gebhart/patrepeval huggingface dataset:
A current affair: electrotherapy in wound healing (2017)

New developments in accelerating wound healing can have immense beneficial socioeconomic impact. The wound healing process is a highly orchestrated series of mechanisms where a multitude of cells and biological cascades are involved. The skin battery and current of injury mechanisms have become topics of interest for their influence in chronic wounds. Electrostimulation therapy of wounds has shown to be a promising treatment option with no-device-related adverse effects. This review presents an overview of the understanding and use of applied electrical current in various aspects of wound healing. Rapid clinical translation of the evolving understanding of biomolecular mechanisms underlying the effects of electrical simulation on wound healing would positively impact upon enhancing patient's quality of life.
Molecular analysis of the RNA and protein components recognized by anti-La(SS-B) autoantibodies. (1985)

The aim of this study was to determine whether sera with autoantibodies to the La(SS-B) nuclear antigen react with the same or different sets of cellular or viral ribonucleoproteins (RNPs) and whether patients with anti-La(SS-B) comprised a homogeneous group with respect to phenotypic and serological markers. The 34 anti-La(SS-B) sera studied were detected in the course of screening 2,000 sera referred from patients with suspected or defined multisystem autoimmune disease. Analysis of the molecular components of the small nuclear (sn) RNPs isolated from immune complexes developed in vitro between the IgG fractions of the anti-La(SS-B) sera and cell lines selected for their content of viral and cellular (non-viral) RNA showed that all 34 anti-La(SS-B) sera reacted with the same group of cellular RNAs and with two viral RNAs encoded by Epstein-Barr virus. The La(SS-B) RNPs contained one major 50,000 dalton antigenic polypeptide that resolved into 5-6 heterogeneously charged isospecies on two-dimensional immunoblots. In addition to anti-La(SS-B) reactivity, all 34 sera were shown to contain anti-Ro(SS-A) activity by counterimmunoelectrophoresis (CIEP); however, with three exceptions, the antigenic Ro(SS-A) polypeptide was not detectable by immunoblotting. The homogeneity of this group with anti-La(SS-B) was indicated by the findings that of the 34 cases 31 (88%) had hypergammaglobulinaemia, 33 (97%) had rheumatoid factor and 27 (of 30 tested, 90%) were HLA-B8. Thus all anti-La(SS-B) sera react with the same set of RNAs associated with an antigenic 50,000 dalton nucleoprotein, and the presence of anti-La(SS-B) autoantibodies identified a homogeneous group of patients with the serological and phenotypic features of primary Sjögren's syndrome.
Concepts in the management of the overactive bladder in women. (2012)

The 'overactive bladder' is a common problem affecting the elderly female population especially after the menopause. Urgency with or without urge incontinence accompanied by frequency of micturition and nocturia are presenting symptoms. The diagnosis is established after excluding other diseases of the lower urinary tract which have similar presenting features. The aetiology is multifactorial and this problem often causes physical, psychological and emotional distress to the patient. Management can be provided by primary care physicians initiating behavioral changes which include life style interventions and bladder drills with or without antimuscarinic drugs. The recalcitrant patient not responding to conventional therapy should be referred for specialist care. Non-conventional treatment using acupressure, neuromodulation and surgical methods are only instituted in indicated cases.
Visible luminescence from silicon surfaces microstructured in air (2002)

We report visible luminescence from SiOx formed by microstructuring silicon surfaces with femtosecond laser pulses in air. Incorporation of oxygen into the silicon lattice occurs only where the laser beam strikes the surface. Laser microstructuring therefore offers the possibility of writing submicrometer luminescent features without lithographic masks. The amount of oxygen incorporated into the silicon surface depends on the laser fluence; the peak wavelength of the primary luminescence band varies between 540 and 630 nm and depends on the number of laser shots. Upon annealing, the intensity of the primary luminescence band increases significantly without any change in the luminescence peak wavelength, suggesting that the luminescence comes from defects rather than quantum confinement.
The GPI anchor of cell-surface proteins is synthesized on the cytoplasmic face of the endoplasmic reticulum. (1994)

Glycosylphosphatidylinositol (GPI) membrane protein anchors are synthesized from sugar nucleotides and phospholipids in the ER and transferred to newly synthesized proteins destined for the cell surface. The topology of GPI synthesis in the ER was investigated using sealed trypanosome microsomes and the membrane-impermeant probes phosphatidylinositol-specific phospholipase C, Con A, and proteinase K. All the GPI biosynthetic intermediates examined were found to be located on the external face of the microsomal vesicles suggesting that the principal steps of GPI assembly occur in the cytoplasmic leaflet of the ER. Protease protection experiments showed that newly GPI-modified trypanosome variant surface glycoprotein was primarily oriented towards the ER lumen, consistent with eventual expression at the cell surface. The unusual topographical arrangement of the GPI assembly pathway suggests that a biosynthetic intermediate, possibly the phosphoethanolamine-containing anchor precursor, must be translocated across the ER membrane bilayer in the process of constructing a GPI anchor.
Mucosal immunity and allergic responses: lack of regulation and/or lack of microbial stimulation? (2005)

Allergic hyperreactivity is defined as an exaggerated immune response [typically immunoglobulin E (IgE) but also non-IgE mediated] toward harmless antigenic stimuli. The prevalence of allergic disease has increased dramatically during the last 20 years, especially in developed countries. Both genetic and environmental factors contribute to susceptibility to allergy. Evidence has emerged supporting the hypothesis that a reduction in antigenic stimulation brought about by widespread vaccination, improvements in standards of hygiene, and extensive use of antibiotics has contributed to the dysregulation of T-helper 2 cell (Th2) type responsiveness that typifies allergy. Regulation of the inherently Th2-biased mucosal immune response is crucial both to the maintenance of homeostasis at this strategic defensive barrier and to the prevention of allergic disease. The ability of Th1 responses to counter-regulate Th2 reactivity is well characterized. More recently, interest has centered on regulatory T cells, which can suppress both Th1 and Th2 cells through the secretion of immunosuppressive cytokines such as interleukin-10 and transforming growth factor-beta. In this review, we discuss the basic cellular mechanisms of allergic diseases at mucosal surfaces, focusing on allergic responses to food, before examining newer work that suggests the induction of allergic hyperreactivity is due to a deficient immunoregulatory network, a lack of microbial stimulation, or both.
Site-directed Mutagenesis of the 100-kDa Subunit (Vph1p) of the Yeast Vacuolar (H+)-ATPase (1996)

Vacuolar (H+)-ATPases (V-ATPases) are multisubunit complexes responsible for acidification of intracellular compartments in eukaryotic cells. V-ATPases possess a subunit of approximate molecular mass 100 kDa of unknown function that is composed of an amino-terminal hydrophilic domain and a carboxyl-terminal hydrophobic domain. To test whether the 100-kDa subunit plays a role in proton transport, site-directed mutagenesis of the VPH1 gene, which is one of two genes that encodes this subunit in yeast, has been carried out in a strain lacking both endogenous genes. Ten charged and twelve polar residues located in the seven putative transmembrane helices in the COOH-terminal domain of the molecule were individually changed, and the effects on proton transport, ATPase activity, and assembly of the yeast V-ATPase were measured. Two mutations (R735L and Q634L) in transmembrane helix 6 and at the border of transmembrane helix 5, respectively, showed greatly reduced levels of the 100-kDa subunit in the vacuolar membrane, suggesting that these mutations affected stability of the 100-kDa subunit. Two mutations, D425N and K538A, in transmembrane helix 1 and at the border of transmembrane helix 3, respectively, showed reduced assembly of the V-ATPase, with the D425N mutation also reducing the activity of V-ATPase complexes that did assemble. Two mutations, H743A and K593A, in transmembrane helix 6 and at the border of transmembrane helix 4, respectively, have significantly greater effects on activity than on assembly, with proton transport and ATPase activity inhibited 40-60%. One mutation, E789Q, in transmembrane helix 7, virtually completely abolished proton transport and ATPase activity while having no effect on assembly. These results suggest that the 100-kDa subunit may be required for activity as well as assembly of the V-ATPase complex and that several charged residues in the last four putative transmembrane helices of this subunit may play a role in proton transport.
CD of the li‐salt of DNA in ethanol/water mixtures: Evidence for the B‐ to C‐form transition in solution (1987)

Abstract The conformational change of Li‐DNA in water/ethanol mixtures is followed by the change in the CD spectrum in solutions containing various percentages of ethanol in the range from 0 to 95%. Two main transitions can be distinguished. The first occurs in the range from 0 to 70% and is represented by a large reduction of the intensity of the positive CD band around 275 nm, which is apparently related to a small change in the number of base pairs per turn. Secondly, at higher percentages of ethanol (&gt; 80%) a conformational change is detected, which is expressed as a reduction of the 245‐nm negative CD intensity. According to x‐ray diffraction experiments of fibers of Li‐DNA, the C‐form is attained in 95% ethanol, while at 70% ethanol a B‐like structure is observed. The CD experiments reported here also show that for DNA in solution the dependence on percentage of ethanol is composed of two main transition regions. The C‐form would then be adopted at high (∼ 95%) ethanol percentage. The 0–70% transition, although strongly expressed in optical CD experiments, has to be related to relatively small structural changes within the B‐family of DNA structures, which probably induce an enhanced contribution of n → π* transitions to the CD spectrum.
Sir2 links chromatin silencing, metabolism, and aging (2000)

Aging is manifested by a progressive decline in vitality over time leading to death. Studies in budding yeast allow aging to be followed in individual pedigrees of cells, that is, those of mother cells, consequent to many rounds of cell division These studies have led to the general conclusion that the silencing protein Sir2 is a limiting component of longevity; deletions of SIR2 shorten life span and an extra copy of this gene increases life span Recent studies have spurred interest in Sir2 as a candidate longevity factor in a broad spectrum of eukaryotic organisms. SIR2 gene homologs have been found in a very wide range of organisms ranging from bacteria to humans Moreover, a biochemical activity of Sir2 likely responsible for chromatin silencing, nicotinamide-adenine dinucleotide (NAD)-dependent histone deacetylase, has recently been discovered and shown to be broadly conserved In this review, I will briefly discuss silencing as it pertains to SIR2 and its relationship to aging. I will then trace the studies that led to the discovery of the NADdependent histone deacetylase. I will next speculate how the regulation of Sir2 by NAD could represent the link between caloric intake and the pace of aging, which is widely observed in many organisms Finally, I will present a speculative model of how a gradual disruption in chromatin silencing may occur and how such a change may cause aging.
Antigenic Variation in gp120s from Molecular Clones of HIV-1 LAI (1993)

To address the relationship between primary sequence variation in HIV-1 gp120 and its antigenic structure in a simple system, we have measured the binding of human and murine monoclonal antibodies (MAbs) to gp120 from four molecular clones of HIV-1 LAI: HxB2, HxB3, Hx10, and NL4-3. Despite the close relationship between these clones, and their relatively conserved gp120 sequences, there is considerable variation in their antigenic structure, judged by MAb reactivities to the V2, V3, and C4 domains and to discontinuous epitopes. Because of our prior studies of the determinants of MAb binding to HxB2 gp120, we can make reasonable estimates of how sequence variation among the LAI clone gp120s affects their binding of some MAbs; for other MAbs our current knowledge of gp120 structure is too limited to allow such estimates. These results indicate that small variations in primary gp120 amino acid sequence can profoundly affect recognition of this glycoprotein by all five groups of defined anti-gp120 neutralizing antibodies.
Status Summary of 3He and Neutron Detection Alternatives for Homeland Security (2010)

This is a short summary whitepaper on results of our alternatives work: Neutron detection is an important aspect of interdiction of radiological threats for homeland security purposes since plutonium, a material used for nuclear weapons, is a significant source of fission neutrons [Kouzes 2005]. Because of the imminent shortage of 3He, which is used in the most commonly deployed neutron detectors, a replacement technology for neutron detection is required for most detection systems in the very near future [Kouzes 2009a]. For homeland security applications, neutron false alarms from a detector can result in significant impact. This puts a strong requirement on any neutron detection technology not to generate false neutron counts in the presence of a large gamma ray-only source [Kouzes et al. 2008].
Immuno- and affinity probes for electron microscopy: a review of labeling and preparation techniques. (1990)

Immuno- and affinity probes are widely used in biology and medicine, and are becoming essential tools for the elucidation of cell structure and function. This article reviews and discusses the bewildering array of probes and preparation techniques now available for the investigation of sectioned material by transmission electron microscopy, with critical analysis of their merits. Emphasis is placed on immunogold probes and methods useful for routine preparation, gathering together information that may be used to improve labeling techniques. New data on inert dehydration for the localization of sensitive epitopes without chemical or cryofixation is presented.
Generation of influenza A viruses entirely from cloned cDNAs (1999)

We describe a new reverse-genetics system that allows one to efficiently generate influenza A viruses entirely from cloned cDNAs. Human embryonic kidney cells (293T) were transfected with eight plasmids, each encoding a viral RNA of the A/WSN/33 (H1N1) or A/PR/8/34 (H1N1) virus, flanked by the human RNA polymerase I promoter and the mouse RNA polymerase I terminator-together with plasmids encoding viral nucleoprotein and the PB2, PB1, and PA viral polymerases. This strategy yielded >1 x 10(3) plaque-forming units (pfu) of virus per ml of supernatant at 48 hr posttransfection. The addition of plasmids expressing all of the remaining viral structural proteins led to a substantial increase in virus production, 3 x 10(4)-5 x 10(7) pfu/ml. We also used reverse genetics to generate a reassortant virus containing the PB1 gene of the A/PR/8/34 virus, with all other genes representing A/WSN/33. Additional viruses produced by this method had mutations in the PA gene or possessed a foreign epitope in the head of the neuraminidase protein. This efficient system, which does not require helper virus infection, should be useful in viral mutagenesis studies and in the production of vaccines and gene therapy vectors.
Synthesis of 2′‐deoxyribofuranosyl indole nucleosides related to the antibiotics SF‐2140 and neosidomycin (1988)

Abstract The 2′‐deoxyribofuranose analog of the naturally occurring antibiotics SF‐2140 and neosidomycin were prepared by the direct glycosylation of the sodium salts of the appropriate indole derivatives, with 1‐chloro‐2‐ deoxy‐3,5‐di‐ O ‐p‐toluoyl‐α‐D‐ erythropentofuranose ( 5 ). Thus, treatment of the sodium salt of 4‐methoxy‐1 H ‐ indol‐3‐ylacetonitrile ( 4a ) with 5 provided the blocked nucleoside, 4‐methoxy‐1‐(2‐deoxy‐3,5‐di‐ O ‐ p ‐toluoyl‐β‐ D‐ erythropentofuranosyl )‐1 H ‐indol‐3‐ylacetonitrile ( 6a ), which was treated with sodium methoxide to yield the SF‐2140 analog, 4‐methoxy‐1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indol‐3‐ ylacetonitrile ( 7a ). The neosidomycin analog ( 8 ) was prepared by treatment of the sodium salt of 1 H ‐indol‐3‐ylacetonitrile ( 4b ) with 5 to obtain the blocked intermediate 1‐(2‐deoxy‐3,5‐di‐ O ‐ p ‐toluoyl‐β‐D‐ erythropentofuranosyl ) −1 H ‐indol‐3‐ylace‐tonitrile ( 6b ) followed by sodium methoxide treatment to give 1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐ indol‐3‐ylacetonitrile ( 7b ) and finally conversion of the nitrile function of 7b to provide 1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indol‐3‐ylacetamide ( 8 ). In a similar manner, indole ( 9a ) and several other substituted indoles including 1 H ‐indole‐4‐carbonitrile ( 9b ), 4‐nitro‐1 H ‐indole ( 9c ), 4‐chloro‐1 H ‐indole‐2‐carboxamide ( 9d ) and 4‐chloro‐1 H ‐indole‐2‐carbonitrile ( 9e ) were each glycosylated and deprotected to provide 1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indole ( 11a ), 1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indole‐4‐ carbonitrile ( 11b ), 4‐nitro‐1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indole ( 11c ), 4‐chloro‐1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐1 H ‐indole‐2‐carboxamide ( 11d ) and 4‐chloro‐1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐ 1 H ‐indole‐2‐carbonitrile ( 11e ), respectively. The 2′‐deoxyadenosine analog in the indole ring system was prepared for the first time by reduction of the nitro group of 11c using palladium on carbon thus providing 4‐amino‐1‐(2‐deoxy‐β‐D‐ erythropentofuranosyl )‐ 1 H ‐indole ( 16 , 1,3,7‐trideaza‐2′‐deoxyadenosine).
Analysis of EphA2 expression and mutant p53 in ovarian carcinoma (2006)

The EphA2 tyrosine kinase receptor is frequently overexpressed in ovarian cancer and this feature is predictive of poor clinical outcome. Preclinical investigation has also linked EphA2 with p53. In our present study, we examined EphA2 and p53 status (both expression and full-length mutation status) in 6 ovarian cell lines and 79 human ovarian cancers to determine potential associations. EphA2 was overexpressed in 80% of ovarian cancer cell lines and in 75% of clinical specimens. In particular, high levels of EphA2 occurred in 91% of tumors with p53 null mutations compared to 68% in tumors with wild-type or missense mutations (p=0.027). EphA2 expression did not relate to critical versus non-critical site missense p53 mutations or the location of mutations on specific p53 exons. We also demonstrated that while EphA2 and p53 can provide independent information regarding clinical status, the combination of EphA2 and p53 status can predict poor clinical outcome. In particular, the combination of EphA2 overexpression and p53 null status was associated with decreased overall patient survival and related to increased incidence of ascites and distant metastasis. Taken together, these data indicate a complex relationship between EphA2 and p53 that appears to regulate EphA2 expression and clinical outcome.
Analysis of the wee gene cluster responsible for the biosynthesis of the polymeric bioemulsifier from the oil-degrading strain Acinetobacter lwoffii RAG-1 The GenBank/EMBL accession number for the sequence analysis of the eight fragments determined in this work is AJ243431. (2001)

A cluster (27 kbp) of genes responsible for the biosynthesis of the amphipathic, polysaccharide bioemulsifier emulsan from the oil-degrading Acinetobacter lwoffii RAG-1 was isolated and characterized. The complete sequence of this cluster, termed wee, consisted of 20 ORFs. One set of 17 ORFs was transcribed in one direction, while a second set of three ORFs, 607 bp upstream of the first, was transcribed in the opposite direction. Mutations in either of the two regions caused defects in emulsan production, yielding specific activities of 5-14% of parental emulsifying activity. Putative functions could be assigned to proteins involved in production of nucleotide amino sugar precursors, transglycosylation, transacetylation, polymerization and transport. However, no JUMPstart or ops sequences, normally found associated with some polysaccharide biosynthetic gene clusters, were identified. Evidence is presented suggesting that the bioemulsifier may be a member of the group 1 or group 4 polysaccharides.
Kaposi's sarcoma-associated herpesvirus-like DNA sequences in multicentric Castleman's disease [see comments] (1995)

Multicentric Castleman's disease (MCD) is an atypical lymphoproliferative disorder defined using clinical and pathologic criteria. A characteristic of the MCD is a close association with Kaposi's sarcoma (KS), which occurs during the clinical course of most human immunodeficiency virus (HIV)-associated MCD cases and also, but less frequently, in HIV-negative patients. Recently, sequences of a putative new Herpesvirus (KSHV) have been isolated and further detected in almost all the acquired immunodeficiency syndrome (AIDS) KS and in most of the non-AIDS KS samples. In this study, we searched for these Herpesvirus-like sequences in MCD samples of 31 patients. KSHV sequences were detected in 14 of 14 cases of HIV-associated MCD, including 5 cases without detectable KS. Moreover, KSHV was detected in 7 of 17 MCD cases in HIV-negative patients, including 1 case associated with a cutaneous KS. In 34 non-MCD reactive lymph nodes (follicular and/or interfollicular hyperplasia) in HIV-negative patients, KSHV was detected in only 1 case. In 1 HIV-negative case of MCD, KSHV was found in both the lymph node and peripheral blood samples. These data suggest that KSHV could play a role in the pathogenesis of MCD, especially in HIV-infected patients.
Practical Aspects of Trapped Ion Mass Spectrometry, Volume IV (2010)

Reflecting the substantial increase in popularity of quadrupole ion traps and Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers, Practical Aspects of Trapped Ion Mass Spectrometry, Volume IV: Theory and Instrumentation explores the historical origins of the latest advances in this expanding field. It covers new methods for trapp
Delaying Acute Graft‐Versus‐Host Disease in Mouse Bone Marrow Transplantation by Treating Donor Cells with Antibodies Directed at l‐Selectin and α4‐Integrin Prior to Infusion (2004)

Acute graft-versus-host disease (GVHD) is still a major hurdle for successful bone marrow transplantation (BMT). Although many immunosuppressive drugs are available, none of them alone or in combination are able to completely abolish acute GVHD. The lifelong immunosuppression profoundly reduces the quality of life of BMT recipients. Therefore, new therapeutic approaches are needed. We previously reported that, in an acute GVHD model using SCID mice as recipient, incubating donor spleen cells with antibodies directed at CD49d and CD62L could significantly delay the occurrence of acute GVHD. To test the potential usefulness of this treatment in BMT, we examined this therapeutic protocol in a mouse BMT model. The present mouse BMT study confirmed our previous results that incubation of donor cells with antibodies directed at CD49d and CD62L prior to infusion into the recipient can effectively delay acute GVHD, allowing the recipients to recover from the side effects of total body irradiation. This one-time treatment is easy and simple and may be modified for clinical usage.