gebhart/patrepeval huggingface dataset:
Characterization of a panel of monoclonal antibodies and their use in the study of the antigenic diversity of bovine viral diarrhea virus (1990)

A panel of 40 monoclonal antibodies (MAb) specific for bovine viral diarrhea virus (BVDV) was produced, and each MAb was characterized and grouped according to its viral protein specificity, immunoglobulin subclass, virus-neutralizing activity, and immunoreactivity with a large collection of BVDV isolates. The MAb were found to be specific for 1 of 3 sets of related viral-induced proteins found in cells infected with the Singer strain of BVDV. Group-1 MAb were specific for the 80- and 118-kilodalton (kD) proteins of BVDV. Group-2 MAb recognized 3 proteins with molecular sizes of 54, 56, and 58 kD. Group-3 MAb recognized a 43- and a 65-kD protein. The MAb belonged to either the IgG1, IgG2a, IgG2b, IgG3 subclasses or the IgE class of mouse immunoglobulin. All MAb in group 2 were able to neutralize BVDV and had neutralization titers that ranged from 24 to 1,600,000. The reactivity of the MAb with numerous field isolates of BVDV was highly variable. Both cytopathic and noncytopathic biotypes of BVDV were examined and had the same degree of antigenic variation. The greatest degree of variation was detected with group-2 MAb. The data demonstrate that BVDV isolates have a high degree of antigenic variation that is largely confined to the envelope glycoproteins associated with virus neutralization. The results also suggest that antigenic variability of this virus is important in the development and severity of the disease it causes.
Endophytic bacteria in grass crop growth promotion and biostimulation (2021)

Plants naturally carry microbes on seeds and within seeds that may facilitate development and early survival of seedlings. Some crops have lost seed-vectored microbes in the process of domestication or during seed storage and seed treatment. Biostimulant microbes from wild plants were used by pre-modern cultures to re-acquire beneficial seed microbes. Today  some companies have developed or are developing the use of microbes obtained from soils or plant sources to stimulate plant development and growth. Many of these biostimulant microbes are endophytic in plants. Biostimulant products also include humic substances, which appear to function as signal molecules in plants, triggering increased internalization of soil microbes into root cells and tissues. In addition, protein coatings on seeds fuel the growth of seed surface-vectored microbes, increasing microbial activity around and within roots. In this article, we provide evidence of the endophytic nature of many biostimulant microbes, and suggest that many of the beneficial effects of microbial biostimulants stem from their action as endophytes or as participants or stimulants of rhizophagy cycle activity.
Extending Relational Database Systems to Automatically Enforce Privacy Policies (2005)

Databases are at the core of successful businesses. Due to the voluminous stores of personal data being held by companies today, preserving privacy has become a crucial requirement for operating a business. This paper proposes how current relational database management systems can be transformed into their privacy-preserving equivalents. Specifically, we present language constructs and implementation design for fine-grained access control to achieve this goal.
Cholesterol-lowering strategies reduce vascular LRP1 overexpression induced by hypercholesterolaemia (2011)

Our results demonstrate that cholesterol-lowering interventions exerted down regulatory effects on vascular LRP1 over expression induced by hypercholesterolemia and that simvastatin did not influence LRP1 expression beyond its cholesterol-lowering effects.
A super-serial Galois fields multiplier for FPGAs and its application to public-key algorithms (2003)

This contribution introduces a scalable multiplier architecture for Galois field GF(2/sup k/) amenable for field programmable gate arrays (FPGAs) implementations. This architecture is well suited for the implementation of public-key cryptosystems which require programmable multipliers in large Galois fields. The architecture trades a reduction in resources with an increase in the number of clock cycles. This architecture is also fine grain scalable in both the time and the area (or logic) dimensions thus facilitating implementations that maximize their use of finite FPGA resources while achieving fast computational speed. This leads to an architecture that requires less resources than traditional bit serial multipliers, which we demonstrated with implementations of multipliers in the field GF(2/sup 167/). Our results demonstrate that for this field one can realize super-serial multipliers that use 2.76 times fewer function generators and 6.84 times fewer flip-flops than their serial multiplier counterparts. We also extrapolated the performance of these multipliers in an elliptic curve cryptosystem.
Design principles and performance of bioresorbable polymeric coronary scaffolds (2009)

Limited clinical data speak to the potential of bioresorbable scaffolds as a new therapy, and future studies will prove critical to inspiring a fourth revolution in PCI.
Lesion size and shape in central vein sign assessment for multiple sclerosis diagnosis: An in vivo and postmortem MRI study (2022)

Lesion-size measures add important information when using CVS+ lesion counts for MS diagnosis. The CVS is a specific biomarker corresponding to intralesional veins on histopathology.
Amino Acid Oligomer Microspheres as Drug Delivery Systems. II. Oligomerization of NCAs Initiated with L-Tyrosine Methyl Ester (1996)

Oligomerizations of various amino acid N-carboxyanhydrides (NCAs) were prepared in the presence of L-tyrosine methyl ester (Tyr.Me). Tyr.Me was found to be an efficient initiator to form oligopeptides consisting of L-aspartic acid, L-glutamic acid, L-phenylalanine, and L-tyrosine with random arrangements of amino acids. In acidic solution, the oligopeptides formed microspheres which were capable of encapsulating macromolecular drugs such as insulin and heparin. These microspheres were considered to be potential oral drug delivery systems.
Human Monoclonal Antibodies Targeting Nonoverlapping Epitopes on Insulin-like Growth Factor II as a Novel Type of Candidate Cancer Therapeutics (2012)

Soluble ligands are important targets for therapy of cancers and other diseases. Therapeutic monoclonal antibodies (mAb) against such ligands block their interactions with corresponding receptors but do not enhance their removal from the circulation and can increase their half-lives because of the long half-lives of the antibodies. We have hypothesized that mAbs targeting two or more nonoverlapping epitopes on the same ligand could form oligomeric antibody-ligand complexes that can bind to cells expressing Fc gamma receptors (FcγRs) with high avidity leading to their fast and irreversible removal from the circulation. Insulin-like growth factor II (IGF-II) is an example of such ligands and an important target for human cancer therapy. We identified two mAbs, m610.27 and m630.3, which bound to nonoverlapping epitopes on IGF-II with nanomolar affinity, and generated a bispecific antibody, m660. m660 inhibited the interaction of human IGF-II (hIGF-II) with the human breast cancer cell line MCF-7, hIGF-II-mediated IGF receptor type I and insulin receptor phosphorylation, and cell growth. In the presence of hIGF-II, large complexes of m660 were formed that bound to FcγRII-expressing BJAB cells much more efficiently than the monospecific antibody-hIGF-II complexes and were presumably phagocytosed by phorbol 12-myristate 13-acetate-stimulated macrophage-like U937 cells. A mixture of m610.27 and m630.3 exhibited similar properties. To our knowledge, these mAbs are the first reported to target nonoverlapping epitopes on a cancer-related ligand and could represent a novel class of candidate therapeutics against cancers. This approach could also be used to irreversibly eliminate other disease-related soluble ligands.
Influence of CSI Feedback Errors on Capacity of Linear Multi-User MIMO Systems (2007)

In this paper, we discuss the influence of feedback channel errors on throughput of linear multi-user multiple-input multiple-output (MIMO) systems employing vector quantization (VQ) algorithms for encoding channel state information (CSI). We consider an approach where the receiver estimates the downlink channel and chooses one of the predefined channel characterization codewords whose indices are transmitted back to the transmitter. In practice, the feedback channel will introduce errors in transmission of the indices and we evaluate the resulting channel capacity loss for different system setups. We demonstrate the performance of two types of systems, one using time division multiplexing of individual users and another transmitting to multiple users. We evaluate two basic error mitigation approaches: the first one with user expurgation using error-detection codes and the second one, based on specially designed VQ indexing. We show that the proposed schemes are very robust to even relatively high bit error rates in the feedback link and that proper VQ indexing may suffice for actual system design, even if the feedback channel is not very reliable.
Odyssey, an optimized personal communications satellite system (1994)

Personal communications places severe demands on service providers and transmission facilities. Customers are not satisfied with the current levels of service and want improvements. Among the characteristics that users seek are: lower service rates, hand held convenience, acceptable time delays, ubiquitous service, high availability, reliability, and high quality. The space industry in developing commercial space systems for providing mobile communications to personal telephones. Provision of land mobile satellite service is fundamentally different from the fixed satellite service provided by geostationary satellites. In fixed service, the earth based antennas can depend on a clear path from user to satellite
A micromachined W-band iris filter (2005)

A micromachined W-band iris filter was successfully demonstrated using micro hot embossing and selective electroplating technologies. The filter design follows the insertion loss method with a Chebyshev polynomial to synthesize the desired spectral responses and numerical simulations were performed using the finite-element tool, high frequency structure simulator (HFSS), to study the effects of iris thickness on the bandwidth and center frequency. The measured prototype filter performance has a transmission loss of -3.49 dB and a return loss of -18 dB at the resonant frequency of 95 GHz. The filter has a bandwidth of 3.5 GHz and a rejection loss of better than -50 dB, while the loaded quality factor is 27.27. This plastic, low-cost manufacturing process opens up opportunities in replacing the expensive metallic components and integrated 3D manufacturing for current and future millimeter-wave systems.
Parameters Affecting the Interaction Among Closely Spaced Hydraulic Fractures (2012)

Summary Placing multiple hydraulic fractures at intervals along horizontal wells has proved to be a highly effective method for stimulation. However, the mechanical interaction between a growing hydraulic fracture and one or more previous hydraulic fractures can affect the fracture geometry such that the final fracture array is suboptimal for stimulation. If the fracture-array geometry is idealized as a set of regular and planar fractures, history matching and production forecasting may be inaccurate. During the treatments, the fractures can curve toward or away from one another, potentially intersecting one another. A detailed parametric study of this phenomenon using a coupled 2D numerical fracturing simulator shows that the curving is associated with a combination of opening and sliding along the previously placed hydraulic fracture, as well as the previous fracture's disturbance of the local stress field because of its propped width. Dimensional analysis and scaling techniques are used to identify the key parameters that are associated with suppression of each mechanism that can lead to hydraulic-fracture curving. The analysis, which is in agreement with available data, results in a clarification of the conditions under which attractive and repulsive curving are expected, as well as the conditions under which curving is expected to be negligible or even completely suppressed. This last case of planar hydraulic-fracture growth is of practical importance and will usually be considered desirable. We present a straightforward method for determining whether planar fracture growth is expected that additionally gives insight into how design parameters can be modified to promote planar hydraulic-fracture growth.
Antibodies against alpha‐synuclein: tools and therapies (2019)

Synucleinopathies including Parkinson's disease, dementia with Lewy bodies and multiple system atrophy are characterized by the abnormal accumulation and propagation of α-synuclein (α-syn) pathology in the central and peripheral nervous system as Lewy bodies or glial cytoplasmic inclusions. Several antibodies against α-syn have been developed since it was first detected as the major component of Lewy bodies and glial cytoplasmic inclusions. Over the years, researchers have generated specific antibodies that alleviate the accumulation of intracellular aggregated α-syn and associated pathology in cellular and preclinical models of synucleinopathies. So far, antibodies have been the first choice as tools for research and diagnosis and currently, a wide variety of antibody fragments have been developed as an alternative to full-length antibodies for increasing its therapeutic usefulness. Recently, conformation specific antibody-based approaches have been found to be promising as therapeutic strategies, both to block α-syn aggregation and ameliorate the resultant cytotoxicity, and as diagnostic tools. In this review, we summarize different α-syn specific antibodies and provide their usefulness in tackling synucleinopathies. This article is part of the Special Issue "Synuclein".
Chemical and Enzymatic Methods for Preparing Circular Single‐Stranded <scp>DNAs</scp> (2000)

Small circular oligonucleotides can be used for diagnostic, therapeutic, and laboratory purposes. These systems have gained considerable attention in recent years because they form unusually strong and specific complexes with RNA and DNA strands. Synthetic circular DNAs of 20 to 200 nucleotides can also serve as catalysts for amplified DNA and RNA synthesis by a rolling circle mechanism. This unit presents methods for synthesizing small circular oligonucleotides. These simple "one-pot" procedures are carried out using short DNA splints that hold the circle together until it is chemically or enzymatically ligated.
A flexible model for resource management in virtual private networks (1999)

As IP technologies providing both tremendous capacity and the ability to establish dynamic secure associations between endpoints emerge, Virtual Private Networks (VPNs) are going through dramatic growth. The number of endpoints per VPN is growing and the communication pattern between endpoints is becoming increasingly hard to forecast. Consequently, users are demanding dependable, dynamic connectivity between endpoints, with the network expected to accommodate any traffic matrix, as long as the traffic to the endpoints does not overwhelm the rates of the respective ingress and egress links. We propose a new service interface, termed a hose , to provide the appropriate performance abstraction. A hose is characterized by the aggregate traffic to and from one endpoint in the VPN to the set of other endpoints in the VPN, and by an associated performance guarantee.Hoses provide important advantages to a VPN customer: (i) flexibility to send traffic to a set of endpoints without having to specify the detailed traffic matrix, and (ii) reduction in the size of access links through multiplexing gains obtained from the natural aggregation of the flows between endpoints. As compared with the conventional point to point (or customer-pipe) model for managing QoS, hoses provide reduction in the state information a customer must maintain. On the other hand, hoses would appear to increase the complexity of the already difficult problem of resource management to support QoS. To manage network resources in the face of this increased uncertainty, we consider both conventional statistical multiplexing techniques, and a new resizing technique based on online measurements.To study these performance issues, we run trace driven simulations, using traffic derived from AT&amp;T's voice network, and from a large corporate data network. From the customer's perspective, we find that aggregation of traffic at the hose level provides significant multiplexing gains. From the provider's perspective, we find that the statistical multiplexing and resizing techniques deal effectively with uncertainties about the traffic, providing significant gains over the conventional alternative of a mesh of statically sized customer-pipes between endpoints.
An object placement advisor for DB2 using solid state storage (2009)

Solid state disks (SSDs) provide much faster random access to data compared to conventional hard disk drives. Therefore, the response time of a database engine could be improved by moving the objects that are frequently accessed in a random fashion to the SSD. Considering the price and limited storage capacity of solid state disks, the database administrator needs to determine which objects (tables, indexes, materialized views, etc.), if placed on the SSD, would most improve the performance of the system. In this paper we propose a tool called "Object Placement Advisor" for making a wise decision for the object placement problem. By collecting profile inputs from workload runs, the advisor utility provides a list of objects to be placed on the SSD by applying heuristics like the greedy knapsack technique or dynamic programming. To show that the proposed approach is effective in conventional database management systems, we have conducted experiments on IBM DB2 with queries and schemas based on the TPC-H and TPC-C benchmarks. The results indicate that using a relatively small amount of SSD storage, the response time of the system can be reduced significantly by considering the recommendation of the advisor.
Targeting the hydrophobic pocket of autotaxin with virtual screening of inhibitors identifies a common aromatic sulfonamide structural motif (2013)

Modulation of autotaxin (ATX), the lysophospholipase D enzyme that produces lysophosphatidic acid, with small-molecule inhibitors is a promising strategy for blocking the ATX-lysophosphatidic acid signaling axis. Although discovery campaigns have been successful in identifying ATX inhibitors, many of the reported inhibitors target the catalytic cleft of ATX. A recent study provided evidence for an additional inhibitory surface in the hydrophobic binding pocket of ATX, confirming prior studies that relied on enzyme kinetics and differential inhibition of substrates varying in size. Multiple hits from previous high-throughput screening for ATX inhibitors were obtained with aromatic sulfonamide derivatives interacting with the hydrophobic pocket. Here, we describe the development of a ligand-based strategy and its application in virtual screening, which yielded novel high-potency inhibitors that target the hydrophobic pocket of ATX. Characterization of the structure-activity relationship of these new inhibitors forms the foundation of a new pharmacophore model of the hydrophobic pocket of ATX.
Framework for GMPLS and Path Computation Element (PCE) Control of Wavelength Switched Optical Networks (WSONs) (2011)

This document provides a framework for applying Generalized Multi-Protocol Label Switching (GMPLS) and the Path Computation Element (PCE) architecture to the control of Wavelength Switched Optical Networks (WSONs).In particular, it examines Routing and Wavelength Assignment (RWA) of optical paths.This document focuses on topological elements and path selection constraints that are common across different WSON environments; as such, it does not address optical impairments in any depth.
Deflection Routing in Slotted Self-Routing Networks With Arbitrary Topology (2004)

A deflection routing scheme for small to medium size future all-optical networks with arbitrary topologies is proposed. The proposed scheme assumes only single-bit all-optical processing and no buffers. The primary output selection and the alternate output choices by a packet at each node are encoded in the packet header in order to reduce the signal processing requirement. Additional features such as priority and time-to-live fields have also been defined. The performance of the deflection routing scheme is studied using the AT&T North America OC-48 optical fiber network topology.
Elimination of basal-plane stacking faults in semipolar/nonpolar GaN and light emitting diodes heteroepitaxially grown on sapphire substrates (2018)

High quality semipolar and nonpolar GaN is crucial in achieving high-performance GaN-based optoelectronic devices, yet it has been very challenging to achieve large-area wafers that are free of basal-plane stacking faults (BSFs). In this work, we report an approach to prepare large-area, stacking-fault-free (SF-free) semipolar GaN on (4-inch) sapphire substrates. A root cause of the formation of BSFs is the emergence of N-polar (000-1) facets during semipolar and non-polar heteroepitaxy. Invoking the concept of kinetic Wulff plot, we succeeded in suppressing the occurrence of N-polar GaN (000-1) facets, and consequently in eliminating the stacking faults generated in (000-1) basal-planes. The result was confirmed by transmission electron microscopy, cathodoluminescence, and low-temperature photoluminescence characterizations. Furthermore, InGaN light emitting diodes with promising characteristics have been produced on the SF-free semipolar (20-21) GaN on sapphire substrates. Our work opens up a new insight about the heteroepitaxial growth of nonpolar/semipolar GaN and provides an approach of producing SF-free nonpolar/semipolar GaN material over large-area wafers which will create new opportunities in GaN optoelectronic and microelectronic research.
1,2,4-Thiadiazino[3,4-b]benzothiazole: A New Cyclic Sulphenimine (1993)

m-3,4-Dihydro-8-trifluoromethoxy-1,2,4-thiadiazino[3,4-blbenzothiazole (2) was prepared in five steps from 6-trifluoromethoxy-2-benzothiazolamine (riluzole, 1).The key final step consisted of an original N-S bond forming reaction between unsubstituted imine and thiol groups, using chloramine-T as reagent (75% yield).The therapeutically useful activities of riluzole (1) (Scheme I), an indirectly-acting excitatory amino acid antagonist,] as well as the need for new pharmaceutical tools to elucidate its mechanisms of action, prompted us t o synthesize analogs of this lead compound.2As pan of this work, we describe herein an efficient and simple synthesis of 3,4-dihydro-8-trifluoromethoxy-1,2,4-thiadiazino[3,4-blbenzothiazole (2) (Scheme 1),3 and a new convenient synthetic approach for the preparation of the cyclic sulphenimine moiety. riluzole