gebhart/patrepeval huggingface dataset:
Heat stability of Mycobacterium leprae immunogenicity (1978)

The protection provided to mice by vaccines administered intradermally was measured after footpad challenge with Mycobacterium leprae. The protection offered by M. leprae suspensions was not decreased when the vaccines were killed by 60 degrees C heat or at the higher temperatures tested, which included 215 degrees C (autoclave). Even highly purified suspensions retained their immunogenicity. In contrast, the vaccine protection provided by intradermal M. bovis (strain BCG) was markedly reduced when heated to 60 degrees C. The enlargement of the lymph nodes regional to the intradermal vaccines was measured and found generally to parallel the vaccine protection provided by M. leprae and by BCG.
Design of a Split Intein with Exceptional Protein Splicing Activity (2016)

Protein trans-splicing (PTS) by split inteins has found widespread use in chemical biology and biotechnology. Herein, we describe the use of a consensus design approach to engineer a split intein with enhanced stability and activity that make it more robust than any known PTS system. Using batch mutagenesis, we first conduct a detailed analysis of the difference in splicing rates between the Npu (fast) and Ssp (slow) split inteins of the DnaE family and find that most impactful residues lie on the second shell of the protein, directly adjacent to the active site. These residues are then used to generate an alignment of 73 naturally occurring DnaE inteins that are predicted to be fast. The consensus sequence from this alignment (Cfa) demonstrates both rapid protein splicing and unprecedented thermal and chaotropic stability. Moreover, when fused to various proteins including antibody heavy chains, the N-terminal fragment of Cfa exhibits increased expression levels relative to other N-intein fusions. The durability and efficiency of Cfa should improve current intein based technologies and may provide a platform for the development of new protein chemistry techniques.
Apically Sorted P2X7 Receptors Mediate Purinergic-Induced Pore Formation Preferentially in Apical Domains of the Plasma Membrane (2006)

Treatment of human epithelial cervical cells CaSki attached on filters with the P2X7-receptor (P2X7-R) agonist BzATP induced acute transient influx of calcium, most likely the result of P2X7-R channel activation, followed by slower sustained calcium influx. In cultures incubated in the presence of ethidium bromide (EB), BzATP induced slow and sustained influx of the dye with a time-course similar to the late slow calcium influx, suggesting P2X7-R pore formation. The acute and late calcium effects of BzATP were greater if the agonist was added to the luminal solution, facing the apical membrane of the cells. The EB effect of BzATP initially occurred in the apical membrane, while effects in the basolateral membrane were delayed and smaller. These results suggest that in polarized epithelial cells under steady-state conditions the P2X7-R is located in the apical membrane, and activation of the receptor induces formation of P2X7-R pores preferentially in the apical membrane.
Function inlining under code size constraints for embedded processors (1999)

Function inlining is a compiler optimization that generally increases performance at the expense of larger code size. However, current inlining techniques do not meet the special demands in the design of embedded systems, since they are based on simple heuristics, and they generate code of unpredictable size. This paper presents a novel approach to function inlining in C compilers for embedded processors, which aims at maximum program speedup under a global limit on code size. The core of this approach is a branch-and-bound algorithm which allows one to quickly explore the large search space. In an application study, we show how this algorithm can be applied to maximize the execution speed of an application under a given code size constraint.
β-Galactosidase-Based Colorimetric Paper Sensor for Determination of Heavy Metals (2011)

We demonstrate a novel approach for rapid, selective, and sensitive detection of heavy metals using a solid-phase bioactive lab-on-paper sensor that is inkjet printed with sol-gel entrapped reagents to allow colorimetric visualization of the enzymatic activity of β-galactosidase (B-GAL). The bioactive paper assay is able to detect a range of heavy metals, either alone or as mixtures, in as little as 10 min, with detection limits as follows: Hg(II) = 0.001 ppm; Ag(I) = 0.002 ppm, Cu(II) = 0.020 ppm; Cd(II) = 0.020 ppm; Pb(II) = 0.140 ppm; Cr(VI) = 0.150 ppm; Ni(II) = 0.230 ppm. The paper-based assay was immune to interferences from nontoxic metal ions such as Na(+) or K(+), could be used to detect heavy metals that were spiked into tap water or lake water, and provided quantitative data that was in agreement with values obtained by atomic absorption. With the incorporation of standard chromogenic metal sensing reagents into a multiplexed bioactive paper sensor, it was possible to identify specific metals in mixtures, albeit with much lower detection limits than were obtained with the enzymatic assay. The paper-based sensor should be valuable for rapid, on-site screening of trace levels of heavy metals in resource limited areas and developing countries.
A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms (2008)

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.
InterPro: the integrative protein signature database (2008)

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).
Actinomycin D Blocks Formation of Memory of Shock-Avoidance in Goldfish (1967)

When 2 micrograms of antinomycin D was injected intracranially into goldfish immediately after a training session, the formation of long-term memory of a shock-avoidance was blocked. The results are discussed in relation to similar findings with acetoxycycloheximide and puromycin in the goldfish and with apparently conflicting results in the mouse.
Regeneration of Zea mays L. from Embryogenic Callus (1985)

Regeneration of corn (Zea mays L.) from embryogenic callus of the inbred line A188 was investigated. Immature zygotic embryos cultured on N6 medium in the dark at 25 C produced a friable, embryogenic callus. Maturation of somatic embryos was enhanced by transferring the embryogenic callus after 3 wk to medium containing 6% sucrose and lacking 2,4-D. During the next 1-2 wk, as the somatic embryos developed, the cultures were transferred to light. When appropriately cultured, between 80% and 90% of the zygotic embryo explants produced embryogenic callus and then plants. An average of seven to eight plants was produced from the callus per zygotic embryo; 70%-80% of these plants were phenotypically normal when evaluated at a height of 7-10 cm. Of ca. 100 plants grown to maturity, 90% exhibited a normal phenotype.
The macroscopic behavior of the TCP congestion avoidance algorithm (1997)

In this paper, we analyze a performance model for the TCP Congestion Avoidance algorithm. The model predicts the bandwidth of a sustained TCP connection subjected to light to moderate packet losses, such as loss caused by network congestion. It assumes that TCP avoids retransmission timeouts and always has sufficient receiver window and sender data. The model predicts the Congestion Avoidance performance of nearly all TCP implementations under restricted conditions and of TCP with Selective Acknowledgements over a much wider range of Internet conditions.We verify the model through both simulation and live Internet measurements. The simulations test several TCP implementations under a range of loss conditions and in environments with both drop-tail and RED queuing. The model is also compared to live Internet measurements using the TReno diagnostic and real TCP implementations.We also present several applications of the model to problems of bandwidth allocation in the Internet. We use the model to analyze networks with multiple congested gateways; this analysis shows strong agreement with prior work in this area. Finally, we present several important implications about the behavior of the Internet in the presence of high load from diverse user communities.
The environmental benefits of water recycling and reuse (2003)

Abstract The world’s supply of fresh water is finite and is threatened by pollution. Rising demands for water to supply agriculture, industry and cities are leading to competition over the allocation of limited fresh water resources. This paper examines how water reuse increases the available supply of water and enables human needs to be met with less fresh water. The paper is illustrated with water reuse case studies in agriculture, urban areas, industry and water resource supplementation in Australia and other countries. The links between water reuse and sustainable water management are examined. Water conservation and water reuse produce substantial environmental benefits, arising from reductions in water diversions, and reductions in the impacts of wastewater discharges on environmental water quality. Some examples are presented demonstrating the environmental benefits in quantitative terms. The paper also describes the economic and environmental benefits identified in a number of recent integrated water cycle planning studies in Australia.
["Surgery first"--a non-routine procedure for the treatment of nasopharyngeal carcinoma]. (2006)

由中华耳鼻咽喉头颈外科杂志编辑部转来司勇锋医师的信,就2005年11月在杂志刊登我们撰写的《放疗在头颈部癌临床治疗中的作用》一文提出一些看法.在该篇文章内,我们提出鼻咽癌应该首选放疗,不应该首选手术的观点,并提供一些我院病例治疗的结果.现就司医师提出的有关问题介绍如下.
“接触性作战”？“非接触性作战”——中俄两国论伊战 (2004)

编者按：最近美国《武装力量》杂志发表了一篇题为《一场非接触-接触战争：中国和俄罗斯从伊拉克战争中看到的》文章。作者是美国长期从事国家安全领域研究的资深研究员。自1977年以来．作者效力美国国防部，一直从事苏联和俄罗斯军事文献研究。该文以一个美国军事专家的视野探讨了中国和俄罗斯两国对伊拉克战争的看法、评估和反应．从一个独特的角度分析了此次战争可能会对两国军事领域产生的重要影响。现摘译其文主要章节，以飨读者。文中所述内容仅代表作者本人观点，特此声明。
Detection of Occult Metastasis in Lymph Nodes From Colorectal Cancer Patients: A Multiple-Marker Reverse Transcriptase-Polymerase Chain Reaction Study (2004)

These results indicate that occult metastases are detectable by reverse transcriptase-polymerase chain reaction in histologically negative lymph nodes from colorectal cancer. The use of a panel of three markers improves the specificity of the method.
Muscle-Derived Neurotrophin-4 as an Activity-Dependent Trophic Signal for Adult Motor Neurons (1995)

The production of neurotrophin-4 (NT-4) in rat skeletal muscle was found to depend on muscle activity. The amounts of NT-4 messenger RNA present decreased after blockade of neuromuscular transmission with alpha-bungarotoxin and increased during postnatal development and after electrical stimulation in a dose-dependent manner. NT-4 immunoreactivity was detected in slow, type I muscle fibers. Intramuscular administration of NT-4 induced sprouting of intact adult motor nerves. Thus, muscle-derived NT-4 acted as an activity-dependent neurotrophic signal for growth and remodeling of adult motor neuron innervation. NT-4 may thus be partly responsible for the effects of exercise and electrical stimulation on neuromuscular performance.
Valproic acid increases SMN levels in spinal muscular atrophy patient cells (2003)

Spinal muscular atrophy (SMA) is an inherited motor neuron disease caused by mutation of the telomeric copy of the survival motor neuron gene (SMN1). Although a centromeric copy of the survival motor neuron gene (SMN2) is retained in all patients with SMA, it differs from SMN1 at a critical nucleotide such that the majority of SMN2 transcripts lack exon 7 and encode an unstable, truncated protein. Here, we show that valproic acid increases levels of exon 7-containing SMN transcript and SMN protein in type I SMA patient-derived fibroblast cell lines. Valproic acid may increase SMN levels both by activating the SMN promoter and by preventing exon 7 skipping in SMN transcripts. Valproic acid and related compounds warrant further investigation as potential treatment for SMA.
Miscellaneous Gram‐Negative Bacteria (2012)

This chapter contains sections titled: Brucella melitensis Bordetella pertussis Francisella tularensis Pasteurella Species Vibrio cholerae Aeromonas Species Campylobacter Species Legionella Species Gardnerella vaginalis Chlamydia Species Rickettsia rickettsii Bacteroides Species Calymmatobacterium granulomatis Cardiobacterium hominis Streptobacillus moniliformis Spirillum minus
Conformational stability of pGEX‐expressed Schistosoma japonicum glutathione S‐transferase: A detoxification enzyme and fusion‐protein affinity tag (1997)

A glutathione S-transferase (Sj26GST) from Schistosoma japonicum, which functions in the parasite's Phase II detoxification pathway, is expressed by the Pharmacia pGEX-2T plasmid and is used widely as a fusion-protein affinity tag. It contains all 217 residues of Sj26GST and an additional 9-residue peptide linker with a thrombin cleavage site at its C-terminus. Size-exclusion HPLC (SEC-HPLC) and SDS-PAGE studies indicate that purification of the homodimeric protein under nonreducing conditions results in the reversible formation of significant amounts of 160-kDa and larger aggregates without a loss in catalytic activity. The basis for oxidative aggregation can be ascribed to the high degree of exposure of the four cysteine residues per subunit. The conformational stability of the dimeric protein was studied by urea- and temperature-induced unfolding techniques. Fluorescence-spectroscopy, SEC-HPLC, urea- and temperature-gradient gel electrophoresis, differential scanning microcalorimetry, and enzyme activity were employed to monitor structural and functional changes. The unfolding data indicate the absence of thermodynamically stable intermediates and that the unfolding/refolding transition is a two-state process involving folded native dimer and unfolded monomer. The stability of the protein was found to be dependent on its concentration, with a delta G degree (H2O) = 26.0 +/- 1.7 kcal/mol. The strong relationship observed between the m-value and the size of the protein indicates that the amount of protein surface area exposed to solvent upon unfolding is the major structural determinant for the dependence of the protein's free energy of unfolding on urea concentration. Thermograms obtained by differential scanning microcalorimetry also fitted a two-state unfolding transition model with values of delta Cp = 7,440 J/mol per K, delta H = 950.4 kJ/mol, and delta S = 1,484 J/mol.
Lactobacillus fermentumBR11 and Fructo-Oligosaccharide Partially Reduce Jejunal Inflammation in a Model of Intestinal Mucositis in Rats (2008)

Although probiotics are beginning to enter mainstream medicine for disorders of the colon, their effects on the small bowel remain largely unexplored. We investigated the recently identified probiotic, Lactobacillus fermentum (L. fermentum) BR11 (BR11) and the prebiotic, fructo-oligosaccharide (FOS), both individually and in synbiotic combination, for their potential to alleviate intestinal mucositis. From Days 0-9, rats consumed skim milk (SM; saline + SM), low dose (LD-BR11; 1 x 10(6)cfu/ml), high dose (HD-BR11; 1 x 10(9)cfu/ml), LD-FOS (3%), HD-FOS (6%), or synbiotic (HD-BR11/FOS). On Day 7, rats were injected with 5-fluorouracil (5-FU; 150 mg/kg). All rats were sacrificed on Day 10. Intestinal tissues were collected for quantitative histology, sucrase, and myeloperoxidase (MPO) determinations. 5-FU decreased sucrase activity, villus height, crypt depth, and crypt cell proliferation compared to controls. Compared to 5-FU + SM, histological damage severity scores were increased for all treatments, although all were effective at reducing jejunal inflammation, indicated by reduced MPO activity (P < 0.05). The combination of BR11 and FOS did not provide additional protection. Moreover, HD-FOS and the synbiotic actually increased clinical mucositis severity (P < 0.05). We conclude that L. fermentum BR11 has the potential to reduce inflammation of the upper small intestine. However, its combination with FOS does not appear to confer any further therapeutic benefit for the alleviation of mucositis.
Pediatric glioma stem cells: biologic strategies for oncolytic HSV virotherapy (2013)

While glioblastoma multiforme (GBM) is the most common adult malignant brain tumor, GBMs in childhood represent less than 10% of pediatric malignant brain tumors and are phenotypically and molecularly distinct from adult GBMs. Similar to adult patients, outcomes for children with high-grade gliomas (HGGs) remain poor. Furthermore, the significant morbidity and mortality yielded by pediatric GBM is compounded by neurotoxicity for the developing brain caused by current therapies. Poor outcomes have been attributed to a subpopulation of chemotherapy and radiotherapy resistant cells, termed "glioma stem cells" (GSCs), "glioma progenitor cells," or "glioma-initiating cells," which have the ability to initiate and maintain the tumor and to repopulate the recurring tumor after conventional therapy. Future innovative therapies for pediatric HGG must be able to eradicate these therapy-resistant GSCs. Oncolytic herpes simplex viruses (oHSV), genetically engineered to be safe for normal cells and to express diverse foreign anti-tumor therapeutic genes, have been demonstrated in preclinical studies to infect and kill GSCs and tumor cells equally while sparing normal brain cells. In this review, we discuss the unique aspects of pediatric GSCs, including markers to identify them, the microenvironment they reside in, signaling pathways that regulate them, mechanisms of cellular resistance, and approaches to target GSCs, with a focus on the promising therapeutic, genetically engineered oHSV.
Perpetuation of the agent of human granulocytic ehrlichiosis in a deer tick-rodent cycle. (1996)

A human-derived strain of the agent of human granulocytic ehrlichiosis, a recently described emerging rickettsial disease, has been established by serial blood passage in mouse hosts. Larval deer ticks acquired infection by feeding upon such mice and efficiently transmitted the ehrlichiae after molting to nymphs, thereby demonstrating vector competence. The agent was detected by demonstrating Feulgen-positive inclusions in the salivary glands of the experimentally infected ticks and from field-derived adult deer ticks. White-footed mice from a field site infected laboratory-reared ticks with the agent of human granulocytic ehrlichiosis, suggesting that these rodents serve as reservoirs for ehrlichiae as well as for Lyme disease spirochetes and the piroplasm that causes human babesiosis. About 10% of host-seeking deer ticks were infected with ehrlichiae, and of these, 20% also contained spirochetes. Cotransmission of diverse pathogens by the aggressively human-biting deer tick may have a unique impact on public health in certain endemic sites.
Nucleotide and Predicted Amino Acid Sequences of the Marek's Disease Virus and Turkey Herpesvirus Thymidine Kinase Genes; Comparison with Thymidine Kinase Genes of Other Herpesviruses (1989)

In this paper we present the nucleotide sequences of the thymidine kinase (TK) genes of two avian herpesviruses: a highly oncogenic strain of Marek's disease virus (MDV strain RB1B) and its serologically related vaccine virus, the herpesvirus of turkeys (HVT strain Fc-126). The predicted coding regions of the two genes are 1029 and 1050 nucleotides respectively, corresponding to polypeptides of 343 and 350 amino acids in length. Putative nucleotide- and nucleoside-binding sites have been identified within the two predicted amino acid sequences. The MDV and HVT TK amino acid sequences exhibit 58.2% amino acid identity. Comparison with other available herpesvirus TK sequences reveals a greater homology to those of the alphaherpesviruses than to those of the gammaherpesviruses. No overall homology was found when compared with the chicken cytoplasmic TK sequence.
Effects of Transmission Delay on Conversational Behavior on Echo-Free Telephone Circuits (1971)

The present study sought to determine the effects of echo-free transmission delays of 600 ms and 1200 ms on conversational behavior when subjects were unaware that delay was present. Sixteen pairs of male subjects conversed 10 minutes each over an echo-free telephone circuit with zero delay and 10 minutes each with 600 ms round-trip delay; a second group of 16 pairs conversed 10 minutes each on zero delay and 1200 ms round-trip delay. Subjects noticed nothing unusual about the circuit, but the delay caused a statistically significant increase in frequency of confusions and in amount of both double talking (simultaneous speech from both speakers) and mutual silence. Analysis by means of an on-off pattern generating model revealed that subjects seem to make some adjustments in their speaking behavior; they tend to wait longer for responses and keep talking longer when interrupted. The two delay values of 600 ms and 1200 ms produced virtually identical effects in the measures made here. All of the subjects in the study were inexperienced with delay circuits; this experiment does not address itself to the possibility that experienced subjects might react differently to the delay. Further work will investigate the effects of training subjects to notice delay.
Compensation of Measurement Overhead in Parallel Performance Profiling (2007)

Performance profiling generates measurement overhead during parallel program execution. Measurement overhead, in turn, introduces intrusion in a program's runtime performance behavior. Intrusion can be mitigated by controlling instrumentation degree, allowing a tradeoff of accuracy for detail. Alternatively, the accuracy in profile results can be improved by reducing the intrusion error due to measurement overhead. Models for compensation of measurement overhead in parallel performance profiling are described. An approach based on rational reconstruction is used to understand properties of compensation solutions for different parallel scenarios. From this analysis, a general algorithm for on-the-fly overhead assessment and compensation is derived.
THE MAGIC LANTERN AND THE CINEMA: ADULT SCHOOLS, EDUCATIONAL SETTLEMENTS AND SECULARISATION IN BRITAIN, C. 1900-1950 (2007)

No abstract available.