gebhart/patrepeval huggingface dataset:
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in <i>Saccharomyces</i> <i>cerevisiae</i> (2006)

Mutations in RRP6 result in the accumulation of aberrant polyadenylated transcripts from small nucleolar RNA genes. We exploited this observation to search for novel noncoding RNA genes in the yeast genome. When RNA from rrp6Delta yeast is compared with wild-type on whole-genome microarrays, numerous intergenic loci exhibit an increased mutant/wild type signal ratio. Among these loci, we found one encoding a new C/D box small nucleolar RNA, as well as a surprising number that gave rise to heterogeneous Trf4p-polyadenylated RNAs with lengths of approximately 250-500 nt. This class of RNAs is not easily detected in wild-type cells and appears associated with promoters. Fine mapping of several such transcripts shows they originate near known promoter elements but do not usually extend far enough to act as mRNAs, and may regulate the transcription of downstream mRNAs. Rather than being uninformative transcriptional "noise," we hypothesize that these transcripts reflect important features of RNA polymerase activity at the promoter. This activity is normally undetectable in wild-type cells because the transcripts are somehow distinguished from true mRNAs and are degraded in an Rrp6p-dependent fashion in the nucleus.
Australian Secondary Teachers' Perceptions of Sexuality Education, Abstinence and Safer Sex: Relevance to US Policy (2002)

This study forms part of an international, comparative study of cultural messages given to young people about adolescent sexual behavior and sexual responsibility. The impetus was the establishment of the United States’ first federal policy on sexuality education in 1996. Through an allocation of $250,000,000 for a five year period that requires an additional 40% state match, the U.S. Congress implemented an abstinence-until-marriage-only (AUMO) sexuality education program for young people (Welfare Reform Act, 1986). Forty-eight states applied for the funds within the first year (Daly & Wong, 1999).
Studies in the biochemistry of micro-organisms (1939)

THE following metabolic products, present in the metabolism solution of Penicillium griseo-fulvum Dierckx when this mould is grown under different cultural conditions and on different culture solutions, have been isolated in this laboratory: 6-hydroxy-2-methylbenzoic acid [Anslow & Raistrick, 1931], 2:5-dihydroxybenzoic acid (gentisic acid), fumaric acid and mannitol The purpose of the present communication is to record observations on a hitherto undescribed chlorine-containing metabolic product of P. griseo-fulvum which has been isolated from the mycelium of this mould and for which the name griseofulvin is proposed.
MEDEA: a hybrid shared-memory/message-passing multiprocessor NoC-based architecture (2010)

The shared-memory model has been adopted, both for data exchange as well as synchronization using semaphores in almost every on-chip multiprocessor implementation, ranging from general purpose chip multiprocessors (CMPs) to domain specific multi-core graphics processing units (GPUs). Low-latency synchronization is desirable but is hard to achieve in practice due to the memory hierarchy. On the contrary, an explicit exchange of synchronization tokens among the processing elements through dedicated on-chip links would be beneficial for the overall system performance. In this paper we propose the Medea NoC-based framework, a hybrid shared-memory/message-passing approach. Medea has been modeled with a fast, cycle-accurate SystemC implementation enabling a fast system exploration varying several parameters like number and types of cores, cache size and policy and NoC features. In addition, every SystemC block has its RTL counterpart for physical implementation on FPGAs and ASICs. A parallel version of the Jacobi algorithm has been used as a test application to validate the methodology. Results confirm expectations about performance and effectiveness of system exploration and design.
Composition and Flavor of Milk Produced by Cows Injected with Recombinant Bovine Somatotropin (1989)

Milk from 10 Holstein cows injected with 30.9 mg/head per d recombinant bovine somatotropin and 11 control cows was analyzed for composition and flavor. Experimental treatments started wk 15 postpartum and continued to the end of lactation. Milk samples were analyzed at wk 14 postpartum (pretreatment for covariant adjustment) and wk 2, Adjusted means for total protein (3.48, 3.49%), true protein (3.28, 3.28%), casein (2.63, 2.58%), NPN (.03, .03%), fat (3.47, 3.52%), freezing point (-.547, -.545"H), titratable acidity (.16, .16%), pH (6.60, 6.64), initial acid degree value (.58, .59), and acid degree value of milk with induced hydrolytic rancidity (3.41, 3.56) were similar for control and somatotropin milk, respectively, whereas serum protein (.65, .71%) and lactose (4.71, 4.80%) were higher and casein as a percent of true protein (80.2, 78.8%) was lower with the somatotropin treatment. Proportions of short-chain (11.6, 10.5%) and medium-chain (58.5, 56.0%) fatty acids were reduced and long-chain fatty acids (26.9, 30.4%) increased for control and somatotropin milks, respectively. In-
Active Contour-Based Visual Tracking by Integrating Colors, Shapes, and Motions (2012)

In this paper, we present a framework for active contour-based visual tracking using level sets. The main components of our framework include contour-based tracking initialization, color-based contour evolution, adaptive shape-based contour evolution for non-periodic motions, dynamic shape-based contour evolution for periodic motions, and the handling of abrupt motions. For the initialization of contour-based tracking, we develop an optical flow-based algorithm for automatically initializing contours at the first frame. For the color-based contour evolution, Markov random field theory is used to measure correlations between values of neighboring pixels for posterior probability estimation. For adaptive shape-based contour evolution, the global shape information and the local color information are combined to hierarchically evolve the contour, and a flexible shape updating model is constructed. For the dynamic shape-based contour evolution, a shape mode transition matrix is learnt to characterize the temporal correlations of object shapes. For the handling of abrupt motions, particle swarm optimization is adopted to capture the global motion which is applied to the contour in the current frame to produce an initial contour in the next frame.
INTERLOCUTOR: conferring with an expert diagnostic consultant in geriatric psychiatry (2003)

The authors discuss INTERLOCUTOR, a diagnostic expert system designed to emulate the typical consultative discourse between clinicians in geriatric psychiatry. Patient data are entered from menus. Domain knowledge is represented as a set of specialists, each containing a firing condition and an implicit action to take when fired. The firing condition is a test for a set of values on the blackboard recording the patient data. Some specialists add information to the blackboard, some initiate the consultative dialogue with the user, and some specify fully or partially supported diagnostic opinions. The data on the blackboard can be stored in their entirety for entry of additional data at a later time or for patient follow up. An English language summary of the diagnostic findings and particulars of the case can be generated from the blackboard values by a text generator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Spread of a Chromosomal Cefixime-Resistant <i>penA</i> Gene among Different <i>Neisseria gonorrhoeae</i> Lineages (2009)

In Neisseria gonorrhoeae, the mosaic type of penA, which encodes penicillin-binding protein 2 (PBP 2), is associated with reduced susceptibility to oral cephalosporins. To investigate the relatedness of N. gonorrhoeae clinical isolates with reduced susceptibility, we sequenced the penA genes of 32 isolates. Five different amino acid sequence types of PBP 2 were identified, but all seemed to be derivatives of pattern X of PBP 2 (PBP 2-X). However, multilocus sequence typing of the isolates showed that the isolates belonged to six different sequence types. As PBP 2-X was identified in three different sequence types, horizontal transfer of the penA allele encoding PBP2-X was suggested. We demonstrated that the penA gene could be transferred from an isolate with reduced susceptibility to a sensitive isolate by natural transformation. Comparison of the sequence of the penA-flanking regions of 12 transformants with those of the donor and the recipient suggested that at least a 4-kb DNA segment, including the penA gene, was transferred. During horizontal transfer, some of the penA alleles also acquired variations due to point mutations and genetic exchange within the allele. Our results provide evidence that the capacity for natural transformation in N. gonorrhoeae plays a role in the spread of chromosomal antibiotic resistance genes and the generation of diversity in such genes.
Potential Impact of Vancomycin Pulmonary Distribution on Treatment Outcomes in Patients with Methicillin‐Resistant <i>Staphylococcus aureus</i> Pneumonia (2006)

Vancomycin as the drug of choice for treatment of methicillin-resistant Staphylococcus aureus (MRSA) pneumonia has been called into question on the basis of therapeutic failures. In patients with MRSA pneumonia, treatment failures are probably due to the complex interplay of variables affecting the host-antimicrobial-pathogen interrelationship. However, it has been suggested that decreased penetration of vancomycin into the lungs may contribute. This review explores physiochemical and physiologic variables that affect pulmonary penetration and describes methods used in quantifying pulmonary vancomycin concentrations. Most important, findings are evaluated in the clinical context of the chemotherapeutic options available for treatment of MRSA pneumonia. The possibility of increased serum vancomycin concentrations as a method to optimize current treatment outcomes is also explored.
Bioluminescent Assay of Total and Brain‐Specific Creatine Kinase Activity in Cerebrospinal Fluid (1982)

A bioluminescent assay based on the firefly luciferase reaction has been used for determination of creatine kinase activity in CSF. Activities as low as 0.1 U/L can be measured. The coefficient of variation at an activity level of 0.3-0.4 U/L was between 5 and 6%. The assay conditions optimized for serum specimens can be used for CSF. The adenylate kinase activity is almost completely inhibited, which simplifies the procedure. The creatine kinase/(CK) isoenzyme distribution was obtained using the bioluminescent assay in combination with immunoinhibition or ion exchange chromatography. All specimens contained both MM and BB activity, but no MB was found. The study indicates that the bioluminescent assay is useful in the determination of CK isoenzymes in CSF. The clinical importance of the observed CK levels will be reported in a separate communication.
Convenient preparation of <i>N</i>‐substituted 2‐amino‐4<i>H</i>‐3,l‐benzoxazin‐4‐ones and 3‐substituted 2,4(1<i>H</i>,3<i>H</i>)‐quinazolinediones (1982)

Abstract Room temperature treatment of 2‐(3‐arylureido)benzoic acids ( 1 ) and methyl 2‐(3‐alkyl‐, or 3‐arylureido)‐ benzoates ( 2 ) with concentrated sulfuric acid leads to N ‐substituted 2‐amino‐4 H ‐3,l‐benzoxazin‐4‐ones ( 3 ) in generally very good yields. The isomeric 3‐substituted 2,4(1 H ,3 H )‐quinazolinediones ( 4 ) are conveniently made in high yield by the action of aqueous‐ethanolic sodium hydoxide on 2.
Safety and Immunogenicity of Improved<i>Shigella</i>O-Specific Polysaccharide-Protein Conjugate Vaccines in Adults in Israel (2001)

Data suggest that the O-specific polysaccharide (O-SP) domain of the lipopolysaccharide (LPS) of Shigella species is both an essential virulence factor and a protective antigen and that a critical level of serum immunoglobulin G (IgG) to this antigen will confer immunity to shigellosis. Because covalent attachment of polysaccharides to proteins increases their immunogenicity, especially in infants and in young children, the O-SP of Shigella species were bound to medically useful proteins, and the safety and immunogenicity of the resultant conjugates were confirmed in adults and 4- to 7-year-old children. Succinylation of the carrier protein improved the immunogenicity of Shigella conjugates in mice and increased their yield. Based on these results, a clinical trial of O-SP conjugates of Shigella sonnei and Shigella flexneri 2a bound to succinylated mutant Pseudomonas aeruginosa exotoxin A (rEPAsucc) or native or succinylated Corynebacterium diphtheriae toxin mutant (CRM9 or CRM9succ) was conducted in healthy adults. The conjugates were safe and immunogenic. S. sonnei-CRM9, S. sonnei-CRM9succ, and S. sonnei-rEPAsucc elicited significant rises of geometric mean (GM) IgG anti-LPS within 1 week of injection (P < 0.001). At 26 weeks, the GM anti-LPS levels elicited by these three conjugates were similar and higher than their prevaccination levels (P < 0.0001). GM IgG anti-LPS levels elicited by S. flexneri 2a-rEPAsucc were significantly higher than those elicited by S. flexneri 2a-rCRM9succ at all intervals after injection. At 26 weeks, the levels of IgG anti-LPS in vaccinees were higher than their prevaccination levels (P < 0.0001). The serum antibody responses were specific, as there was no significant rise of anti-LPS to the heterologous O-SP in any vaccinee. Both conjugates elicited statistically significant rises of serum antibodies to the injected carrier protein. At 6 months, these five Shigella conjugates elicited higher fold rises than similar conjugates (D. N. Taylor et al., Infect. Immun. 61:3678-3687, 1993). Based on these data, we chose S. sonnei-CRM9 and S. flexneri 2a-rEPAsucc for evaluation in children.
Different Clinical Features of Malaria (2012)

Malaria is a major public health problem in India, accounting for sizeable morbidity, mortality and economic loss. Apart from preventive measures, early diagnosis and complete treatment are the important modalities that have been adopted to contain the disease the other causes should also be suspected and investigated in the presence of following manifestations: Running nose, cough and other signs of respiratory infection Diagnosis can be done by Microscopy,RDT etc The treatment of P. falciparum malaria is based on areas identified as chloroquine resistant/ sensitive as ACT Clinical features are Severe manifestations can develop in P. falciparum infection over a span of time as short as 12 – 24 hours and may lead to death, if not treated promptly and adequately Specific antimalarial treatment of severe malaria is an emergency and treatment should be given promptly Parenteral artemisinin derivatives or quinine should be used irrespective of chloroquine sensitivity
Immunosurveillance modelled in vitro: naive and memory T cells spontaneously migrate across unstimulated microvascular endothelium (1997)

As a model for T cell immigration into non-lymphoid tissue we set up an in vitro assay that would allow us to investigate the phenotype of T lymphocytes from peripheral lymph nodes (PLN), mesenteric lymph nodes (MLN) or peripheral blood (PBL) of mice, which were able to spontaneously migrate across unstimulated microvascular endothelium. The transendothelial migrating T cell population was enriched for T lymphocytes expressing a "recently activated/memory' phenotype: LFA-1/CD44/ICAM-1high, but also contained CD45RBhigh and LFA-1low T cells, which in the case of MLN T cells were phenotyped as CD4+ and thus characterized as naive T cells. Transmigrated T cells could be further distinguished from their original populations and from each other by their distinct but heterogeneous expression patterns for L-selectin, alpha 4 beta 7-integrin and PECAM-1. This observation suggests the presence of phenotypically different migratory T cells among MLN, PLN and PBL. Additional studies provided evidence that the capacity to migrate across unstimulated microvascular endothelium was a characteristic of a T cell population that could phenotypically be differentiated from activated T cells. The endothelial cells were found to play an active role in selecting the traversing T cell population, as they controlled the number and phenotype of spontaneously transmigrating T cells. Our studies suggest that the capacity to transmigrate across unstimulated microvascular endothelium and hence to immigrate into non-lymphoid tissue is owned by a phenotypically heterogeneous T cell population, which is enriched for memory T cells but not devoid of naive T cells.
Extracellular Matrix Metalloproteinase Inducer Stimulates Tumor Angiogenesis by Elevating Vascular Endothelial Cell Growth Factor and Matrix Metalloproteinases (2005)

Matrix metalloproteinases (MMPs) are endopeptidases that play pivotal roles in promoting tumor disease progression, including tumor angiogenesis. In many solid tumors, MMP expression could be attributed to tumor stromal cells and is partially regulated by tumor-stroma interactions via tumor cell-associated extracellular matrix metalloproteinase inducer (EMMPRIN). The role of EMMPRIN during tumor angiogenesis and growth was explored by modulating EMMPRIN expression and activity using recombinant DNA engineering and neutralizing antibodies. In human breast cancer cells, changes in EMMPRIN expression influenced vascular endothelial growth factor (VEGF) production at both RNA and protein levels. In coculture of tumor cells and fibroblasts mimicking tumor-stroma interactions, VEGF expression was induced in an EMMPRIN- and MMP-dependent fashion, and was further enhanced by overexpressing EMMPRIN. Conversely, VEGF expression was inhibited by suppressing EMMPRIN expression in tumor cells, by neutralizing EMMPRIN activity, or by inhibiting MMPs. In vivo, EMMPRIN overexpression stimulated tumor angiogenesis and growth; both were significantly inhibited by antisense suppression of EMMPRIN. Expression of both human and mouse VEGF and MMP, derived from tumor and host cells, respectively, was regulated by EMMPRIN. These results suggest a novel tumor angiogenesis mechanism in which tumor-associated EMMPRIN functionally mediates tumor-stroma interactions and directly contributes to tumor angiogenesis and growth by stimulating VEGF and MMP expression.
Identification of novel bladder tumour suppressor genes (1999)

Many genetic alterations have recently been identified in transitional cell carcinoma (TCC) of the bladder. These include alterations to known proto-oncogenes and tumour suppressor genes and the identification of multiple sites of nonrandom chromosomal deletion which are predicted to define the location of as yet unidentified tumour suppressor genes. This review summarises recent efforts to define the location of novel bladder tumour suppressor genes using loss of heterozygositiy (LOH) and homozygous deletion analyses and to isolate the genes targeted by these deletions. For three of the four regions of deletion on chromosome 9, the most frequently deleted chromosome in TCC, candidate genes have been identified. It is anticipated that the identification of the genes and/or genetic regions which are frequently altered in TCC will provide useful tools for diagnosis, prediction of prognosis, patient monitoring and novel therapies.
Identification of novel genetic causes of Rett syndrome-<i>like</i> phenotypes (2016)

Network analysis reveals that these genes interact by means of protein interactions with each other and with the known RTT genes. These findings expand the phenotypical spectrum of previously known NDD genes to encompass RTT-like clinical presentations and identify new candidate genes for RTT-like phenotypes.
Effect of caffeine on hyperoxic lung injury of premature rats and its relationship with p38 motigen-activated protein kinase signal pathway (2019)

Objective
To study the effect of caffeine on hyperoxic lung injury of premature rats and its relationship with p38 motigen-activated protein kinase(MAPK) signal pathway.


Methods
Sixty Wistar premature rats were divided into 4 groups(n=15) according to the random number table: air + normal saline group(A+ N group), air + caffeine group(A+ C group), hyperoxia + normal saline group(H+ N group), and hyperoxia + caffeine group(H+ C group). Among them, H+ N group and H+ C group were continually exposed to hyperoxia(oxygen concentration was 60%~70%). For A+ C group and H+ C group, the premature rats were injected with caffeine of 29 mg/(kg·d) into their peritoneal cavities every day after birth.For A+ N group and H+ N group, the premature rats were injected with normal saline of the same volume into their peritoneal cavities.In each group, the lung tissues of 5 premature rats were randomly selected on the third, seventh and fourteenth day respectively.The pathological changes of lung tissue, radiated alveolar count(RAC) and collagen content in lung tissue were observed under a light microscope.The wet/dry ratio(W/D) was measured.Two-step immunohistochemistry was used to detect the distribution of p38MAPK in lung tissue.The content of phosphorylated p38MAPK(p-p38MAPK) protein was detected by western blot.


Results
Compared with the air groups, the lung tissues of premature rats in high oxygen exposure groups showed different degree of inflammatory changes on the third, seventh, and fourteenth day.The changes were more obvious with the prolonged exposure to hyperoxia.Pulmonary fibrosis was visible on the fourteenth day, which was improved after caffeine intervention.The RAC value of premature rats in hyperoxia exposure groups was significantly lower than that in air-exposure groups(P<0.05), and the W/D ratio and collagen content in lung tissue increased significantly(P<0.05), which were improved after caffeine intervention(P<0.05). The results of two-step immunohistochemistry showed that the number of p-p38MAPK positive cells in the lung tissue of premature rats in hyperoxia exposure groups increased and widely distributed, but decreased after caffeine intervention.The results of western blot showed that the content of p-p38MAPK protein in lung tissue of premature rats in hyperoxia exposure groups was significantly higher than that of air groups(P<0.05), but it decreased after caffeine intervention(P<0.05).


Conclusion
Hyperoxia can promote the formation of pulmonary fibrosis by activating p38MAPK signal pathway.Caffeine can interdict the expression of p38MAPK to alleviate the fibrosis of lung tissue exposed to hyperoxia and thus protects the lung tissue.


Key words: 
Hyperoxia; Lung injury; Caffeine; p38 motigen-activated protein kinase; Premature rats
External Reference Electrodes for Use in High Temperature Aqueous Systems (1979)

Potentials for the thermal cell (25°C) as a function of the concentration of and temperature are reported. The thermal cell potentials are combined with isothermal potentials for the silver‐silver chloride electrode at elevated temperatures to calibrate external electrodes as pseudothermodynamic standards for the investigation of electrochemical processes in high temperature aqueous systems.
Supramolecular chemistry of flexible, dendritic-based structures employing molecular recognition (1996)

G. R. Newkome, B. D. Woosley, E. He, C. N. Moorefield, R. Güther, G. R. Baker, G. H. Escamilla, J. Merrill and H. Luftmann, Chem. Commun., 1996, 2737 DOI: 10.1039/CC9960002737
Overexpression of BCL-x protein in primary breast cancer is associated with high tumor grade and nodal metastases. (1997)

These findings suggest that expression of BCL-x protein is increased in a significant fraction of invasive breast cancers. In contrast to BCL2 expression, up-regulation of BCL-x protein may be a marker of tumor progression. Additional data including larger numbers of patients, more uniform treatments, and longer follow-up are needed to define the prognostic significance of overexpression of BCL-x during breast cancer progression.