gebhart/patrepeval huggingface dataset:
The complex amino acid diet of Francisella in infected macrophages (2015)

Francisella tularensis, the agent of the zoonotic disease tularemia, is a highly infectious bacterium for a large number of animal species and can be transmitted to humans by various means. The bacterium is able to infect a variety of cell types but replicates in mammalian hosts mainly in the cytosol of infected macrophages. In order to resist the stressful and nutrient-restricted intracellular environments, it encounters during its systemic dissemination, Francisella has developed dedicated stress resistance mechanisms and adapted its metabolic and nutritional needs. Recent data form our laboratory and from several other groups have shown that Francisella simultaneously relies on multiple host amino acid sources during its intracellular life cycle. This review will summarize how intracellular Francisella use different amino acid sources, and their role in phagosomal escape and/or cytosolic multiplication and systemic dissemination. We will first summarize the data that we have obtained on two amino acid transporters involved in Francisella phagosomal escape and cytosolic multiplication i.e., the glutamate transporter GadC and the asparagine transporter AnsP, respectively. The specific contribution of glutamate and asparagine to the physiology of the bacterium will be evoked. Then, we will discuss how Francisella has adapted to obtain and utilize host amino acid resources, and notably the contribution of host transporters and autophagy process in the establishment of a nutrient-replete intracellular niche.
Development of F-18-labeled fluoroerythronitroimidazole as a PET agent for imaging tumor hypoxia. (1995)

F-18-labeled FETNIM can help detect tumor hypoxia and is easier to prepare, less costly, and more hydrophilic than F-18-labeled FMISO.
Phenotypic and Molecular Characteristics of Carbapenem-Resistant Enterobacteriaceae in a Health Care System in Los Angeles, California, from 2011 to 2013 (2014)

Carbapenem-resistant Enterobacteriaceae (CRE) are a concern for health care in the United States but remain relatively uncommon in California. We describe the phenotype, clonality, and carbapenemase-encoding genes present in CRE isolated from patients at a Californian tertiary health care system. CRE for this study were identified by evaluating the antibiograms of Enterobacteriaceae isolated in the UCLA Health System from 2011 to 2013 for isolates that were not susceptible to meropenem and/or imipenem. The identification of these isolates was subsequently confirmed by matrix-associated laser desorption ionization-time of flight, and broth microdilution tests were repeated to confirm the CRE phenotype. Real-time PCR for bla(KPC), bla(SME), bla(IMP), bla(NDM-1), bla(VIM), and bla(OXA-48) was performed. Clonality was assessed by repetitive sequence-based PCR (repPCR) and multilocus sequence typing (MLST). Of 15,839 nonduplicate clinical Enterobacteriaceae isolates, 115 (0.73%) met the study definition for CRE. This number increased from 0.5% (44/8165) in the first half of the study to 0.9% (71/7674) in the second (P = 0.004). The most common CRE species were Klebsiella pneumoniae, Enterobacter aerogenes, and Escherichia coli. A carbapenemase-encoding gene was found in 81.7% (94/115) of CRE and included bla(KPC) (78.3%), bla(NDM-1) (0.9%), and bla(SME) (2.6%). The majority of bla(KPC) genes were in K. pneumoniae isolates, which fell into 14 clonal groups on typing. bla(KPC) was identified in more than one species of CRE cultured from the same patient in four cases. Three bla(SME)-carrying Serratia marcescens isolates and one bla(NDM-1) carrying Providencia rettgeri isolate were detected. CRE are increasing in California, and carbapenemases, particularly KPC, are a common mechanism for carbapenem resistance in this region.
(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol: A Potent New Neuroprotectant Which Blocks N-Methyl-D-Aspartate Responses (1995)

(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol (20, CP-101,606) has been identified as a potent and selective N-methyl-D-aspartate (NMDA) antagonist through a structure activity relation (SAR) program based on ifenprodil, a known antihypertensive agent with NMDA antagonist activity. Sites on the threo-ifenprodil skeleton explored in this report include the pendent methyl group (H, methyl, and ethyl nearly equipotent; propyl much weaker), the spacer group connecting the C-4 phenyl group to the piperidine ring (an alternating potency pattern with 0 and 2 carbon atoms yielding the greatest potency), and simple phenyl substitution (little effect). While potent NMDA antagonists were obtained with a two atom spacer, this arrangement also increased alpha 1 adrenergic affinity. Introduction of a hydroxyl group into the C-4 position on these piperidine ring resulted in substantial reduction in alpha 1 adrenergic affinity. The combination of these observations was instrumental in the discovery of 20. This compound potently protects cultured hippocampal neurons from glutamate toxicity (IC50 = 10 nM) while possessing little of the undesired alpha 1 adrenergic affinity (IC50 approximately 20 microM) of ifenprodil. Furthermore, 20 appears to lack the psychomotor stimulant effects of nonselective competitive and channel-blocking NMDA antagonists. Thus, 20 shows great promise as a neuroprotective agent and may lack the side effects of compounds currently in clinical trials.
Efficacy and Validity of Radiofrequency Neurotomy for Chronic Lumbar Zygapophysial Joint Pain (2000)

Lumbar medial branch neurotomy is an effective means of reducing pain in patients carefully selected on the basis of controlled diagnostic blocks. Adequate coagulation of the target nerves can be achieved by carefully placing the electrode in correct position as judged radiologically. Electrical stimulation before lesioning is superfluous in assuring correct placement of the electrode.
Coercivity change in an FePt thin layer in a Hall device by voltage application (2011)

The coercivity (Hc) of a perpendicularly magnetized FePt layer was modulated by applying the voltage (Vapp) to a Hall device through MgO and Al–O insulating layers. A change in ∼40 Oe in Hc was observed by changing Vapp from −13 to 13 V. From the quantitative analysis of the voltage effect on Hc, the change in the anisotropy energy by voltage application was evaluated to be 18.6 fJ/V m, which was of the same order as the theoretical prediction. The role of the MgO layer for the voltage effect was also discussed.
Ultraviolet B Light Stimulates lnterleukin‐20 Expression by Human Epithelial Keratinocytes (2006)

The proinflammatory cytokine interleukin-20 (IL-20) may exert the majority of its activity in the skin. We examined the effect of various treatments including several forms of phototherapy on IL-20 expression using cultured normal human epithelial keratinocytes (NHEK). Broadband UVB light, recombinant (r) IL-1 and rIL-8 increased, while hydrocortisone reduced, NHEK supernatant IL-20 levels. Elevation of NHEK IL-20 mRNA and maximal supernatant IL-20 levels occurred with a UVB light dose (40 mJ cm(-2)) that reduced cell viability by approximately 50%. While this UVB light dose also elevated supernatant IL-1 alpha and IL-8 levels, antibody neutralization studies indicated that neither of these cytokines was directly responsible for this increase in IL-20 expression. However, the elevation in IL-20 levels was fully inhibited by the p38 mitogen-activated protein kinase (MAPK) inhibitor SB-203580, suggesting involvement of this stress signaling pathway in this UVB light response. Photodynamic therapy (PDT) with the photosensitizer lemuteporfin, UVA light, cisplatin, lipopolysaccharide (LPS), tumor necrosis factor-alpha (TNF-alpha) or recombinant interferon-gamma (rIFN-gamma) either had little effect or decreased NHEK supernatant IL-20 levels. Reduced IL-20 levels paralleled the cytotoxic actions of PDT, UVA light or cisplatin and the antiproliferative effect of rIFN-gamma. Neither rIL-20 supplementation nor anti-IL-20 antibody treatments affected cell viability indicating that soluble IL-20 did not affect the short-term survival of UVB light-irradiated NHEK. Stimulation of IL-20 expression in keratinocytes by UVB light suggests that this cytokine might participate in skin responses to this ever-present environmental factor and potentially has a role in UV light-associated dermatoses.
Isolation and characterization of ethanol-producing yeasts from fruits and tree barks (2008)

Environmental isolates of yeasts which could convert xylose to ethanol could form the basis for bio-fuel production and proper utilization of xylan rich agricultural and forest wastes.
Macrophage Mediated Suppression of Granulocyte and Macrophage Growth After Burn Wound Infection Reversal by Means of Anti-PGE2 (2000)

The production and release of granulocytes and macrophages, crucial elements of the host defense system, are significantly impaired after burn injury and sepsis. Prostaglandin E2 (PGE2) is known to be myelosuppressive. We hypothesized that the macrophages contributed to myelopoietic suppression by means of increased PGE2 production, which is induced by thermal injury and sepsis. In this study, peritoneal macrophages were elicited at day 3 from normal mice and from mice who underwent a 15% total body surface area dorsal scald burn with or without Pseudomonas aeruginosa burn wound infection. The macrophages were incubated with or without endotoxin and with or without PGE2 polyclonal antiserum (anti-PGE2) for 18 hours. Macrophage supernatants were then used in co-cultures of bone marrow cells in a clonogenic assay of granulocyte-macrophage colony-forming cells (GM-CFCs) to determine the effect of burn wound infection on the alteration of the proliferative status of the GM-CFCs. Burn wound infection and endotoxin both caused marked reductions in GM-CFC growth in culture (20%-40% as compared with normal, P < .05-.01). The inhibition of GM-CFC growth induced by burn, burn plus infection, or endotoxin was significantly reversed by the addition of anti-PGE2 to the cultures (30%-40% increase in GM-CFC colony growth as compared with cultures without anti-PGE2). These results suggest that PGE2 is a key mediator in the gram-negative sepsis-induced macrophage suppression of granulocyte and macrophage production. The ability of anti-PGE2 to neutralize PGE2 activity may provide a useful means of mitigating myeloid depression that follows postburn sepsis.
Purification of a Ciliary Neurotrophic Factor from Bovine Heart (1987)

A neurotrophic factor that promotes the survival of cholinergic parasympathetic ciliary neurons has been purified approximately 20,000-fold from bovine cardiac tissue under nondenaturing conditions using heparin-affinity chromatography. Up to 22 micrograms of purified factor having a specific activity of 4 X 10(5) trophic units/mg can be obtained from 250 g of heart muscle. Sodium dodecyl sulfate (SDS)-polyacrylamide gels of the purified material show a broad band that is sometimes resolvable into a closely spaced pair of bands of 22 and 23 kilodaltons. Partially purified factor can be resolved into two peaks of activity (pI 5.6 and 5.0) by high-resolution anion-exchange chromatography and chromatofocusing, although these procedures have not proved useful as purification methods because of the large losses of activity incurred. It is likely that these two peaks represent the two bands seen on SDS-polyacrylamide gels. The bovine cardiac factor(s) differs from similar factors purified from chick optic tissues and pig brain in that it is irreversibly denatured by SDS.
Dabco-Catalysed Reactions of Salicylaldehydes with Acrylate Derivatives (1996)

Abstract Treatment of salicylaldehydes with acrylate derivatives in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) has been shown to afford both coumarin and chromene derivatives, and factors influencing the product distributions have been investigated.
SpotON: An Indoor 3D Location Sensing Technology Based on RF Signal Strength (2000)

Providing a reliable technology and architecture for determining the location of real world objects and people will undoubtedly enable applications, customization, and inference not currently possible. This paper documents the creation of SpotON, a new tagging technology for three dimensional location sensing based on radio signal strength analysis. Although there are many aspects to the topic of location sensing and several of them will be briefly discussed, this paper is primarily concerned with the hardware and embedded system development of such a system.
Multidrug-Resistant Typhoid in Children: Presentation and Clinical Features (1991)

Typhoid accounts for 8% of pediatric admissions to the Aga Khan University Hospital in Karachi, Pakistan. Over a 4-year period (1986-1989), 355 children had typhoid documented by culture of blood or bone marrow. Strains of Salmonella, resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole accounted for 20% of these cases. Compared with children infected by drug-susceptible strains of Salmonella, children with multiresistant infection were generally sicker at presentation and were more likely to be assessed as appearing "toxic" (P less than .001), as having disseminated intravascular coagulation (P less than .01), and as exhibiting hepatomegaly (P less than .01). The mortality was 4.2% among children with multiresistant infection and 1.4% among those infected with strains susceptible to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole; the higher mortality in the former group was probably due to a longer duration of illness (P less than .05) and to ineffectual oral antimicrobial therapy before hospitalization.
RETRACTED: Breast Tumor Cells with PI3K Mutation or HER2 Amplification Are Selectively Addicted to Akt Signaling (2008)

These data demonstrate that breast cancers with PI3K mutation or HER2 amplification are selectively dependent on Akt signaling, and that effective inhibition of Akt in tumors is feasible and effective in vivo. These findings suggest that direct inhibition of Akt may represent a therapeutic strategy for breast and other cancers that are addicted to the pathway including tumors with resistant to Herceptin.
Cellular uptake of magnetic fluid particles and their effects on human adenocarcinoma cells exposed to AC magnetic fieldsin vitro (1996)

Suspensions of coated superparamagnetic particles (magnetic fluids, MF) in AC magnetic fields have a pronounced specific absorption rate (SAR) per mass compared to multidomain particles. The aim of the present study was to investigate cellular uptake and the biological effects of AC magnetic field excited bio-compatible magnetic fluids on human carcinoma cells in vitro. One of the fluids tested was a dextran magnetite, which has a very low cyto-toxicity with survival fractions (SF) between 0.8 and 0.9 at concentrations of up to 5 mg ferrite per ml. Human carcinoma cells intracellularly accumulate up to 1 pg ferrite/cell which has been demonstrated by electron microscopy (TEM), X-ray spectroscopy and measurements of intracellular iron. It has been shown that the ferrite core is not altered intracellularly, but many of the dextran shells are degraded which yields particle chains and other aggregates observed in TEM. Semi-solid pellets of the tumour cells were treated with AC magnetic fields (520 kHz, 4-12.5 kA/m) or waterbath hyperthermia at 43 and 45 degrees C, in presence of extracellular and/or intracellular magnetic fluid particles. Although MF heating is produced from individual particles, the survival fractions of MF heated and water bath heated cells are equal. In fact, the extracellular MF particle distribution is homogeneous enough to obtain similar inactivation. In contrast to earlier reports intracellular dextran magnetite particles in AC magnetic fields did not induce cell inactivation. Since the amount of intracellular ferrite should be indeed large enough for cell inactivation, the loss of dextran shells is most probably the main cause of limited effectiveness of the intracellular magnetite particles. The present work has demonstrated that: (1) MFH is able to inactivate tumour cells in vitro to at least the same extent as water bath hyperthermia; and (2) that there is a sensitizer effect of ferrofluids at 43 degrees C probably caused by free ferric ions which induce oxidative stress; and (3) that there is no cytotoxic effect of intracellular dextran magnetite particles 30-180 min excited with AC magnetic fields used in this study. For the new method the term 'magnetic fluid hyperthermia (MFH)' is proposed.
Engineering Superconducting Phase Qubits (1999)

The superconducting phase qubit combines Josephson junctions into superconducting loops and defines one of the promising solid state device implementations for quantum computing. While conventional designs are based on magnetically frustrated superconducting loops, here we discuss the advantages offered by $π$-junctions in obtaining naturally degenerate two-level systems. Starting from a basic five-junction loop, we show how to construct degenerate two-level junctions and superconducting phase switches. These elements are then effectively engineered into a superconducting phase qubit which operates exclusively with switches, thus avoiding permanent contact with the environment through external biasing. The resulting superconducting phase qubits can be understood as the macroscopic analogue of the `quiet' s-wave-d-wave-s-wave Josephson junction qubits introduced by Ioffe {\it et al.} [Nature {\bf 398}, 679 (1999)].
Profiling of amyloid beta peptide variants using SELDI Protein Chip arrays. (1999)

The profile of amyloid beta (A beta) peptide variants secreted into the media of human cultured cells that express the amyloid precursor protein was examined by Surface Enhanced Laser Desorption/Ionization (SELDI) ProteinChip technology from Ciphergen Biosystems using biologically active ProteinChip Arrays. An anti-A beta polyclonal antibody (anti-NTA4) was used to capture and purify multiple immunoreactive A beta fragments from a single microliter of media onto the ProteinChip Array. Fragments retained on the surface of the ProteinChip Array were detected directly by mass in the ProteinChip System to provide detailed information on the identity of different A beta variants secreted from the cultured cells. We discuss existing and potential applications of this immunoassay for the detection and relative quantitation of A beta species from both cultured cell systems and clinical samples.
The gastrointestinal tract and its indigenous microbiota (2004)

The gastrointestinal tract (GIT) and the accessory digestive organs (teeth, tongue, salivary glands, liver, gallbladder, and pancreas) together constitute the digestive system whose function is to break down dietary constituents into small molecules and then to absorb these molecules for subsequent distribution throughout the body. The GIT is, basically, a continuous tube extending from the mouth to the anus (Figure 7.1). The main regions of the GIT include the oral cavity, the oropharynx, and laryngopharynx (which are also part of the respiratory tract), oesophagus, stomach, small intestine (duodenum, jejunum, and ileum), and the large intestine (caecum, colon, and rectum). Because of differences in their anatomy, physiology, organisation, and location, each of these regions provides a different set of environmental conditions for potential microbial colonisers and has, therefore, a distinctive microbiota. Although each of these regions is distinctly different, the oral cavity has some unique features (e.g., a complex anatomy leading to a great variety of habitats, the presence of non–shedding surfaces; i.e., teeth, which enable biofilm formation and a high oxygen content), which render it very different from the rest of the GIT. In contrast, the other regions of the GIT have a far simpler structure (basically, tubular in nature), which results in a lower habitat diversity within a particular region, non–shedding surfaces are absent, most regions (below the stomach) are anaerobic, and many regions (within the large intestine) have a lumen which is usually filled with material.
Tandem oligonucleotide synthesis using linker phosphoramidites (2005)

Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623-631] is added to the 5'-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3'-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5'- and 3'-terminal OH ends and other oligonucleotides with 5'-phosphorylated and 3'-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.
Japanese-English Translation Selection Using Vector Space Model. (2003)

SENSEVAL-2日本語翻訳タスクは, 日本語単語の語義をその訳語の異なりとして定義・分類し, 新たな表現に含まれる日本語単語の語義を判別する課題である. 実際の課題としては, 語義分類の定義として日英対訳用例を収集した翻訳メモリ (TM) が与えられ, 語義の選択はTM中から適切な用例を選択するか, 対象となる日本語単語の翻訳結果を示すことで解くことができる. 我々は, 入力表現の対象語周辺文脈が最も似ているTMの日本語表現を選択する単言語の問題と見なし, 本タスクを解くシステムを開発した. 対象語周辺文脈の類似度は, 対象語周辺文脈を特徴づける要素である「文脈素性」の出現を各次元に配置した「文脈素性ベクタ」を用い, ベクタ空間モデルを用いて計算する. 文脈素性は, 対象語周辺文脈の特徴を, 対象語との構文的/位置的関係と単語の形態的/意味的属性の組で表現したもので, これにより, TM表現問の文脈の違いを詳細に表現できる. SENSEVAL-2参加システムは, 形態素・構文解析器にJUMAN+KNP, シソーラスに日本語彙体系を用い, 精度・再現率はともに45.8%を達成した. 各素性の有効性について分析した結果, シソーラスからた意味属性に関する文脈素性が性能に最も寄与しており, 係り受けに関する素性は限定的にしか寄与していないことがわかった.
HTRA1, an age‐related macular degeneration protease, processes extracellular matrix proteins EFEMP1 and TSP1 (2018)

High-temperature requirement protein A1 (HTRA1) is a serine protease secreted by a number of tissues including retinal pigment epithelium (RPE). A promoter variant of the gene encoding HTRA1 is part of a mutant allele that causes increased HTRA1 expression and contributed to age-related macular degeneration (AMD) in genomewide association studies. AMD is characterized by pathological development of drusen, extracellular deposits of proteins and lipids on the basal side of RPE. The molecular pathogenesis of AMD is not well understood, and understanding dysregulation of the extracellular matrix may be key. We assess the high-risk genotype at 10q26 by proteomic comparison of protein levels of RPE cells with and without the mutation. We show HTRA1 protein level is increased in high-risk RPE cells along with several extracellular matrix proteins, including known HTRA1 cleavage targets LTBP-1 and clusterin. In addition, two novel targets of HTRA1 have been identified: EFEMP1, an extracellular matrix protein mutated in Doyne honeycomb retinal dystrophy, a genetic eye disease similar to AMD, and thrombospondin 1 (TSP1), an inhibitor of angiogenesis. Our data support the role of RPE extracellular deposition with potential effects in compromised barrier to neovascularization in exudative AMD.