sites at the surface of the cells. The molecular action of glucocorticoids results in genomic and nongenomic effects. Direct and indirect transcriptional and post-transcriptional effects related to the cytosolic glucocorticoid receptor account for the genomic effects. Nongenomic effects are probably subsequent to cytosolic interaction between the glucocorticoid receptor and proteins, or to interaction between glucocorticoids and specific membrane binding sites.
Natural ligands for CD33-related Siglecs? (2009)

Finding natural ligands involved in protein–protein interactions is relatively easy, and false-positives are rare. In contrast, the natural ligands for glycan-binding proteins (GBPs) can be quite elusive, and artifacts are common. For example, it took almost 10 years from the detection of P-selectin's glycan binding properties (Moore et al. 1991) to reach the definitive conclusion that a certain specific posttranslationally modified form of the polypeptide PSGL-1 was the functionally relevant natural ligand for this GBP (Epperson et al. 2000). There are many reasons for such difficulties, including the fact that glycan binding is often of relatively low affinity and relies on multivalency to achieve adequate avidity, as well as the complexities of local rebinding effects such as the recently described “jump and bind” mechanisms for lectin–mucin interactions (Dam and Brewer 2008). Meanwhile, investigators continue to incorrectly state that “PSGL-1 is the ligand for P-selectin,” without realizing that while the PSGL-1 polypeptide backbone is expressed in many cell types (Laszik et al. 1996), it is only the correctly sialylated, fucosylated, and tyrosine-sulfated form found in certain cells that can function as a P-selectin ligand. In this regard, an excellent prior suggestion is to define the ligand as the glycan(s) bound by the GBP, the protein or lipid to which the glycan(s) are bound as the “carrier,” and the composite of the glycan and the carrier as the “counter–receptor” (Crocker and Feizi 1996) (see Notes).
Detecting and Preventing Fraud with Data Analytics (2015)

Abstract Although fraud is not a new issue, the current financial crisis has enlightened that fraud occurs mainly during a recession, as compared with normal periods of economic growth. In counterbalance to the slow economic recovery, managers need to start a series of antifraud measures, as a leverage of cost control, while reducing available resources. Fraud involves inclusively significant financial risks which may threaten profitability, and the image of an economic entity. In these circumstances, in which development of the IT systems plays a central role in the creation of competitive companies, the amount of processed data has grown exponentially. Internal control team members should need to look at every transaction that takes place, but, unfortunately this issue can no longer be manually performed, requiring the use of data analysis tools and programs. Since the companies usually operate with large volumes of data, it is absolutely necessary to implement such processes of continuous monitoring, in order to identify anomalies in the data stream or behavioral patterns, potentially fraudulent. Such new and significant information will be later used in directing investigations, as well as to make recommendations to improve the control activities. We strive to provide an overview of the way in which technology can be implemented to improve fraud prevention and detection, inside of a public or private economic entity.
Optimal Training Signals for Joint Estimation of Channel Response and Frequency Offset in Multiuser OFDM (2007)

In this paper, a new method for pilot-tone design is presented for multiuser orthogonal frequency division multiplexing(OFDM) systems. We first compute the mean square error (MSE) of the ML channel estimate, then we derive optimal pilot sequences and optimal placement of the pilot tones with respect to this MSE. It is shown that the optimal pilot sequences are equipowered and phase shift orthogonal. Through simulations, it is shown that the optimal pilot sequences derived in this paper outperform the random pilot sequences for joint estimation of channel response and frequency offset in multiuser OFDM systems. Simultaneously, by using the modified maximum likelihood (ML) algorithm can reduce the complex of computation. Simulations indicate that this scheme is especially useful for the system has small frequency offset.
Oxygen Effects in Anaerobic Digestion – A Review (2011)

This article reviews the experimental and theoretical studies conducted on the possible effects of oxygen in biogas generating anaerobic digesters. The interactions of oxygen with various biochemical processes associated with anaerobic digestion are discussed together with other relevant aspects. The conventional perception of oxygen being merely toxic in anaerobic digestion (AD) is refuted. Digesters can withstand significant levels of oxygenation without drastic negative impacts. Limited quantities of oxygen can even lead to improved AD reactor performance under certain operating conditions. Co-existence of anaerobic and aerobic cultures in a single bioreactor environment has been demonstrated. It is shown that the partial aeration assisted AD can serve as a beneficial treatment strategy for simultaneous waste treatment and energy generation, for a multitude of organic waste categories.
A Cost-Effective and QoS-Aware Approach to Scheduling Real-Time Workflow Applications in PaaS and SaaS Clouds (2015)

The ever increasing popularity of cloud computing has relieved many consumers and businesses from the burden of acquiring, maintaining and monitoring expensive hardware and software infrastructure. In this paper, we focus on Platform as a Service (PaaS) and Software as a Service (SaaS) clouds, where users submit their workflow applications in order to be executed within strict timing constraints. It is assumed that the target cloud platform is based on a multi-tenant approach, where applications of different users may share the same virtual machines. We propose a list scheduling heuristic for the scheduling of real-time workflow applications in a heterogeneous PaaS (or SaaS) cloud that incorporates imprecise computations and bin packing techniques. Our scheduling approach has two objectives: (a) to guarantee that all applications will meet their deadline, providing high quality results and (b) to minimize the execution time of each workflow application and thus the cost charged to the user. The proposed approach is compared to a baseline list scheduling algorithm via simulation, for workflow applications with various communication to computation ratios. The simulation results show that the proposed scheduling strategy outperforms the baseline policy, providing promising results.
Effects of proteoglycan extraction on the tensile behavior of articular cartilage (1990)

We undertook an interdisciplinary biomechanical and biochemical study to explore the extent and manner in which the total pool of proteoglycans influences the kinetic and static behavior of bovine articular cartilage in tension. Two biomechanical tests were used: (a) the viscoelastic creep test and (b) a slow constant-rate uniaxial tension test; and two enzymatic proteoglycan extraction procedures were used: (a) chondroitinase ABC treatment and (b) a sequential enzymatic treatment with chondroitinase ABC, trypsin, and Streptomyces hyaluronidase. We found that the viscoelastic creep response of all cartilage specimens may be divided into two distinct phases: an initial phase (less than 15 s), characterized by a rapid increase in strain following load application, and a late phase (15 s less than or equal to t less than 25,000 s), characterized by a more gradual increase in strain. A major finding of this study is that the kinetics of the creep response is greatly influenced by the glycosaminoglycan content of the tissue. For untreated and control specimens, the initial response comprises about 50% of the total strain, while for chondroitinase ABC and sequentially extracted specimens, the initial response comprises up to 83% of the total strain. Furthermore, most untreated and control specimens did not reach equilibrium within the 25,000 s test period, while enzymatically digested specimens often reached equilibrium in less than 100 s. Thus, we conclude that through their physical restraints on collagen, the bulk of proteoglycan present in the tissue acts to retard fibrillar reorganization and alignment under tensile loading, thereby effectively preventing sudden extension of the collagen network. In contrast, the results of our slow constant-rate uniaxial tension experiment show that essentially complete extraction of proteoglycan glycosaminoglycans does not affect the intrinsic tensile stiffness and strength of cartilage specimens or the collagen network in a significant manner. Hence, an important function of the bulk proteoglycans (i.e., the large aggregating type) in cartilage is to retard the rate of stretch and alignment when a tensile load is suddenly applied. This mechanism may be useful in protecting the cartilage collagen network during physiological situations, where sudden impact forces are imposed on a joint.
Performance evaluation of dynamic cloud resource migration based on temporal and capacity-aware policy for efficient resource sharing (2013)

This paper elaborates on practical considerations, such as location and capacity issues to offload resources, by adopting a rack based approach for the implementation. The proposed cooperative migration of resources enables efficient resource manipulation without any intermittent execution of the claimed tasks by the mobile devices, while it significantly reduces crash failures that lead all servers to become unavailable within a rack. In addition, this paper presents a modular resource migration scheme for failure-aware resource allocation, where according to the estimated performance of the resource sharing process (e.g. access time, service delay etc.) resources are migrated to another cloud rack based on the associated performance-oriented metrics. The proposed architecture is thoroughly evaluated through simulation tests for the resource migration policy used in the context of cloud rack failures for delay-bounded resource availability of mobile users, as well as for the efficiency of the proposed resource migration scheme.
The MethDet: a technology for biomarker development (2011)

Early detection and diagnosis of a disease in its presymptomatic form has to rely on biomarkers, and multiple laboratories are involved in their development and validation. In this article, we describe our work on a platform technology for a genome-wide analysis of DNA methylation while still using a small amount of sample - a biopsy, a section from a formalin-fixed paraffin-embedded tissue or a small volume (0.4 ml) of plasma from blood. This technology (methylation detection or MethDet) allows genome-wide association studies similar to the analysis of single-nucleotide polymorphisms. Instead of mostly static genetic differences, the MethDet technology tests disease-dependent changes of epigenetic makeup, which is closely related to the gene expression pattern of a disease. The MethDet assay has the capacity to utilize highly fragmented DNA (e.g., cell-free circulating DNA from plasma) to identify disease-specific changes, effects of treatment or changes in the disease activity.
A Statistical Approach to Estimate the Wind Speed Distribution: The Case of Gelibolu Region (2008)

Wind energy is renewable and environment friendly. It is an alternative clear energy source compared to the fossil fuels that pollute the lower layer of atmosphere. The most important parameter of the wind energy is the wind speed. Statistical methods are useful for estimating wind speed because it is a random phenomena. For this reason, wind speed probabilities can be estimated by using probability distributions. An accurate determination of probability distribution for wind speed values is very important in evaluating wind speed energy potential of a region. In this study, first, we tried to determine appropriate theoretical pdf (probability density function) by comparing 10 pdf for the wind speed data measured for Gelibolu region. In determining proper pdf , an approach consisting of 3 goodness of fit tests and fitted graphics have been used.
Nonlinear analysis of EEG signals at different mental states (2004)

It is found that the measures are significantly lower when the subjects are under sound or reflexologic stimulation as compared to the normal state. The dimension increases with the degree of the cognitive activity. This suggests that when the subjects are under sound or reflexologic stimuli, the number of parallel functional processes active in the brain is less and the brain goes to a more relaxed state
Structure-Function Analysis of Tritrypticin, an Antibacterial Peptide of Innate Immune Origin (1999)

The structural requirements for the antibacterial activity of a pseudosymmetric 13-residue peptide, tritrypticin, were analyzed by combining pattern recognition in protein structures, the structure-activity knowledge-base, and circular dichroism. The structure-activity analysis, based on various deletion analogs, led to the identification of two minimal functional peptides, which by themselves exhibit adequate antibacterial activity against Escherichia coli and Salmonella typhimurium. The common features between these two peptides are that they both share an aromatic-proline-aromatic (ArProAr) sequence motif, and their sequences are retro with respect to one another. The pattern searches in protein structure data base using the ArProAr motif led to the identification of two distinct conformational clusters, namely polyproline type II and beta-turn, which correspond to the observed solution structures of the two minimal functional analogs. The role of different residues in structure and function of tritrypticin was delineated by analyzing antibacterial activity and circular dichroism spectra of various designed analogs. Three main results arise from this study. First, the ArProAr sequence motif in proteins has definitive conformational features associated with it. Second, the two minimal bioactive domains of tritrypticin have entirely different structures while having equivalent activities. Third, tritrypticin has a beta-turn conformation in solution, but the functionally relevant conformation of this gene-encoded peptide antibiotic may be an extended polyproline type II.
<title>Newly Developed Glass Devices For Image Transmission</title> (1973)

Through the improvement of quality and manufacturing process of glass device named "SELF001W, which was introduced at SPIE of January, 1970, the several kinds of new SELFOOV lenses, in which SELFOCO lenses having different view angles, SELFOd lens of large diameter, SELFOOt4 lens with low chromatic abberation and high quality SELF0a) lens array are included, have been developed. We also succeeded in developing fused fiber plate and flexible image bundle of high quality and low cost by improving the manufacturing process. At the same time, we developed several types of unique endoscopes whose image transmitting devices were composed of the optical glass devices mentioned above. In those unique endoscopes, there are an arthroscope having the thinnest inserting needle in the world and flexible endoscopes for industrial and medical purposes of which costs are very low in spite of their high performances.
Smart guide: lithium niobate large index contrast waveguides fabricated by crystal ion slicing and wafer bonding (2005)

Recently large index contrast optical waveguides are considered for the fabrication of integrated optical components. Electro-optical waveguides are particularly interesting since they have the potential to be used for switching devices. In this paper we introduce a new method for fabrication of large index contrast lithium niobate waveguides. The waveguides are fabricated using crystal ion slicing and wafer bonding. This allows the fabrication of high refractive index contrast waveguides with lithium niobate as the core and silicon dioxide as the low refractive index cladding. Electrodes can also be deposited between the layers for applying an electric field to the waveguide in the vertical direction. The structure can be fabricated on any substrate. Waveguides with a thickness of 700nm suitable for single mode operation at lambda=1.55micron have been successfully produced. The thin films are analyzed using different analytical techniques including atomic force microscopy and Rutherford backscattering (RBS). The RBS spectrum shows that the crystal structure of the fabricated thin films is very similar to bulk lithium niobate and the quality of the crystalline waveguide is excellent. Optical waveguiding and electro-optical modulation is demonstrated using the prism-coupling method. It is shown that the fabricated waveguide refractive indices and electro-optic coefficients are identical to bulk lithium niobate crystals. These large index contrast waveguides are ideal for fabrication of devices such as electro-optic micro-ring resonators, Mach-Zehnder interferometric modulators with reduced half wave voltage and nonlinear optical waveguide devices for second harmonic generation or parametric amplification. It is shown that this waveguide structure is an ideal structure for the fabrication of integrated optical components due to the good optical properties of lithium niobate and large index contrast achieved by the fabrication method.
Design and evaluation of the combined input and crossbar queued (cicq) switch (2004)

Packet switches are used in the Internet to forward information between a sender and receiver and are the critical bottleneck in the Internet. Without faster packet switch designs, the Internet cannot continue to scale-up to higher data rates. Packet switches must be able to achieve high throughput and low delay. In addition, they must be stable for all traffic loads, must efficiently support variable length packets, and must be scalable to higher link data rates and greater numbers of ports. This dissertation investigates a new combined input and crossbar queued (CICQ) switch architecture.\nSome unbalanced traffic loads result in instability for input queued (IQ) and CICQ switches. This instability region was modeled, and the cause of the instability was found to be a lack of work conservation at one port. A new burst stabilization protocol was investigated that was shown to stabilize both IQ and CICQ switches. As an added benefit, this new protocol did not require a costly internal switch speed-up. Switching variable length packets in IQ switches requires the segmentation of packets into cells. The process also requires an internal switch speed-up which can be costly. A new method of cell-merging in IQ switches reduced this speed-up. To improve fairness for CICQ switches, a block and transfer method was proposed and evaluated.\nImplementation feasibility of the CICQ switch was also investigated via a field programmable gate array (FPGA) implementation of key components. Two new designs for round robin arbiters were developed and evaluated. The first of these, a proposed priority-encoder-based round robin arbiter that uses feedback masking, has a lower delay than any known design for an FPGA implementation. The second, an overlapped round robin arbiter design that fully overlaps round robin polling and scheduling, was proposed and shown to be scalable, work conserving, and fair.\nTo allow for multi-cabinet implementation and minimization of the size of the cross point buffers, a distributed input port queue scheduler was investigated. This new scheduler minimizes the amount of buffering needed within the crossbar.\nThe two primary contributions of this dissertation are 1) a complete understanding of the performance characteristics of the CICQ switch, and 2) new methods for improving the performance, stability,and scalability of the CICQ switch. This work has shown that the CICQ switch can be the switch architecture of the future.