gebhart/patrepeval huggingface dataset:
A Multivalent Adsorption Apparatus Explains the Broad Host Range of Phage phi92: a Comprehensive Genomic and Structural Analysis (2012)

Bacteriophage phi92 is a large, lytic myovirus isolated in 1983 from pathogenic Escherichia coli strains that carry a polysialic acid capsule. Here we report the genome organization of phi92, the cryoelectron microscopy reconstruction of its virion, and the reinvestigation of its host specificity. The genome consists of a linear, double-stranded 148,612-bp DNA sequence containing 248 potential open reading frames and 11 putative tRNA genes. Orthologs were found for 130 of the predicted proteins. Most of the virion proteins showed significant sequence similarities to proteins of myoviruses rv5 and PVP-SE1, indicating that phi92 is a new member of the novel genus of rv5-like phages. Reinvestigation of phi92 host specificity showed that the host range is not limited to polysialic acid-encapsulated Escherichia coli but includes most laboratory strains of Escherichia coli and many Salmonella strains. Structure analysis of the phi92 virion demonstrated the presence of four different types of tail fibers and/or tailspikes, which enable the phage to use attachment sites on encapsulated and nonencapsulated bacteria. With this report, we provide the first detailed description of a multivalent, multispecies phage armed with a host cell adsorption apparatus resembling a nanosized Swiss army knife. The genome, structure, and, in particular, the organization of the baseplate of phi92 demonstrate how a bacteriophage can evolve into a multi-pathogen-killing agent.
Two-dimensional correction for min-sum decoding of irregular LDPC codes (2006)

Two-dimensional (2-D) correction schemes are proposed to improve the performance of conventional min-sum (MS) decoding of irregular low density parity check codes. An iterative procedure based on parallel differential optimization is presented to obtain the optimal 2-D factors. Both density evolution analysis and simulation show that the proposed method provides a comparable performance as belief propagation (BP) decoding while requiring less complexity. Interestingly, the new method exhibits a lower error floor than that of BP decoding. With respect to conventional MS and 1-D normalized MS decodings, the 2-D normalized MS offers a better performance. The 2-D offset MS decoding exhibits a similar behavior.
Industrial restructuring : policy and practice (1990)

Industrial restructuring involves actions by enterprises to bridge gaps between their current performance and what is required to become internationally competitive. This paper examines the reasons for restructuring and oulines the policies and institutions needed to make it effective. The evolution of Bank lending for industrial restructuring is described, with lessons learned from past operations highlighted. The purpose of the paper is to provide guidance on the design and implementation of Bank supported industrial restructuring programs. The paper identifies key industry and trade policies; outlines elements of successful approaches to subsector and enterprise restructuring; and describes the financial instruments and institutions required to promote industrial restructuring.
Electron and hole relaxation pathways in semiconductor quantum dots (1999)

Femtosecond (fs) broad-band transient absorption (TA) is used to study the intraband relaxation and depopulation dynamics of electron and hole quantized states in CdSe nanocrystals (NC's) with a range of surface properties. Instead of the drastic reduction in the energy relaxation rate expected due to a ``phonon bottleneck,'' we observe a fast subpicosecond $1P$-to-$1S$ electron relaxation, with the rate exceeding that due to phonon emission in bulk semiconductors. The energy relaxation is enhanced with reducing the NC's radius, and does not show any dependence on the NC surface properties (quality of the surface passivation). These data indicate that electron energy relaxation occurs by neither multiphonon emission nor by coupling to surface defects, but is likely meditated by Auger-type electron-hole energy transfer. We use fs infrared TA to probe electron and hole intraband transitions, which allows us to distinguish between electron and hole relaxation pathways leading to the depopulation of NC quantized states. In contrast to the electron relaxation, which is controlled by NC surface passivation, the depopulation of hole quantized states is extremely fast (sub-ps-to-ps time scales) in all types of samples, independent of NC surface treatment (including NC's overcoated with a ZnS layer). Our results indicate that ultrafast hole dynamics are not due to trapping at localized surface defects such as a vacancy, but rather arise from relaxation into intrinsic NC states or intrinsically unpassivated interface states.
Surface immobilization of galactose onto aliphatic biodegradable polymers for hepatocyte culture (2002)

A novel surface modification method of biodegradable polymers was investigated for inducing the attachment of specific cells onto the polymer surface via ligand-receptor interactions. Galactose, a targeting ligand specific to asialoglycoprotein receptors present on cell membrane of hepatocytes, was introduced on the surface of poly(D,L-lactic-co-glycolic acid) (PLGA) films. A terminal end group of carboxylic acid in PLGA was activated by dicyclohexylcarbodiimide and N-hydroxysuccinimide for the direct conjugation of lactose by reductive amination reaction. Di-block copolymers of PLGA-b-poly(ethylene glycol) (PEG) having a free terminal amine group were also synthesized and used for the conjugation of galactose for the introduction of a PEG spacer between PLGA and galactose. The presence of galactose moieties on the blend film surface was characterized by measuring water contact angle and X-ray photon spectroscopy, and the amount of galactose was indirectly determined by a specific lectin-binding assay. With increasing the galactose concentration on the blend film surface, the initial attachment as well as the cell viability of hepatocyates concomitantly increased. The introduction of PEG spacer reduced the cell attachment and viability. Albumin secretion rate from hepatocytes was enhanced for galactose modified surfaces, whereas it was reduced for the surfaces not having galactose moieties.
Stem cell transplantation into the central nervous system and the control of differentiation (2001)

Recent advances in stem cell biology, including methods of cell amplification and control of differentiation in vitro, provide us with new and powerful tools with which to explore the cellular, molecular, and genetic factors affecting cell survival, proliferation, differentiation, and differentiation potential. Mitigating this vein of enthusiasm are the results of stem cell transplantation studies, which highlight our inability to control the fate of stem cell populations following transplantation to the central nervous system (CNS). Differentiation of transplanted cells is strongly influenced by the environmental signals and cellular deficiencies operating at the site of implantation, over which we can exert little or no control. Where stem cell transplantation-mediated repair of the injured CNS has been demonstrated most successfully, the transplant environments have invariably been simplistic, and transplantation into the complex and reactive environment of a CNS injury site generally results in migration from the site of implantation followed by glial cell differentiation. Together, these findings suggest that the most significant advances for the stem cell transplantation field will come from research strategies that include predifferentiation of stem cells prior to transplant and studies that further our understanding of the factors affecting stem cell differentiation in the complex environment of the CNS in vivo.
Expanding the Use of Magnetic Resonance in the Assessment of Tumor Response to Therapy: Workshop Report (2005)

Although dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and magnetic resonance spectroscopy (MRS) have great potential to provide routine assessment of cancer treatment response, their widespread application has been hampered by a lack of standards for use. Thus, the National Cancer Institute convened a workshop to assess developments and applications of these methods, develop standards for methodology, and engage relevant partners (drug and device industries, researchers, clinicians, and government) to encourage sharing of data and methodologies. Consensus recommendations were reached for DCE-MRI methodologies and the focus for initial multicenter trials of MRS. In this meeting report, we outline the presentations, the topics discussed, the ongoing challenges identified, and the recommendations made by workshop participants for the use of DCE-MRI and 1H MRS in the clinical assessment of antitumor therapies.
A human monoclonal macroglobulin with specificity for alpha(2----8)-linked poly-N-acetyl neuraminic acid, the capsular polysaccharide of group B meningococci and Escherichia coli K1, which crossreacts with polynucleotides and with denatured DNA. (1986)

We have described an IgM antibody from a patient with macroglobulinemia specifically reacting with poly-alpha(2----8)N-acetyl neuraminic acid (NeuNAc) the capsular polysaccharide of two important human pathogens, group B meningococcus and E. coli K1. This antibody has a narrowly defined specificity in its interactions with polysaccharides, being unable to bind poly-alpha(2----9)NeuNAc or alternating poly-alpha(2----8)alpha(2----9)NeuNAc. However, it shows interesting crossreactivity with seemingly unrelated polynucleotides and denatured DNA, supporting the hypothesis that charged groups with a given spacing may determine the specificity of antigen-antibody interactions on otherwise dissimilar molecular structures. Despite the crossreactivity with denatured DNA and polynucleotides, the antibody does not appear to have adverse effects in the patient. The antibody protects newborn rats against E. coli K1 infection, as well as the standard horse antiserum H46, and one would expect it to prove useful in humans as an adjunct to antibiotic therapy in infections with group B meningococcus and E. coli K1. We have attempted to clone the antibody-producing cells from peripheral blood, and have shown that the relevant cells are present and can be cultured.
Stem cells in the treatment of diabetes (2005)

Clinical islet transplantation trials based on cadaveric allogenic islets have demonstrated that it is indeed possible to restore near-physiological insulin secretion capacity in a type 1 diabetic patient through transplantation of insulin-producing cells. In order to develop this form of therapy to become available for the vast majority of patients with diabetes, new sources of transplantable insulin-producing cells need to be identified. Stem cells provide the best potential to achieve this goal. Controversial results have been presented concerning the existence and nature of pancreatic islet stem or precursor cells. An increasing body of evidence suggests that the pancreatic and hepatic cell types (hepatocytes, islet, acinar and ductal cells) have remarkable plasticity and can de- and trans-differentiate into each other under appropriate conditions. Elucidation of the molecular mechanisms regulating these processes could lead to clinically applicable ways of either inducing pancreatic islet regeneration in situ or to expanding the insulin-producing cells in vitro for transplantation. The emergence of human embryonic stem cells has led to an active area of research aiming to achieve targeted differentiation of these cells into a safely transplantable beta-like cell. After initial excitement, it appears that much basic research is still required before this goal could be achieved.
Neuropeptides: implications for alcoholism (2004)

The role of neuromodulatory peptides in the aetiology of alcoholism has been relatively under-explored; however, the development of selective ligands for neuropeptide receptors, the characterization and cloning of receptors, and the development of transgenic mouse models have greatly facilitated this analysis. The present review considers the most recent preclinical evidence obtained from animal models for the role of two of the opioid peptides, namely b-endorphin and enkephalin; corticotropin-releasing factor (CRF), urocortin I and neuropeptide Y (NPY) in deleterious and excessive alcohol consumption, focussing on specific brain regions, in particular the central nucleus of the amygdala, that appear to be implicated in the pathophysiology of alcoholism. The review also outlines potential directions for further research to clarify neuropeptide involvement in neuromodulation within discrete brain nuclei pertinent to behavioural patterns.
Western Corn Rootworm1Adult and Spotted Cucumber Beetle1Associations withCucurbitaandCucurbitacins (1976)

The western corn rootworm (WCR), Diabrotica virgifera LeConte, demonstrated strong affinities for aggregation and feeding on the foliage of certain wild Cucurbita species with relatively high concentrations of cucurbitacin “bitter principles.” Most preferred were xerophytic species of the Digitata group— C. digitata Gray, C. cylindrata Bailey and C. palmata Wats. and mesophytic species of the Lundelliana group— C. lundelliana Bailey, C. okeechobeensis Bailey and C. ecuadorensis Cutler and Whitaker. Xerophytic species were more susceptible to injury and seldom survived continuous 24-h exposure to natural infestations. The spotted cucumber beetle (SCB), D. undecimpunctata howardi Barber, exhibited similar aggregation and feeding responses to wild mesophytic Cucurbita species with high cucurbitacin foliage but showed a more consistent feeding preference for cultivated species than the WCR. Both species preferred fruits of feral C. texana Gray and C. andreana Naud. with high cucurbitacin over non-bitter fruits of their cultivated relatives, C. pepo L. and C. maxima Duchesne, respectively. The combined plant and insect factors which interact to bring about the SCB-WCR/ Cucurbita associations observed here are discussed.
The rapid detection of clonal T-cell proliferations in patients with lymphoid disorders. (1991)

A series of T-cell proliferations in peripheral blood, bone marrow, or tissue samples were analyzed for clonality. The technique used employs the polymerase chain reaction to amplify portions of the rearranged T-cell receptor beta chain genes, using primers recognizing conserved sequences of the variable, diversity, and joining region segments. We examined 17 cases of T-cell lymphoma or leukemia; a clone was identified in 13 cases (76%) overall and in 7 of 8 cases (87.5%) in which both beta-chain alleles were known to be rearranged, as shown by restriction enzyme analysis. No clonal rearrangements were detected in samples from 13 non-T-cell disorders, including B-cell lymphomas, reactive lymphoid proliferations, and nonlymphoid tumors. This method is useful for detecting clones in thymic and post-thymic T-cell malignancies and has the advantages of being extremely rapid (a result is obtained within hours of the biopsy procedure), requiring no radiolabeling, using only a small amount of tissue, and being applicable to formalin-fixed, paraffin-embedded tissue.
Inhibition of NF-κB activity enhanced cytosine arabinoside induced apoptosis in leukemic cell line HL60-N (2003)

Objective: To explore the effects of dexamethasone (DXM) and vincristine (VCR) on cytosine arabinoside (Ara-C) induced apoptosis and activation of nuclear factor-K-gene binding (NF-κB) in leukemic cell line HL60-n. Methods: Apoptosis of HL60-n cells was analysed by TdT-mediated X-dUTP nick and end labeling (TUNEL) and DNA electrophoresis. NF-κB activity of HL60-n cells was detected by electrophoretic mobility shift assay (EMSA). Results: There was slight activation of NF-κB in HL60-n cells without drug induction. Ara-C at 1 (µmol/L significantly enhanced the activation of NF-κB in HL60-n cells. The level of NF-κB activation induced by DXM at 1 µmol/L or VCR at 0.1 µmol/L had no significant difference compared with that of the control group. However, in HL60-n cells pre-treated with 1 µmol/L of DXM or 0.1 µmol/L of VCR, the activation of NF-κB induced by 1 µmol/L of Ara-C was significantly suppressed with inhibition rates of 31.0% and 47.0%, respectively. The apoptosis rates of HL60-n cells induced by 1.0 µmol/L, 10 µmol/L and 100 µmot/L Ara-C were 45.00±3.16%, 61.88±3.40% and 77.62±4.75%, respectively. The apoptotic rates of HL60-n cells induced by DXM at 1 µmol/L or VCR at 0.1 µmol/L were similar to that of the control group. However, either DXM at 1 µmol/L or VCR at 0.1 µmol/L could enhance the apoptosis of HL60-n cells induced by Ara-C at 1 µmol/L with rates of 39.1 % and 59.2%, respectively. Conclusion: Ara-C can induce apoptosis and activation of NF-κB in HL60-n cells. The mechanism of increased apoptosis of HL60-n cells by DXM or VCR may be related to suppression of NF-κB activation.
Vericiguat in patients with worsening chronic heart failure and preserved ejection fraction: results of the SOluble guanylate Cyclase stimulatoR in heArT failurE patientS with PRESERVED EF (SOCRATES-PRESERVED) study (2016)

Vericiguat was well tolerated, did not change NT-proBNP and LAV at 12 weeks compared with placebo but was associated with improvements in quality of life in patients with HFpEF. Given the encouraging results on quality of life, the effects of vericiguat in patients with HFpEF warrant further study, possibly with higher doses, longer follow-up and additional endpoints.
운동영양학 / 비타민 E 투여와 식이제한이 흰쥐의 T-cell , MDA 및 조직내 항산화효소에 미치는 영향 (2000)

본 연구는 비타민 E 및 식이제한이 T-cell, MDA 및 조직내 SOD, CAT, GPX에 미치는 영향을 알아보고자 SD계 흰쥐(rat) 40마리를 대상으로 집단별 10마리씩 무선배정하여 8주간 트레드밀 운동을 실시한 결과 다음과 같은 결론을 얻었다.
1. 집단별 T-cell, 폐 SOD, 간, 폐CAT, 간GPX는 비타민 E 투여 집단에서 가장 높은 것으로 나타났으며, 통계적으로 유의한 차이가 있는 것으로 나타났다.
2. 집단별 MDA는 운동집단에서 가장 높은 것으로 나타났으며, 통계적으로 유의한 차이가 있는 것으로 나타났다.
3. 집단별 간 SOD는 비타민 E, 식이제한 집단에서 가장 높은 것으로 나타났으며, 통계적으로 유의한 차이가 있는 것으로 나타났다.
이상의 결과를 종합해보면 비타민 E는 면역세포인 T-cell에 영향을 주는 것으로 밝혀졌으나 이에 대해선 투여량이나 항산화제의 복합투여 그리고 이에 따른 T-cell의 증식반응과 관련된 연구가 선행되어야 한다고 본다. 한편 운동시 생성되는 라디칼이나 반응성 산소화합물은 항산화제인 비타민 E에 의해 제거될 수 있으며, 항산화 효소 역시 비타민 E에 영향을 받는 것으로 나타났다. 따라서 운동시 비타민 E를 투여함으로 인해 라디칼로부터 세포손상을 억제함은 물론 각종 질병예방과 운동수행력 증대에 도움이 될 것으로 생각된다.
Reduction of Lipofuscin-like Autofluorescence in Fluorescently Labeled Tissue (1999)

The fluorescent pigment lipofuscin accumulates with age in the cytoplasm of cells of the CNS. Because of its broad excitation and emission spectra, the presence of lipofuscin-like autofluorescence complicates the use of fluorescence microscopy (e.g., fluorescent retrograde tract tracing and fluorescence immunocytochemistry). In this study we examined several chemical treatments of tissue sections for their ability to reduce or eliminate lipofuscin-like autofluorescence without adversely affecting other fluorescent labels. We found that 1-10 mM CuSO4 in 50 mM ammonium acetate buffer (pH 5) or 1% Sudan Black B (SB) in 70% ethanol reduced or eliminated lipofuscin autofluorescence in sections of monkey, human, or rat neural tissue. These treatments also slightly reduced the intensity of immunofluorescent labeling and fluorescent retrograde tract tracers. However, the reduction of these fluorophores was far less dramatic than that for the lipofuscin-like compound. We conclude that treatment of tissue with CuSO4 or SB provides a reasonable compromise between reduction of lipofuscin-like fluorescence and maintenance of specific fluorescent labels.
Receptor activation of G proteins (1988)

G proteins are a highly conserved family of membrane-associated proteins composed of alpha, beta, and gamma subunits. The alpha subunit, which is unique for each G protein, binds GDP or GTP. Receptors such as those for beta- and alpha-adrenergic catecholamines, muscarinic agonists, and the retinal photoreceptor rhodopsin, catalyze the exchange of GDP for GTP binding to the alpha subunit of a specific G protein. G alpha.GTP regulates appropriate effector enzymes such as adenylyl cyclase or the cyclic GMP phosphodiesterase. The beta gamma-subunit complex of G proteins is required for efficient receptor-catalyzed alpha subunit guanine nucleotide exchange and also functions as an attenuator of alpha subunit activation of effector enzymes. Recent elucidation of both receptor and G protein primary sequence has allowed structural predictions and new experimental approaches to study the mechanism of receptor-catalyzed G protein regulation of specific effector systems and the control of cell function including metabolism, secretion, and growth.
ThepstOperon ofBacillus subtilisIs Specifically Induced by Alkali Stress (2003)

To cope with a sudden increase in the external pH value to 8.9, Bacillus subtilis cells induce about 80 genes which can be divided into two classes. Most of these genes are members of the sigma(W) regulon, while some are under the control of so-far-unknown transcriptional regulators. The genes of the pst operon belong to the second class. Here, we attempted to answer the questions of why and how the genes of this operon are induced. Using transcriptional fusions to two of the five genes of this operon, we confirmed their induction after alkali stress. Furthermore, a Northern blot experiment revealed that the complete operon was alkali inducible, that the transcriptional start site used was identical to that used after phosphate starvation, and that induction was prevented in a phoR background. Most interestingly, increasing the phosphate concentration within the medium prevented alkali induction of the pst operon, and phoA, another member of the PhoRP regulon, did not respond to alkali stress. In the end, we showed that alkali treatment completely prevented phosphate uptake. These results are discussed to explain alkali induction of the pst operon.
Purification and characterization of human recombinant interleukin-1 beta. (1987)

A human interleukin-1 (IL-1) beta cDNA was cloned, and the region coding for the mature protein was expressed in Escherichia coli. The 17-kDa biologically active product was purified in 40% yield to apparent homogeneity, without chaotropes, from the soluble fraction of sonicated cell lysates. The recombinant IL-1 beta was characterized by amino acid analysis, NH2- and COOH-terminal sequence analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, spectroscopy, and biological assay. Specific biological activity was 4.6 X 10(8) units/mg in a co-mitogenic IL-2 induction assay using cultured EL-4 T-lymphocytes. The molar extinction coefficient was determined to be 10,300 cm-1 M-1 at 280 nm. NH2-terminal sequence analysis revealed that 70% of the product begins with the Ala corresponding to the NH2 terminus of the natural protein, while 30% begins with the following Pro. No initiator Met was observed. Both of the sulfhydryl groups are reactive to Ellman's reagent and to iodoacetamide under nonreducing conditions, indicating that the Cys residues do not form disulfide bonds. S-Carboxamidomethyl-Cys-rIL-1 beta retained biological activity in the IL-2 induction assay. Circular dichroism suggested an extensive beta sheet structure for rIL-1 beta.