gebhart/patrepeval huggingface dataset:
Functional characterization of the first two actinomycete 4-amino-4-deoxychorismate lyase genes (2009)

In some antibiotic producers, p-aminobenzoic acid (PABA) or its immediate precursor, 4-amino-4-deoxychorismate (ADC), is involved in primary metabolism and antibiotic biosynthesis. In Streptomyces sp. FR-008, a gene pabC-1 putatively encoding a fold-type IV pyridoxal 5'-phosphate (PLP)-dependent enzyme was found within the antibiotic FR-008/candicidin biosynthetic gene cluster, whose inactivation significantly reduced the productivity of antibiotic FR-008 to about 20% of the wild-type level. Its specific role in PABA formation was further demonstrated by the successful complementation of an Escherichia coli pabC mutant. Moreover, a free-standing gene pabC-2, probably encoding another fold-type IV PLP-dependent enzyme, was cloned from the same strain. Inactivation of pabC-2 reduced antibiotic FR-008 yield to about 57% of the wild-type level in the mutant, and the complementation of the E. coli pabC mutant established its involvement in PABA biosynthesis. Furthermore, a pabC-1/pabC-2 double mutant only retained about 4% of the wild-type antibiotic FR-008 productivity, clearly indicating that pabC-2 also contributed to biosynthesis of this antibiotic. Surprisingly, apparently retarded growth of the double mutant was observed on minimal medium, which suggested that both pabC-1 and pabC-2 are involved in PABA biosynthesis for primary metabolism. Finally, both PabC-1 and PabC-2 were shown to be functional ADC lyases by in vitro enzymic lysis with the release of pyruvate. pabC-1 and pabC-2 appear to represent the first two functional ADC lyase genes identified in actinomycetes. The involvement of these two ADC lyase genes in both cell growth and antibiotic FR-008 biosynthesis sets an example for the interplay between primary and secondary metabolisms in bacteria.
DNA Nicks and Nodes and Nanotechnology (2000)

The properties that make DNA such an effective molecule for genetic material also make it a superb molecule for nanotechnology, when stable, stiff branched species are combined with cohesive interactions. Reciprocal crossovers between single strands of duplex or complex molecules lead to a panoply of motifs that can be used for DNA nanotechnology. A general derivation of these molecules is shown here, including components of devices and periodic or algorithmic arrays.
Nearfield synthesis of complex sources with high-order ambisonics, and binaural rendering. (2007)

Cardiac function analysis is critical in the management of patients with cardiovascular diseases. The two most common non-invasive techniques used nowadays to evaluate cardiac function are ultrasonography and magnetic resonance imaging (MR). The parameters to be determined with both techniques include the systolic volume of the left ventricle, the cardiac mass, myocardial thickness and ejection fraction. Ultrasound images have high resolution and they do not need any cardiac or respiratory gating. It has limitations in obese patients, patients with pulmonary obstructive disease or patients after thoracic surgery. MR has a high spatial and temporal resolution. There are different sequences we can use to determine cardiac function parameters, Gradient Echo sequences are used to analyze the ventricular volume and the ejection fraction. Myocardial tagging sequences are used to quantify the myocardial wall motion. Computed Tomography constitutes other alternative that can be used in patients with claustrophobia or pace markers to evaluate cardiac function.
Reduction of postprandial triglyceridemia in humans by dietary n-3 fatty acids (1988)

Long chain n-3 fatty acids present in fish oils have been shown to reduce fasting plasma triglyceride and very low density lipoprotein levels in normal and hyperlipidemic human subjects. The present studies were designed to examine whether dietary n-3 fatty acids influence chylomicron formation and metabolism in healthy volunteers. In the first study seven subjects were fed either saturated fat, vegetable oil, or fish oil-based diets for 4 weeks each, and test meals containing 50 g of the background fat were administered after the second week of each diet. The postprandial rise in triglyceride levels was significantly lower following the fish oil test meal as compared to the saturated fat or vegetable oil test meals. In the second study, six subjects eating their usual home diets were given two fat tolerance tests. The first contained saturated fat and the second, given 1 week later, contained fish oil. There was no difference in the postprandial triglyceride response between the fish oil and the saturated fat meals. A third study was then conducted with eight volunteers in which saturated fat and fish oil test meals were administered during saturated fat and fish oil background diets in a crossover design. The presence of fish oil in the background diet reduced postprandial lipemia regardless of the type of fat in the test meal. Although there was no effect of the fish oil diet on the lipoprotein lipase and hepatic lipase activity of postheparin plasma measured in vitro, stimulation of in vivo lipolysis was not ruled out. Our results suggest that chronic (but not acute) intake of fish oil may inhibit the synthesis or secretion of chylomicrons from the gut. However, accelerated clearance due to decreased VLDL competition cannot be excluded.
[Morphology and delta-endotoxin proteins of Bacillus thuringiensis from soils and their toxicities to insects]. (1992)

94 strains of Bacillus thuringiensis were isolated from soils in southwest and northwest of China. The morphology of cells, spores and parasporal crystals of these strains was investigated under transmission and scanning electro-microscope. Proteins of delta-endotoxins from all strains were analysed by rapid SDS-PAGE. 9 species of insects in Lepidoptera, Coleoptera and Diptera were tested for assay of delta-endotoxins. Some kinds of parasporal crystals were quite different in form and in composition of protein from those reported before. Most of strains were nontoxic to all of 9 species used in bio-assay. Some strains were very effective in species of Coleoptera or Noctuidae.
Serum and urine vitamin D metabolite analysis in early preeclampsia (2017)

Vitamin D deficiency is common in pregnant women and may contribute to adverse events in pregnancy such as preeclampsia (PET). To date, studies of vitamin D and PET have focused primarily on serum concentrations vitamin D, 25-hydroxyvitamin D3 (25(OH)D3) later in pregnancy. The aim here was to determine whether a more comprehensive analysis of vitamin D metabolites earlier in pregnancy could provide predictors of PET. Using samples from the SCOPE pregnancy cohort, multiple vitamin D metabolites were quantified by liquid chromatography–tandem mass spectrometry in paired serum and urine prior to the onset of PET symptoms. Samples from 50 women at pregnancy week 15 were analysed, with 25 (50%) developing PET by the end of the pregnancy and 25 continuing with uncomplicated pregnancy. Paired serum and urine from non-pregnant women ( n = 9) of reproductive age were also used as a control. Serum concentrations of 25(OH)D3, 25(OH)D2, 1,25(OH) 2 D3, 24,25(OH) 2 D3 and 3-epi-25(OH)D3 were measured and showed no significant difference between women with uncomplicated pregnancies and those developing PET. As previously reported, serum 1,25(OH) 2 D3 was higher in all pregnant women (in the second trimester), but serum 25(OH)D2 was also higher compared to non-pregnant women. In urine, 25(OH)D3 and 24,25(OH) 2 D3 were quantifiable, with both metabolites demonstrating significantly lower ( P &lt; 0.05) concentrations of both of these metabolites in those destined to develop PET. These data indicate that analysis of urinary metabolites provides an additional insight into vitamin D and the kidney, with lower urinary 25(OH)D3 and 24,25(OH) 2 D3 excretion being an early indicator of a predisposition towards developing PET.
Age-Related Susceptibility to Apoptosis in Human Retinal Pigment Epithelial Cells Is Triggered by Disruption of p53–Mdm2 Association (2012)

Our studies suggest that aging in the RPE leads to alterations of specific checkpoints in the apoptotic pathway, which may represent important molecular targets for the treatment of RPE-related aging disorders such as AMD.
Lentiviral delivery of HIV-1 Vpr protein induces apoptosis in transformed cells (1999)

Most current anticancer therapies act by inducing tumor cell stasis followed by apoptosis. HIV-1 Vpr effectively induces apoptosis of T cells after arrest of cells at a G(2)/M checkpoint. Here, we investigated whether this property of Vpr could be exploited for use as a potential anticancer agent. As a potentially safer alternative to transfer of genes encoding Vpr, we developed a method to efficiently introduce Vpr protein directly into cells. Vpr packaged into HIV-1 virions lacking a genome induced efficient cell cycle arrest and apoptosis. Introduction of Vpr into tumor cell lines of various tissue origin, including those bearing predisposing mutations in p53, XPA, and hMLH1, induced cell cycle arrest and apoptosis with high efficiency. Significantly, apoptosis mediated by virion-associated Vpr was more effective on rapidly dividing cells compared with slow-growing cells, thus, in concept, providing a potential differential effect between some types of tumor cells and surrounding normal cells. This model system provides a rationale and proof of concept for the development of potential cancer therapeutic agents based on the growth-arresting and apoptotic properties of Vpr.
Discovery of Mer Specific Tyrosine Kinase Inhibitors for the Treatment and Prevention of Thrombosis (2013)

The role of Mer kinase in regulating the second phase of platelet activation generates an opportunity to use Mer inhibitors for preventing thrombosis with diminished likelihood for bleeding as compared to current therapies. Toward this end, we have discovered a novel, Mer kinase specific substituted-pyrimidine scaffold using a structure-based drug design and a pseudo ring replacement strategy. The cocrystal structure of Mer with two compounds (7 and 22) possessing distinct activity have been determined. Subsequent SAR studies identified compound 23 (UNC2881) as a lead compound for in vivo evaluation. When applied to live cells, 23 inhibits steady-state Mer kinase phosphorylation with an IC50 value of 22 nM. Treatment with 23 is also sufficient to block EGF-mediated stimulation of a chimeric receptor containing the intracellular domain of Mer fused to the extracellular domain of EGFR. In addition, 23 potently inhibits collagen-induced platelet aggregation, suggesting that this class of inhibitors may have utility for prevention and/or treatment of pathologic thrombosis.
Inhibition of Staphylococcus aureus Biofilms by a Novel Antibacterial Envelope for Use with Implantable Cardiac Devices (2009)

Biofilm formation on representative implantable medical devices using a known human pathogen (Staphylococcus aureus) was significantly reduced (p < 0.01) at all time points measured (24,48, and 72 hours) by employing a novel antibacterial envelope (AIGIS Rx). The result was demonstrated using a standard US Centers for Disease Control (CDC) bioreactor model and the results were confirmed by Scanning Electron Microscopy (SEM). The antibacterial envelope used in the study is coated with a proprietary combination broad spectrum antibiotics (rifampin and minocycline) embedded in a resorbable polymeric coating. The antibiotics are designed to elute out of the coating over a multi-day period for controlled, site-specific drug delivery. The infection rate for patients receiving pacemakers and defibrillators is increasing faster than the rate of new implants and the growing resistance of S. aureus strains suggests that conventional, systemic antibiotic prophylaxis may have limited future utility. Moreover, emerging evidence suggests that bacterial biofilms result in infections of implantable medical devices. These findings demonstrate the in vitro efficacy of a new means to address potential biofilm-derived Hospital Acquired Infections (HAIs) related to implantable medical devices composed of titanium inclusive of pacemakers and defibrillators by means of a locally delivered, low dose, combination antibacterial treatment.
Chapter 1: Getting Star ted (2015)

There are compelling reasons to use R. Enthusiastic users, programmers, and contributors support R and its development. A dedicated core team of R experts maintains the language. R is accurate, produces excellent graphics, has a variety of built-in functions, and is both a functional language and an object-oriented one. There are (literally) thousands of contributed packages available to R users for specialized data analyses.
Synthesis and Biological Evaluation of EC140:  A Novel Folate-Targeted Vinca Alkaloid Conjugate (2006)

A novel folate conjugate of desacetylvinblastine monohydrazide (DAVLBH), herein referred to as EC140, was designed and evaluated for biological activity against folate receptor (FR)-positive cells and tumors. EC140 was produced by coupling a peptidic analogue of the vitamin folic acid to DAVLBH via an acylhydrazone bond. This water-soluble conjugate was found to retain high affinity for FR-positive cells, and it produced specific, dose-responsive activity in vitro. Initial in vivo tests confirmed EC140's activity in both syngeneic and xenograft models. Hence, enduring complete responses were observed in animals bearing established, subcutaneous tumors prior to therapy using regimens that produced minor toxicity. In contrast, treatment with the unconjugated DAVLBH drug produced nominal efficacy when dosed at its MTD. Overall, EC140's performance in vitro and in vivo warrants further preclinical study before this novel targeted chemotherapeutic is considered for clinical investigation.
Polysomnographic Characteristics in Normal Preschool and Early School-Aged Children (2006)

Developmental changes occur in several polysomnographic measures among normal children from 3 to 7 years of age, particularly during transition from preschool to early school age. Our findings in a large number of healthy community children comprise the most extensive compilation of normative reference values for laboratory-based pediatric polysomnography to date.
A sentiment-based meta search engine (2006)

This study is in the area of sentiment classification: classifying online review documents according to the overall sentiment expressed in them. This paper presents a prototype sentiment-based meta search engine that has been developed to perform sentiment categorization of Web search results. It assists users to quickly focus on recommended or non-recommended information by classifying Web search results into four categories: positive, negative, neutral, and non-review documents. It does this by using an automatic classifier based on a supervised machine learning algorithm, Support Vector Machine (SVM). This paper also discusses various issues we have encountered during the prototype development, and presents our approaches for resolving them. A user evaluation of the prototype was carried out with positive responses from users.
Query Focused Abstractive Summarization: Incorporating Query Relevance, Multi-Document Coverage, and Summary Length Constraints into seq2seq Models (2018)

Query Focused Summarization (QFS) has been addressed mostly using extractive methods. Such methods, however, produce text which suffers from low coherence. We investigate how abstractive methods can be applied to QFS, to overcome such limitations. Recent developments in neural-attention based sequence-to-sequence models have led to state-of-the-art results on the task of abstractive generic single document summarization. Such models are trained in an end to end method on large amounts of training data. We address three aspects to make abstractive summarization applicable to QFS: (a)since there is no training data, we incorporate query relevance into a pre-trained abstractive model; (b) since existing abstractive models are trained in a single-document setting, we design an iterated method to embed abstractive models within the multi-document requirement of QFS; (c) the abstractive models we adapt are trained to generate text of specific length (about 100 words), while we aim at generating output of a different size (about 250 words); we design a way to adapt the target size of the generated summaries to a given size ratio. We compare our method (Relevance Sensitive Attention for QFS) to extractive baselines and with various ways to combine abstractive models on the DUC QFS datasets and demonstrate solid improvements on ROUGE performance.
여대생의 커피 섭취량에 따른 영양섭취 및 식사의 질 평가 (2009)

The purpose of this study was to assess nutrient intake and dietary quality in female college students according to their coffee consumption. The survey was conducted through questionnaires and 3-day dietary records with 353 students. The subjects were divided into three groups: students who didn`t consume coffee (non-coffee group, N=119), students who consumed ＜250 ml coffee (light-coffee group, N=140), and students who consumed ≥250 ml coffee (moderate-coffee group, N=94). There were no significant differences in age, weight, height, and BMI among the three groups. The mean daily energy intake was 1800.8 kcal in the non-coffee group, 1724.9 kcal in the light-coffee group, and 1729.7 kcal in the moderate-coffee group. The moderate-coffee group consumed a significantly higher amount of alcohol than the light-coffee group (p＜0.05). The average intakes of dietary fiber, vitamin A, β-carotene, and folate in the non-coffee group were significantly higher than those in the light-coffee and moderate-coffee groups. Indexes of Nutritional Quality (INQ) for vitamin A, niacin, and vitamin B6 were significantly higher in the non-coffee group than in the light-coffee group. Also the non-coffee group consumed a significantly higher amount of vegetables compared to the light-coffee group. There was no significant difference in the Dietary Diversity Scores (DDS) among the three groups. These results suggest that coffee consumption affects food and nutrient intake in female college students.
Thienamycin: development of imipenem-cilastatin (1983)

Thienamycin, a natural product produced by Streptomyces cattleya is the first representative of a unique class of beta-lactam antibiotics, the carbapenems. Despite its outstanding potency and antibacterial spectrum, thienamycin was itself unsuited for further development because of its chemical instability in concentrated solution and in the solid state. Synthesis of the amidine derivative, N-formimidoyl thienamycin (imipenem, MK0787) resulted in a crystalline product with much improved stability and with antibacterial properties significantly superior to thienamycin. Imipenem has an unusually broad antimicrobial spectrum. A high order of bactericidal activity is found against Pseudomonas aeruginosa, Serratia, Bacteroides fragilis, enterococci and numerous other species intrinsically resistant to other antibiotics. Imipenem is refractory to hydrolysis by all important classes of bacterial beta-lactamases and thus exhibits no cross-resistance with penicillins or cephalosporins. Imipenem is distinguished from the new generation of extended-spectrum cephems by its unusually high potency against Gram-positive as well as Gram-negative organisms. Offsetting these excellent antimicrobial properties was an unusual susceptibility exhibited by imipenem to renal metabolism in animal species and in man. Very low urinary recoveries resulted without, however, any significant reduction in the serum half-life of imipenem. A brush-border dipeptidase, dehydropeptidase-I, was shown to be responsible for renal metabolism. Metabolism has been countered with the development of cilastatin (MK0791), a substituted amino-propenoate inhibitor of dehydropeptidase which is specific, potent and well matched in its pharmacokinetic properties for co-administration with imipenem. With the imipenem/cilastatin combination, uniformly high urinary concentrations and recovery are obtained regardless of the varying but often extensive metabolism suffered by imipenem in human populations. An additional benefit conferred by cilastatin results from its ability to exclude imipenem competitively from entry into and subsequent metabolism within the proximal tubular epithelium of the kidney. The tubular necrosis induced by imipenem alone when it is administered at very high doses to susceptible mammalian species is thereby eliminated. Thus the imipenem/cilastatin combination affords reliability and enhanced safety in the application of the antibiotic's unusual antibacterial potential in the treatment of difficult infections regardless of the site of disease.
Detecting Protein–Protein Interactions with the Split-Ubiquitin Sensor (2011)

A detailed understanding of a cellular process requires the knowledge about the interactions between its protein constituents. The Split-Ubiquitin technique allows to monitor and detect interactions of very diverse proteins, including transcription factors and membrane-associated proteins. The technique is based on unique features of ubiquitin, the enzymes of the ubiquitin pathway, and the reconstitution of a native-like ubiquitin from its N- and C-terminal fragments. Using Ura3p as a reporter for the reconstitution of the ubiquitin fragments, methods are presented that enable to screen in yeast for interaction partners of a given protein with either a randomly generated expression library or a defined but more limited array of protein fusions.
The Complexity of Stoquastic Local Hamiltonian Problems (2006)

We study the complexity of the Local Hamiltonian Problem (denoted as LH-MIN) in the special case when a Hamiltonian obeys conditions of the Perron-Frobenius theorem: all off-diagonal matrix elements in the standard basis are real and non-positive. We will call such Hamiltonians, which are common in the natural world, stoquastic. An equivalent characterization of stoquastic Hamiltonians is that they have an entry-wise non-negative Gibbs density matrix for any temperature. We prove that LH-MIN for stoquastic Hamiltonians belongs to the complexity class AM -- a probabilistic version of NP with two rounds of communication between the prover and the verifier. We also show that 2-local stoquastic LH-MIN is hard for the class MA. With the additional promise of having a polynomial spectral gap, we show that stoquastic LH-MIN belongs to the class POSTBPP=BPPpath -- a generalization of BPP in which a post-selective readout is allowed. This last result also shows that any problem solved by adiabatic quantum computation using stoquastic Hamiltonians lies in PostBPP.
Creatine supplementation in Huntington’s disease (2003)

One year of Cr intake, at a rate that can improve muscle functional capacity in healthy subjects and patients with neuromuscular disease (5 g/day), did not improve functional, neuromuscular, and cognitive status in patients with stage I to III HD.
Lifetime Analysis of Hospitalizations and Survival of Patients Newly Admitted With Heart Failure (2012)

Among newly discharged patients with HF, cardiovascular events were clustered at early postdischarge and prefatal time periods, and were increased among those with ischemic etiology.
급속 냉각 전로슬래그 골재를 이용한 콘크리트의 차폐특성에 관한 실험적 연구 (2013)

This study experimentally evaluated the radiation shielding capacity and mechanical properties of concretes made with rapid chilled converter slag(RCCS) aggregate. Air content, slump test and unit volume weight test were performed for fresh concretes and compressive strength test, chloride penetration test and radiation shielding capacity test were performed for the harden concretes. Compressive strength and chloride penetration resistance of RCCS aggregate concrete was higher and lower than normal concrete, aggregate can be effectively used for the radiation shielding concrete.