gebhart/patrepeval huggingface dataset:
Degradation of Proteins with Acetylated Amino Termini by the Ubiquitin System (1989)

A free NH2-terminal group has been previously shown to be an obligatory signal for recognition and subsequent degradation of proteins in a partially fractionated and reconstituted ubiquitin proteolytic system. Naturally occurring proteins with acetylated NH2-termini--most cellular proteins fall in this category--were not degraded by this system. Other studies have suggested that the identity of the NH2-terminal residue is important in determining the metabolic stability of a protein in vivo (N-end rule). Whole reticulocyte lysate and antibodies directed against the ubiquitin-activating enzyme (E1) have now been used to show that such acetylated proteins are degraded in a ubiquitin-dependent mode. Although fractionation of lysate does not affect its proteolytic activity toward substrates with free NH2-termini, it completely abolishes the activity toward the blocked substrates, indicating that an important component of the system was either removed or inactivated during fractionation. An NH2-terminal "unblocking" activity that removes the blocking group, thus exposing a free NH2-terminus for recognition according to the N-end rule, does not seem to participate in this pathway. Incubation of whole lysate with labeled histone H2A results in the formation of multiple ubiquitin conjugates. In contrast, the fractionated system is devoid of any significant conjugating activity. These results suggest that a novel conjugating enzyme (possibly a ubiquitin-protein ligase) may be responsible for the degradation of these acetylated proteins by recognizing structural features of the substrate that are downstream and distinct from the NH2-terminal residue.
MicroRNAs in Renal Cell Carcinoma: Diagnostic Implications of Serum miR-1233 Levels (2011)

MicroRNA levels are distinctly increased in cancer patients, although only a small subset of circulating microRNAs has a tumor-specific origin. We identify circulating miR-1233 as a potential biomarker for RCC patients. Larger-scaled studies are warranted to fully explore the role of circulating microRNAs in RCC.
Coherent phase combining of 64 fibers (2011)

In this Communication, we present coherent phase combining of 64 independent fibers, selectively amplified by 4 optical amplifiers. This is to our knowledge the highest number of combined fibers ever demonstrated. In order to achieve this result, we have developed specific collective components for phase measurement of a large number of fibers, arrays of phase modulators, and an array of collimated fibers.
High active device density Quasi-Optical amplifier (1996)

A quasi-optical amplifier using narrow slot antenna is designed with high active device density. The natural coupling of the microstrip and slotline is exploited for power combining/dividing without any appreciable increase in circuit real-estate. Measured EIPG in the transmission mode agrees well with theoretical prediction.
[Family of multiple peptide fragments derived from angiotensin and their interaction]. (2005)

It is well established that renin-angiotensin system (RAS) is the major regulatory network that maintains blood pressure, fluid and electrolyte balance and the homeostasis of cardiovascular system. Most studies in the last decades centered on the pivotal members of RAS, that is, angiotensin II (Ang II ) and angiotensin converting enzyme (ACE). Recent identification of ACE-2, the homology of ACE, and the identification of the multiple products degraded from angiotensin I, including Ang III, Ang IV, Ang(1-9), Ang(1-7), Des-Asp-angiotensin I(DAA I), etc, have proved that Ang II is not the only biological active compound of RAS. Peptides derived from angiotensinogen,that is, family of angiotensins,display independent and pleiotropic biological activities in vivo, and interact with each other both in metabolism pathway and the biologic effects. The imbalance of the network of angiotensin metabolites exhibits significant pathophysiological role in cardiovascular disease.
Heterocyclic synthesis: A convenient route to some 2‐mercepto 1,3,4‐oxadiazole and green chemistry microwave‐induced one‐pot synthesis of 2‐aryl 1,3,4‐oxadiazole in quinazolone and their antibacterial and antifungal activity (2005)

Abstract Several 6‐substituted‐3‐[(5‐mercepto‐1,3,4‐oxadiazol‐2‐yl)methyl]‐2‐substituted quinazolin‐4(3 H )‐one or 6‐substituted‐3‐[4‐(5‐mercepto‐1,3,4‐oxadiazol‐2‐yl)phenyl]‐2‐substituedquinazolin‐4(3 H )‐one 2(a‐l) and 6‐substituted‐3‐[(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl)methyl]‐2‐substitutedquinazolin‐4(3 H )‐one or 6‐substi‐tuted‐3‐[4‐(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl) phenyl]‐2‐substitutedquinazolin‐4(3 H )‐one 3(a‐l) were synthesized using conventional and microwave techniques respectively and were screened for antibacterial and antifungal activity.
Superconducting electronics (1981)

The pioneers of superconducting electronics are accumulating an impressive record of achievement. For example, they have now gained the high-performance lead in the important field of digital electronics. Logic delays of 13 picoseconds and switching times of 9 picoseconds have been experimentally demonstrated. The same basic devices, Josephson junctions, also make the most sensitive microwave detectors, the most sensitive magnetometers (or current sensors) and the most stable voltage sources. Although each of these developments is an important independent accomplishment, the combination of these developments in a single technology merits special attention.
Multiple Organ Failure Syndrome in the 1990s (1994)

OBJECTIVE--This review of the systemic inflammatory response syndrome (SIRS) and multiple organ dysfunction syndrome (MODS) provides an overview of a common but complex problem found in critically ill patients. It emphasizes definitions, common clinical patterns, metabolic responses, and pathophysiological changes. A brief discussion of treatment concepts is also included. DATA SOURCES--Data for this review were gathered from peer-reviewed journals, review articles by experts in SIRS/MODS, and selections from reference volumes written on SIRS/MODS. STUDY SELECTION--Reference selections were chosen on the basis of quality of research. Peer-reviewed journals were given primary consideration. Those review articles cited were felt to be essential to any discussion of SIRS/MODS. DATA EXTRACTION--Where possible, randomized, controlled, prospective studies were reviewed and conclusions used in this overview of SIRS/MODS. CONCLUSION--Our ability to care for critically ill patients has led to a new problem, SIRS and eventually MODS, which may become progressive organ failure and death. Unfortunately, these conditions are extremely frequent and carry high mortality rates. Increased oxygen consumption demands highlight the physiological response. The typical metabolic responses are characterized by hyperglycemia and accelerated protein catabolism. Unrecognized perfusion deficits, an uncontrolled septic focus, a persistent source of inflammation, or injured tissue is commonly present with SIRS/MODS and should be corrected. Restoration of oxygen transport and metabolic support are also important components of treatment. The cause of SIRS/MODS is complex and not fully understood, but multiple mediators and stimulated macrophages likely are important components and areas where treatment may well be focused.
The diabetic foot. (2000)

Foot complications in diabetics often lead to amputation. Ulceration is the most common complication in the diabetic forefoot and underlies more than 90% of cases of pedal osteomyelitis. The diagnosis of osteomyelitis is, nevertheless, difficult, and imaging is an important part of the work-up. Plain radiographs, although useful for anatomical information, are neither sensitive nor specific. Three-phase bone scintigraphy is sensitive but not specific. Labelled leucocyte scintigraphy and MRI are both useful and are complementary to one another. Labelled leucocyte scintigraphy is valuable for diagnosis as well as follow-up of pedal osteomyelitis. MRI offers exquisite anatomical detail, which is invaluable for guiding surgical management. The principal complication in the mid and hind foot is the neuropathic or Charcot joint. Although infection of the neuropathic joint is infrequent, its diagnosis is difficult. The extensive bony changes that accompany this disorder severely diminish the value of radiography and bone scintigraphy. It is not always possible to distinguish the marrow oedema of neuropathy from that of osteomyelitis and the role of MRI in the evaluation of this entity is still uncertain. Uptake of labelled leucocytes in the absence of infection may occur and is owing, at least in part, to haematopoietically active marrow. Combined leucocyte/marrow scintigraphy holds considerable promise for identifying the infected Charcot joint.
Experimental evaluation of EMTP-based current transformer models for protective relay transient study (1994)

This paper describes an EPRI study of current transformer (CT) digital models intended for protective relay transient performance analysis. Experimental evaluation of CT models implemented using the Electromagnetic Transient Program (EMTP) was carried out. Two relaying CTs with 600/5 and 2000/5 ratios were used in the study. Experiments in a high power laboratory were performed to obtain transient responses. Simulation of the CT response to the same transient events was set up using three different CT models. They were implemented based on the saturable transformer and nonlinear reactor models available in an EMTP. Comparison of laboratory and simulation results indicates that CT models developed based on the EMTP program give satisfactory results for most of the cases. It has also been discovered that in some instances EMTP models need further improvements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fetal fraction‐based risk algorithm for non‐invasive prenatal testing: screening for trisomies 13 and 18 and triploidy in women with low cell‐free fetal DNA (2018)

For pregnancies with a FF too low to receive a result on standard NIPT, the FFBR algorithm identified a subset of cases at increased risk for trisomy 13, trisomy 18 or triploidy. For the remainder of cases, the risk of a fetal chromosomal abnormality was unchanged from that expected based on MA and GA. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
Induction of an epitope-specific humoral immune response by lipopeptide—hapten conjugates: enhancement of the anti-melittin response by a synthetic T helper (T<sub>h</sub>)-cell epitope (1997)

Lipopeptides of bacterial origin constitute potent immunoadjuvants when combined with antigens. After the immunization with lipopeptides covalently coupled to non-immunogenic low-molecular-mass antigens or haptens, a hapten-specific humoral immune response can often be obtained. The response against synthetically prepared melittin fragments was further enhanced by the additional introduction of a T helper (Th)-cell epitope into the lipopeptide-hapten conjugate. The Th-cell epitope applied, which is presented by the MHC class II molecule of the BALB/c (H-2d) haplotype, consisted of a synthetic 16-amino-acid oligopeptide derived from sperm whale myoglobin. The immune-enhancing effect was most pronounced for the melittin-derived peptide fragments [Mel(1-16)] and [Mel(17-26)-CONH2]. Antibodies obtained after 3 immunizations with the conjugates recognized the synthetic as well as the native melittin molecule. Our results show that it is possible to markedly enhance a weak hapten-specific immune response by coupling the haptens to a lipopeptide conjugated to a haplotype-specific T helper-cell epitope. The novel conjugates are well suited for the optimization of immunization procedures, and for the development of novel synthetic vaccines.
Intrusion Tolerant Systems Characterization and Acceptance Monitor Design (2001)

Intrusion detection research has been so far mostly concentrated on techniques that effectively identify the malicious behaviors. No assurance can be assumed once a system is compromised. Intrusion tolerance, on the other hand, focuses on providing the desired services even when some components have been compromised. A DARPA-funded research project named SITAR (A Scalable Intrusion-Tolerant Architecture for Distributed Services) investigates the intrusion tolerance further in distributed systems to provide reliable services. Two specific challenges are addressed in this project: the first is how to take advantage of fault tolerant techniques in intrusion tolerant systems; the second is how to deal with possible attacks and compromised components so as to continue providing the service. This thesis represents part of the on-going development of the SITAR project. First, a state transition model is developed to describe the dynamic behavior of an intrusion tolerant system. Second, the Acceptance Monitor is designed to detect the system compromises from the request-response stream. Third, various kinds of vulnerabilities on Web-based COTS services are investigated and one specific design of the Acceptance Monitor is proposed and implemented for a Web-based COTS service to show the effectiveness of the proposed approach. We hope by utilizing the fault tolerance methodologies on the intrusion tolerance system we can solve the problem of providing reliable distributed services that are invulnerable to both known and unknown intrusions.
The Optimization of the Formation Process for Lead-acid Battery (2005)

To the same type exide battery, the operation of changing current density and time, controlling the temperature of the electrolyte and adding the sulfuric acid two times yields optimum parameters for the formation process. It reduces sharply the period of the formation process, improving the productivity and saving energy sources.
All-optical demultiplexing of 80 to 10 Gb/s signals with monolithic integrated high-performance Mach-Zehnder interferometer (1998)

A novel high-performance monolithic integrated Mach-Zehnder interferometer with semiconductor optical amplifiers (SOA's) in its arms has been realized and 80-Gb/s all-optical demultiplexing demonstrated. Penalty-free operation for 40-10 Gb/s demultiplexing has also been achieved. Dynamic range with respect to the input signal power for error-free operation at 40 Gb/s is more than 17 dB and fiber-to-fiber loss less than 2 dB. A theoretical model which takes into consideration amplifier gain dynamics and pulse propagation describes the demultiplexing experiments and predicts the device performances also at higher bit rates.
Ductile-Regime Grinding: A New Technology for Machining Brittle Materials (1991)

Because of recent advances in precision engineering that allow controlled grinding infeed rates as small as several nanometers per grinding wheel revolution, it is possible to grind brittle materials so that the predominant material-removal mechanism is plastic-flow and not fracture. This process is known as ductile-regime grinding. When brittle materials are ground through a process of plastic deformation, surface finishes similar to those achieved in polishing or lapping are produced. Unlike polishing or lapping, however, grinding is a deterministic process, permitting finely controlled contour accuracy and complex shapes. In this paper, the development of a research apparatus capable of ductile-regime grinding is described. Furthermore, an analytical and experimental investigation of the infeed rates necessary for ductile-regime grinding of brittle materials is presented. Finally, a model is proposed, relating the grinding infeed rate necessary for ductile material-removal with the properties of the brittle workpiece material.
Collaborative scoring with dishonest participants (2010)

Consider a set of players that are interested in collectively evaluating a set of objects. We develop a collaborative scoring protocol in which each player evaluates a subset of the objects, after which we can accurately predict each players' individual opinion of the remaining objects. The accuracy of the predictions is near optimal, depending on the number of objects evaluated by each player and the correlation among the players' preferences.
Fabrication of submicrometre 3D periodic structurescomposed of Si/SiO <sub>2</sub> (1997)

The successful fabrication of 3D periodic structures composed of two transparent materials in the submicrometre range is reported for the first time. The material system comprises a-Si (n = 3.26) and SiO2 (n = 1.46), and sputter-etching leads to ‘high-fidelity’ layer-to-layer propagation of a concave-convex pattern.
Neuroprotective effects of<i>Triticum aestivum</i>L. against β‐Amyloid‐induced cell death and memory impairments (2009)

beta-Amyloid (A beta) is a key component of senile plaques, neuropathological hallmarks of Alzheimer's disease (AD) and has been reported to induce cell death via oxidative stress. This study investigated the protective effects of Triticum aestivum L. (TAL) on A beta-induced apoptosis in SH-SY5Y cells and cognitive dysfunctions in Sprague-Dawley (SD) rats. Cells treated with A beta exhibited decreased viability and apoptotic features, such as DNA fragmentation, alterations in mitochondria and an increased Bax/Bcl-2 ratio, which were attenuated by TAL extract (TALE) pretreatment. To elucidate the neuroprotective mechanisms of TALE, the study examined A beta-induced oxidative stress and cellular defense. TALE pretreatment suppressed A beta-increased intracellular accumulation of reactive oxygen species (ROS) via up-regulation of glutathione, an essential endogenous antioxidant. To further verify the effect of TALE on memory impairments, A beta or scopolamine was injected in SD rats and a water maze task conducted as a spatial memory test. A beta or scopolamine treatment increased the time taken to find the platform during training trials, which was decreased by TALE pretreatment. Furthermore, one of the active components of TALE, total dietary fiber also effectively inhibited A beta-induced cytotoxicity and scopolamine-caused memory deficits. These results suggest that TALE may have preventive and/or therapeutic potential in the management of AD.
Analysis of Androgen Receptor Rapid Actions in Cellular Signaling Pathways: Receptor/Src Association (2011)

Much evidence indicates that, with few exceptions, non-genomic actions of steroids are mediated by receptors universally known as nuclear receptors. Steroid receptors do not exhibit intrinsic tyrosine kinase activity. Nevertheless, they stimulate different signaling pathways in cytoplasm of target cells, including those dependent on Src, a cytoplasmic tyrosine kinase. Steroid-induced Src activation regulates cell cycle progression, survival, migration, and associated processes, such as cell growth and differentiation. Androgen stimulation of human prostate cancer-derived LNCaP cells triggers cell cycle progression and proliferation. The key event in this process is the association of androgen receptor (AR) with Src. This association triggers activation of the Src/Ras/Erk pathway and finally impacts cell cycle. Androgen stimulation of fibroblasts also induces AR/Src association, which triggers DNA synthesis. Prevention of this association by a receptor-derived peptide competing for AR interaction with Src specifically inhibits the androgen receptor-dependent proliferative effect in vitro and in vivo.
A Quantitative Tool to Distinguish Isobaric Leucine and Isoleucine Residues for Mass Spectrometry-Based De Novo Monoclonal Antibody Sequencing (2014)

De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.
The US army IETM one year later (1995)

SAIC and the US Army have created a new approach to diagnostic testing that is both economical to develop and capable of tackling real world trouble shooting problems. This technology resulted in the development of a set of Interactive Electronic Technical Manuals (IETMs) for a new breed of heavy trucks also developed by the Army. The original concept was first presented in the 1993 Proceedings of AutoTestCon when the IETMs were still under development and the architecture was fluid. This paper is a follow up on the completion of the project. It analyzes the effectiveness of the various multimedia techniques used in the IETM such as sound, video clips, text to speech translation, hyper-text and hyper-procedures. It also presents a series of metrics collected on the IETMs such as mass storage space requirements, authoring problems encountered and other lessons learned about developing IETMs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On Constraints for Path Computation in Multi-Layer Switched Networks (2007)

This paper considers optical transport and packet networks and discusses the constraints and solutions in computation of traffic engineering paths. We categorize the constraints into prunable or non-prunable classes. The former involves a simple metric which can be applied for filtering to determine the path. The latter requires a methodic consideration of more complicated network element attributes. An example of this type of constraints is path loss in which the metric can be evaluated only on a path basis, as opposed to simply applying the metric to the link. Another form of non-prunable constraint requires adaptation and common vector operation. Examples are the switching type adaptation and wavelength continuity, respectively. We provide possible solutions to cases with different classes of constraints and address the problem of path computation in support of traffic engineering in multi-layer networks where a set of constrains are concurrently present. The solutions include the application of channel graph and common vector to support switching type adaptation and label continuity, respectively.