gebhart/patrepeval huggingface dataset:
Some Features of Base Pair Mismatch and Heterology Repair in <i>Escherichia coli</i> (1987)

We have used artificially constructed heteroallelic heteroduplex molecules of bacteriophage lambda DNA to transfect Escherichia coli, and E. coli mutants deficient in various functions involved in the adenine methylation-directed mismatch repair system, MutL, MutS, MutH, and UvrD (MutU). Analysis of the allele content of single infective centers shows that this repair system often acts on several mismatches, separated by as many as 2000 bp, on one of the strands of a heteroduplex molecule. When the methyl-directed mismatch repair system is disabled by mutH or uvrD mutations, localized mismatch repair becomes prominent. This prominent localized repair that can result in separation of very closely linked markers requires the functions MutL and MutS, is independent of adenine methylation, and appears to reflect another mechanism of mismatch repair. Heterology-containing heteroduplex molecules with a deletion in one strand often escape processing. However, when the heterology includes the stem and loop structure of a transposon, Tn10, the transposon is lost.
Gene Polymorphisms of OPRM1 A118G and ABCB1 C3435T May Influence Opioid Requirements in Chinese Patients with Cancer Pain (2013)

The OPRM1 A118G single nucleotide polymorphism (SNP) is a key contributor for the inter-individual variability in opioidrequirements in Chinese cancer pain patients. This may possibly extend to the ABCB1 C3435T SNP.
A zero-overhead IC identification technique using clock sweeping and path delay analysis (2012)

The counterfeiting of integrated circuits (ICs) has become a major issue for the electronics industry. Counterfeit ICs that find their way into the supply chains of critical applications can have a major impact on the security and reliability of those systems. This paper presents a new method for uniquely identifying ICs through path delay analysis. There is no overhead in terms of area, timing, or power for this method, since it extracts the intrinsic path delay variation information of the IC. Simulation results from 90nm technology and experimental results from 90nm FPGAs demonstrate the effectiveness of our technique.
Critical care nurses' and doctors' attitudes to parasuicide patients. (1995)

The aim of this study was to investigate the attitudes of critical care nurses and doctors to parasuicide patients. A survey was conducted of 299 nurses and 81 doctors working in emergency departments and intensive care units of nine Victorian hospitals. Data obtained from responses to a Likert-type questionnaire were assessed in order to explore relationships between the doctors' and nurses' attitudes and demographic and other variables. The survey showed that the nurses' and doctors' attitudes to parasuicide patients were generally negative and that respondents did not enjoy caring for parasuicide patients. Nurses were significantly more likely than doctors to think that nurses' attitudes to parasuicide patients were poor. Nurses were also significantly more likely than doctors to self report that they were afraid of saying the wrong thing to these patients. Eighty three percent of nurses and 61% of doctors stated that they would benefit from suicide related education. Addressing this expressed need must be a high a priority for critical care units if parasuicide patients are to receive more individual and appropriate care and if their carers are to experience greater work satisfaction.
Automated Trigger Activation by Repeated Maximal Clique Sampling (2020)

Hardware Trojans are serious threat to security and reliability of computing systems. It is hard to detect these malicious implants using traditional validation methods since an adversary is likely to hide them under rare trigger conditions. While existing statistical test generation methods are promising for Trojan detection, they are not suitable for activating extremely rare trigger conditions in stealthy Trojans. To address the fundamental challenge of activating rare triggers, we propose a new test generation paradigm by mapping trigger activation problem to clique cover problem. The basic idea is to utilize a satisfiability solver to construct a test corresponding to each maximal clique. This paper makes two fundamental contributions: 1) it proves that the trigger activation problem can be mapped to clique cover problem, 2) it proposes an efficient test generation algorithm to activate trigger conditions by repeated maximal clique sampling. Experimental results demonstrate that our approach is scalable and it outperforms state-of-the-art approaches by several orders-of-magnitude in detecting stealthy Trojans.
Polymerization of a peptide-based enzyme substrate (2013)

Polymers of norbornenyl-modified peptide-based enzyme substrates have been prepared via ring-opening metathesis polymerization (ROMP). Peptides displayed on water-soluble homopolymers retain the ability to be enzymatically processed by a disease-associated enzyme. In contrast, when the peptides are densely arrayed on a nanoparticle derived from a self-assembled amphiphilic block-copolymer, they function with reduced activity as enzymatic substrates.
Multi-agent application of substation protection coordination with distributed generators (2005)

This paper presents new explorations into the use of agent technology applied to substation protection coordination of power systems. The impact of distributed generators on protection coordination in substation with different locations is firstly discussed. Then a coordination multi-agent system is proposed with the functions of the agents described. In the proposed system, communication plays an important role to provide more information for the relay coordination besides the relay settings. Relay coordination strategy is also discussed and communication simulation has been carried out on the Java agent development framework (JADE) platform. The simulation results shows that proper protection coordination can be achieved by the proposed coordination strategy and information communication.
Perceptually Motivated Audio Equalization Using Fixed-Pole Parallel Second-Order Filters (2008)

In audio, equalizer design should take into account the frequency resolution of the auditory system. In this paper, this is accomplished by the fixed-pole design of parallel second-order filters. The design process has two steps: first, the poles of the filter are set according to the desired frequency resolution. Then, the feedforward coefficients of the second-order filters are determined by a linear least squares solution. The proposed parallel filter achieves effectively the same equalization results as the Kautz filter, but it requires 33% fewer multiplications and additions.
The involvement of macrophage‐derived tumour necrosis factor and lipoxygenase products on the neutrophil recruitment induced by <i>Clostridium difficile</i> toxin B (1997)

Clostridium difficile (Cd) toxins appear to mediate the inflammatory response in pseudomembranous colitis and/or colitis associated with the use of antibiotics. In contrast to Cd Toxin A (TxA), Cd Toxin B (TxB) has been reported not to promote fluid secretion or morphological damage in rabbits and hamsters and also does not induce neutrophil chemotaxis in vitro. However, TxB is about 1000 times more potent than TxA in stimulating the release of tumour necrosis factor-alpha (TNF-alpha) by cultured monocytes. In the present study, we investigated the ability of TxB to promote neutrophil migration into peritoneal cavities and subcutaneous air-pouches of rats. We also examined the role of resident peritoneal cells in this process as well as the inflammatory mediators involved. TxB caused a significant and dose-dependent neutrophil influx with a maximal response at 0.1 microgram/cavity after 4 hr. Depleting the peritoneal resident cell population by washing the peritoneal cavity or increasing this population by pretreating the animals with thioglycollate blocked and amplified the TxB-induced neutrophil migration, respectively. Pretreating the animals with MK886 (a lipoxygenase inhibitor), NDGA (a dual cyclo- and lipoxygenase inhibitor) or the glucocorticoid, dexamethasone, but not with indomethacin (a cyclo-oxygenase inhibitor), or BN52021 (a platelet-activating factor antagonist), inhibited the neutrophil migration evoked by TxB. Pretreatment with dexamethasone or the administration of anti-TNF-alpha serum into the air-pouches also significantly reduced the TxB-induced neutrophil migration. Supernatants from TxB-stimulated macrophages induced neutrophil migration when injected into the rat peritoneal cavity. This effect was attenuated by the addition of either MK886 or dexamethasone to the macrophage monolayer and by preincubating the supernatants with anti-TNF-alpha serum. TxB also stimulated the release of TNF-alpha by macrophages. Overall, these results suggest that TxB induces an intense neutrophil migration which is mediated by macrophage-derived TNF-alpha and lipoxygenase products.
Randomized Clinical Trial of Lumbar Instrumented Fusion and Cognitive Intervention and Exercises in Patients with Chronic Low Back Pain and Disc Degeneration (2003)

The main outcome measure showed equal improvement in patients with chronic low back pain and disc degeneration randomized to cognitive intervention and exercises, or lumbar fusion.
Optical waveguide cable connection (1976)

The requirements for a practical optical waveguide cable connector are reviewed. The sources of loss in fiber-to-fiber coupling, both intrinsic (fiber-related) and extrinsic (connector-related), are discussed and quantified. A multiple channel, single-fiber-per-channel connector concept, termed the overlap connector, is then described, with emphasis on the relationship of its individual design features to practical connector requirements. Experimental results with prototype overlap connectors are presented, showing that a mean extrinsic loss of less than 0.6 dB is obtained, with a standard deviation of 0.1 dB, as a result of intermating different connector halves (twelve combinations). Losses from fiber distortions are shown to account for 0.2 dB of this extrinsic loss, and, since these distortion losses are specific deficiencies of the prototype hardware (correctable in a straightforward manner), this overlap connector hardware is taken as demonstrating an extrinsic loss of 0.4 dB. Variations in joint loss and the possibility of damage to waveguides resulting from remating are also discussed. The standard deviation of joint loss obtained in a remating test is 0.09 dB.
Human neural stem cell growth and differentiation in a gradient-generating microfluidic device (2005)

This paper describes a gradient-generating microfluidic platform for optimizing proliferation and differentiation of neural stem cells (NSCs) in culture. Microfluidic technology has great potential to improve stem cell (SC) cultures, whose promise in cell-based therapies is limited by the inability to precisely control their behavior in culture. Compared to traditional culture tools, microfluidic platforms should provide much greater control over cell microenvironment and rapid optimization of media composition using relatively small numbers of cells. Our platform exposes cells to a concentration gradient of growth factors under continuous flow, thus minimizing autocrine and paracrine signaling. Human NSCs (hNSCs) from the developing cerebral cortex were cultured for more than 1 week in the microfluidic device while constantly exposed to a continuous gradient of a growth factor (GF) mixture containing epidermal growth factor (EGF), fibroblast growth factor 2 (FGF2) and platelet-derived growth factor (PDGF). Proliferation and differentiation of NSCs into astrocytes were monitored by time-lapse microscopy and immunocytochemistry. The NSCs remained healthy throughout the entire culture period, and importantly, proliferated and differentiated in a graded and proportional fashion that varied directly with GF concentration. These concentration-dependent cellular responses were quantitatively similar to those measured in control chambers built into the device and in parallel cultures using traditional 6-well plates. This gradient-generating microfluidic platform should be useful for a wide range of basic and applied studies on cultured cells, including SCs.
Second-harmonic generation of poled BaTiO3 thin films (1993)

Second-harmonic generation of 1.064 μm incident light was measured on BaTiO3 thin films prepared by metalorganic chemical vapor deposition. Upon corona poling of the film, the second-harmonic signal was significantly enhanced. The second-order nonlinear optical susceptibility, d, of the poled film reaches ∼7.5 times that of the quartz. The enhanced second-harmonic generation shows a very slow decay at room temperature.
Transgene containment by maternal inheritance: Effective or elusive? (2007)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Liquid crystal lens prepared utilizing patterned molecular orientations on cell walls (2006)

A liquid crystal (LC) lens prepared using patterned molecular orientations on cell walls is proposed. On each wall, the LC directors in a circular area are aligned to be parallel, while those outside the area are perpendicular, to the wall. A spatially varying director orientation and a lenslike distribution of refractive index may appear in the LC layer. The LC cell then becomes an optical lens even in the absence of any applied voltages. The focal length of the lens is electrically tunable. The size of the lens prepared in this way can become very small.
Minichromosome maintenance protein 2 expression in normal kidney and renal cell carcinomas: relationship to tumor dormancy and potential clinical utility. (2002)

This is the first study examining Mcm2 protein in normal and tumor kidney samples, and the first to perform histological subgroup analysis. It shows that Mcm2 is a superior marker to Ki-67 in the assessment of cell cycle entry in histological archival material and that normal kidney has a subset of cells within the glomerular and tubular compartments that are in cycle. It demonstrates that the frequency of cells in cycle in tumors formed from stable or labile epithelial populations mirrors that in the nonneoplastic epithelium. This study additionally demonstrates that the number of cells in cycle in tumors is limited by the angiogenic phenotype and supports animal models that show angiogenesis determines the likelihood of tumor dormancy. Additional study to confirm the clinical utility of Mcm2 as a prognostic marker is now indicated.
Cloud Migration: A Case Study of Migrating an Enterprise IT System to IaaS (2010)

This case study illustrates the potential benefits and risks associated with the migration of an IT system in the oil & gas industry from an in-house data center to Amazon EC2 from a broad variety of stakeholder perspectives across the enterprise, thus transcending the typical, yet narrow, financial and technical analysis offered by providers. Our results show that the system infrastructure in the case study would have cost 37% less over 5 years on EC2, and using cloud computing could have potentially eliminated 21% of the support calls for this system. These findings seem significant enough to call for a migration of the system to the cloud but our stakeholder impact analysis revealed that there are significant risks associated with this. Whilst the benefits of using the cloud are attractive, we argue that it is important that enterprise decision-makers consider the overall organizational implications of the changes brought about with cloud computing to avoid implementing local optimizations at the cost of organization-wide performance.
Pathogenesis, imaging and clinical characteristics of CF and non-CF bronchiectasis (2018)

Bronchiectasis is a common feature of severe inherited and acquired pulmonary disease conditions. Among inherited diseases, cystic fibrosis (CF) is the major disorder associated with bronchiectasis, while acquired conditions frequently featuring bronchiectasis include post-infective bronchiectasis and chronic obstructive pulmonary disease (COPD). Mechanistically, bronchiectasis is driven by a complex interplay of inflammation and infection with neutrophilic inflammation playing a predominant role. The clinical characterization and management of bronchiectasis should involve a precise diagnostic workup, tailored therapeutic strategies and pulmonary imaging that has become an essential tool for the diagnosis and follow-up of bronchiectasis. Prospective future studies are required to optimize the diagnostic and therapeutic management of bronchiectasis, particularly in heterogeneous non-CF bronchiectasis populations.
Systematic review of progesterone for the prevention of preterm birth in singleton pregnancies (2009)

In women with a singleton pregnancy and previous preterm delivery, progesterone reduces the rates of preterm delivery before 32 weeks, perinatal death, as well as respiratory distress syndrome and necrotizing enterocolitis in the newborn. Women with a short cervix or preterm labor may also benefit from progesterone, but further evidence is needed to support such a recommendation. Follow-up studies should focus on possible metabolic complications in the mother or the offspring.
Identification of a Fertility-Associated Protein in Bull Seminal Plasma As Lipocalin-Type Prostaglandin D Synthase1 (1998)

The objective of this study was to characterize a 26-kDa seminal plasma protein previously shown to be prevalent in bulls of high fertility. Spots of this protein, excised and electroeluted from two-dimensional SDS-PAGE gels, were used for N-terminal amino acid sequencing and for preparation of antiserum in rabbits. The N-terminal amino acid sequence (ALQPNFEEDKFLGRWFTSGL) was 75% identical and 100% homologous to lipocalin-type prostaglandin (PG) D synthase isolated from human cerebrospinal fluid (CSF). Western blots of purified 26-kDa protein cross-reacted with polyclonal antibodies against lipocalin-type PGD synthase isolated from rat brain and human CSF. Immunoreactive bands at 26 kDa appeared in Western blots of seminal plasma and cauda epididymal fluid (CEF). A 29-kDa band appeared in blots of rete testis fluid (RTF). PGD synthase activity was detected in seminal plasma, CEF, and RTF. The cDNA for bovine lipocalin-type PGD synthase, isolated by reverse transcription-polymerase chain reaction, contained a coding region of 573 base pairs corresponding to 191 amino acids. The amino acid sequence was 63-80% identical to that of the enzyme of other mammals. These results establish that the 26-kDa fertility-associated protein in bull seminal plasma is lipocalin-type PGD synthase. Although we do not yet know the role of lipocalin-type PGD synthase in the male genital tract, we speculate that this protein may play an important role in both the development and the maturation of sperm.
Biotin Uptake by Rabbit Corneal Epithelial Cells: Role of Sodium-Dependent Multivitamin Transporter (SMVT) (2006)

Results obtained from both in vitro and exvivo studies suggest the possible role of SMVT expressed on corneal epithelial cells for the uptake of biotin, which co-transports pantothenic acid and lipoic acid. Further, the presence of biotin in tears suggests the physiological significance of this transporter in rabbit corneal epithelium.
Enantioselective alkylation of carbonyl compounds. From stoichiometric to catalytic asymmetric induction (1988)

Abstract
PbS quantum-dot-doped glasses for ultrashort-pulse generation (2000)

We investigate the use of PbS quantum-dot-doped glasses as saturable absorbers for ultrashort-pulse lasers by means of absorption bleaching experiments and numerical analysis of the pulse shaping process using the Haus’ master equation. We explain the mode-locking mechanism and the limitations of these absorbers. The generation of transform-limited fs pulses is predicted by soliton mode locking initiated by the absorption saturation of higher excited states of the quantum-dot saturable absorber.
Insecticide Resistance in the Bed Bug: A Factor in the Pest’s Sudden Resurgence? (2007)

Infestations of the bed bug, Cimex lectularius L. (Heteroptera: Cimicidae), are increasing around the world at an alarming rate and have become a major public health concern. The evolution of insecticide resistance could be a primary factor in explaining this resurgence. Extremely high levels of resistance to two pyrethroid insecticides, deltamethrin and lambda-cyhalothrin, relative to a susceptible colony, were detected in populations collected from human dwellings in Kentucky and Ohio. Offspring of a cross between a resistant and susceptible colony had intermediate susceptibility. Evaluations of populations from across the United States indicate that resistance to pyrethroid insecticides is already widespread. Without the development of new tactics for bed bug management, further escalation of this public health problem should be expected.
Glycoprotein Ib Has a Partial Role in Platelet-von Willebrand Factor Collagen Interaction (1988)

The adhesion of human fixed washed platelets (FWP) to collagen was decreased after treatment with Serratia marcescens protease (SP), which removed 95% of the glycocalicin from platelet membrane glycoprotein (GP) Ib. However, the diminished adhesion of SP treated FWP to collagen could still be increased in the presence of purified von Willebrand factor (vWF). This ability to vWF to increase FWP adhesion to collagen is defined as collagen cofactor (CCo). The adhesion of FWP to collagen was not affected by a monoclonal antibody (MAb) to GP IIb/IIIa (10E5), that inhibits ADP and collagen induced platelet aggregation. On the other hand, it was decreased by 50% by a MAb to GP Ib (6D1), that inhibits ristocetin induced platelet aggregation. Adhesion of FWP in buffer to collagen was completely inhibited by Ricinus communis agglutinin I or concanavalin A, while Lens culinalis agglutinin and wheat germ agglutinin showed 50% inhibition. The FWP adhesion to collagen in the presence of vWF (normal plasma) was unaffected by MAbs to GP IIb/IIIa (10E5, P2, HPL1) but was decreased to 32-38% by MAbs to GP Ib (6D1, AN51, HPL11). A MAb to vWF (CLB-RAg 35), that inhibits ristocetin induced binding of vWF to platelets, decreased the CCo of normal plasma by 70%. The MAb, CLB-RAg 201, that inhibits the binding of vWF to collagen, completely inhibited the CCo of normal plasma.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure of a legume lectin from the bark of <i>Robinia pseudoacacia</i> and its complex with N‐acetylgalactosamine (2001)

The structure of the bark lectin RPbAI (isoform A4) from Robinia pseudoacacia has been determined by protein crystallography both in the free form and complexed with N-acetylgalactosamine. The free form is refined at 1.80 A resolution to an R-factor of 18.9% whereas the complexed structure has an R-factor of 19.7% at 2.05 A resolution. Both structures are compared to each other and to other available legume lectin structures. The polypeptide chains of the two structures exhibit the characteristic legume lectin tertiary fold. The quaternary structure resembles that of the Phaseolus vulgaris lectin, the soybean agglutinin, and the Dolichos biflorus lectin, but displays some unique features leading to the extreme stability of this lectin.