gebhart/patrepeval huggingface dataset:
Oligomeric β‐amyloid(1‐42) induces the expression of Alzheimer disease‐relevant proteins in cholinergic SN56.B5.G4 cells as revealed by proteomic analysis (2008)

Alzheimer's disease (AD) is characterized by cholinergic dysfunction and progressive basal forebrain cell loss which has been hypothesized to be associated with extensive accumulation of beta-amyloid (Abeta). To reveal whether oligomeric Abeta displays a particular toxicity for cholinergic neurons, the cholinergic cell line SN56.B5.G4 (SN56) was used as a model. Recently performed microarray analyses demonstrated that genes affected by exposure of SN56 cells with 50 microM oligomeric Abeta(1-42) for 24 h were involved in protein modification and degradation [Heinitz, K., Beck, M., Schliebs, R., Perez-Polo, J.R., 2006. Toxicity mediated by soluble oligomers of beta-amyloid(1-42) on cholinergic SN56.B5.G4 cells. J. Neurochem. 98, 1930-1945]. Using a proteomic approach, we compared the levels of proteins and specially of phosphorylated proteins in cytosolic fractions of cell lysates from cholinergic SN56 cells exposed to 50 microM Abeta(1-42) for 24h to those in control incubations. We show here that the levels of calreticulin, and mitogen-activated protein kinase (MAPK) kinase 6c were up-regulated in cholinergic SN56 cells exposed to Abeta(1-42), while gamma-actin appeared down-regulated. Abeta(1-42) exposure of cholinergic SN56 cells led to decreased phosphorylation of phosphoproteins, such as the Rho GDP dissociation inhibitor, the ubiquitin carboxyl terminal hydrolase-1, and the tubulin alpha-chain isotype Malpha6, as compared to untreated control lysates. The proteins identified have also been reported to be affected in brains of AD patients, suggesting a potential role of Abeta in influencing the integrity and functioning of the proteome in AD.
Prognostic factors of tumor recurrence in completely resected non-small cell lung cancer (2013)

IVI, tumor diameter more than 5 cm, and tumor necrosis are prognostic factors of tumor recurrence in completely resected NSCLC. Therefore, NSCLC patients, with or without nodal involvement, who have one or more prognostic factors of tumor recurrence may benefit from adjuvant chemotherapy for prevention of tumor recurrence.
Core/Single‐Crystal‐Shell Nanospheres for Controlled Drug Release via a Magnetically Triggered Rupturing Mechanism (2008)

Core/single-crystal-shell nanospheres are constructed from a poly-(N-vinyl- 2-pyrrolidone) (PVP)-modified silica core with an outer layer of single-crystal iron oxide shell. The nanospheres show outstanding release-and-zero-release characteristics via the addition and removal, respectively, of an external high-frequency magnetic field.
Mass Spectrometry for Species or Strain Identification after Culture or without Culture: Past, Present, and Future (2006)

This minireview discusses the use of mass spectrometry in biomarker discovery, the current utility of these markers for bacterial identification after culture, and the potential for non-culture-based diagnosis of infectious diseases. The bases of these thoughts are the independent revolutions that
Adenosine A2B Receptor Blockade Slows Growth of Bladder and Breast Tumors (2011)

The accumulation of high levels of adenosine in tumors activates A(2A) and A(2B) receptors on immune cells and inhibits their ability to suppress tumor growth. Deletion of adenosine A(2A) receptors (A(2A)ARs) has been reported to activate antitumor T cells, stimulate dendritic cell (DC) function, and inhibit angiogenesis. In this study, we evaluated the effects of intermittent intratumor injection of a nonselective adenosine receptor antagonist, aminophylline (AMO; theophylline ethylenediamine) and, for the first time to our knowledge, a selective A(2B)AR antagonist, ATL801. AMO and ATL801 slowed the growth of MB49 bladder and 4T1 breast tumors in syngeneic mice and reduced by 85% metastasizes of breast cancer cells from mammary fat to lung. Based on experiments with A(2A)AR(-/-) or adenosine A(2B) receptor(-/-) mice, the effect of AMO injection was unexpectedly attributed to A(2B)AR and not to A(2A)AR blockade. AMO and ATL801 significantly increased tumor levels of IFN-γ and the IFN-inducible chemokine CXCL10, which is a ligand for CXCR3. This was associated with an increase in activated tumor-infiltrating CXCR3(+) T cells and a decrease in endothelial cell precursors within tumors. Tumor growth inhibition by AMO or ATL801 was eliminated in CXCR3(-/-) mice and RAG1(-/-) mice that lack mature T cells. In RAG1(-/-) mice, A(2B)AR deletion enhanced CD86 expression on CD11b(-) DCs. Bone marrow chimera experiments demonstrated that CXCR3 and A(2B)AR expression on bone marrow cells is required for the antitumor effects of AMO. The data suggest that blockade of A(2B)ARs enhances DC activation and CXCR3-dependent antitumor responses.
Results of a phase II clinical trial of 6-mercaptopurine (6MP) and methotrexate in patients with BRCA-defective tumours (2019)

NCT01432145 http://www.ClinicalTrials.gov.
Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity (2007)

Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (PI3K) pathway is frequently activated in solid tumors; however, currently, no reliable test for PI3K pathway activation exists for human tumors. Taking advantage of the observation that loss of PTEN, the negative regulator of PI3K, results in robust activation of this pathway, we developed and validated a microarray gene expression signature for immunohistochemistry (IHC)-detectable PTEN loss in breast cancer (BC). The most significant signature gene was PTEN itself, indicating that PTEN mRNA levels are the primary determinant of PTEN protein levels in BC. Some PTEN IHC-positive BCs exhibited the signature of PTEN loss, which was associated to moderately reduced PTEN mRNA levels cooperating with specific types of PIK3CA mutations and/or amplification of HER2. This demonstrates that the signature is more sensitive than PTEN IHC for identifying tumors with pathway activation. In independent data sets of breast, prostate, and bladder carcinoma, prediction of pathway activity by the signature correlated significantly to poor patient outcome. Stathmin, encoded by the signature gene STMN1, was an accurate IHC marker of the signature and had prognostic significance in BC. Stathmin was also pathway-pharmacodynamic in vitro and in vivo. Thus, the signature or its components such as stathmin may be clinically useful tests for stratification of patients for anti-PI3K pathway therapy and monitoring therapeutic efficacy. This study indicates that aberrant PI3K pathway signaling is strongly associated with metastasis and poor survival across carcinoma types, highlighting the enormous potential impact on patient survival that pathway inhibition could achieve.
A vibration energy harvesting device with bidirectional resonance frequency tunability (2008)

Vibration energy harvesting is an attractive technique for potential powering of wireless sensors and low power devices. While the technique can be employed to harvest energy from vibrations and vibrating structures, a general requirement independent of the energy transfer mechanism is that the vibration energy harvesting device operate in resonance at the excitation frequency. Most energy harvesting devices developed to date are single resonance frequency based, and while recent efforts have been made to broaden the frequency range of energy harvesting devices, what is lacking is a robust tunable energy harvesting technique. In this paper, the design and testing of a resonance frequency tunable energy harvesting device using a magnetic force technique is presented. This technique enabled resonance tuning to ± 20% of the untuned resonant frequency. In particular, this magnetic-based approach enables either an increase or decrease in the tuned resonant frequency. A piezoelectric cantilever beam with a natural frequency of 26 Hz is used as the energy harvesting cantilever, which is successfully tuned over a frequency range of 22–32 Hz to enable a continuous power output 240–280 µW over the entire frequency range tested. A theoretical model using variable damping is presented, whose results agree closely with the experimental results. The magnetic force applied for resonance frequency tuning and its effect on damping and load resistance have been experimentally determined.
Lactam bridge stabilization of α‐helical peptides: Ring size, orientation and positional effects (1995)

A series of 14 residue amphipathic alpha-helical peptides, in which the sidechains of glutamic acid and lysine have been covalently joined, was synthesized in order to determine the effect of spacing, position and orientation of these lactam bridges. It was found that although an (i, i+3) spacing would position the lactam bridge on the same face of the helix, these lactams with 18-member rings were actually helix-destabilizing regardless of position or location. On the other hand, (i, i+4) lactams with 21-member rings were helix-stabilizing but this was dependent on orientation. Glutamic acid-lysine lactams increased the helical content of the peptide when compared with their linear homologue in benign conditions (50 mM KH2PO4, 100 mM KCl, pH 7). Two Glu-Lys (i, i+4) lactams located at the N- and C-termini gave rise to a peptide with greater than 99% helical content in benign conditions. Peptides with Lys-Glu oriented lactams were random structures in benign conditions but in the presence of 50% TFE could be induced into a helical conformation. The stability of the single-stranded alpha-helices, as measured by thermal denaturations in 25% TFE indicated that Glu-Lys oriented lactam bridges stabilized the helical conformation relative to the linear unbridged peptide. One Glu-Lys lactam in the middle of the peptide was more effective at stabilizing helical structure than two Glu-Lys lactams positioned one at each end of the molecule. The lactams with the Lys-Glu orientation were destabilizing relative to the unbridged peptide. This study demonstrates that correct orientation and position of a lactam bridge is critical in order to design peptides with high helical content in aqueous media.
A rare cryptic translation product is presented by Kb major histocompatibility complex class I molecule to alloreactive T cells. (1995)

The identity of allogeneic peptide/major histocompatibility complex (MHC) complexes that elicit vigorous T cell responses has remained an interesting problem for both practical and theoretical reasons. Although a few abundant MHC class I-bound peptides have been purified and sequenced, identifying the unique T cell-stimulating peptides from among the thousands of existing peptides is still a very difficult undertaking. In this report, we identified the antigenic peptide that is recognized by an alloreactive bm1 anti-B6 T cell clone using a novel genetic strategy that is based upon measurement of T cell receptor occupancy in single T cells. Using lacZ-inducible T cells as a probe, we screened a splenic cDNA library in transiently transfected antigen-presenting cells (APCs) and isolated a cDNA clone that allowed expression of the appropriate peptide/Kb MHC complex in APC. The antigenic octapeptide (SVVEFSSL) exactly matched the consensus Kb MHC motif, but was surprisingly encoded by a non-ATG defined translation reading frame. Furthermore, the abundance of the naturally processed analog in untransfected cells was estimated to be <10 copies per cell. These results illustrate a novel strategy for identifying T cell-stimulating antigens in general and directly show that alloreactive T cells can respond to rather rare peptide/MHC complexes. These results also suggest that the total pool of processed peptides expressed on the APC surface may include those generated by cryptic translation of normally expressed transcripts.
Allelic losses at loci on chromosome 10 are associated with metastasis and progression of human prostate cancer (1996)

DNA samples from tumors and paired normal tissues from 48 patients with prostate cancer (stage B, 16 cases; stage C, 14 cases; stage D, 18 cases) were examined with 26 polymorphic markers spanning chromosome 10. Allelic losses were observed in 17 of the 46 cases (37%) that were informative with at least one of the markers. Detailed deletion mapping identified two distict commonly deleted regions on the long arm of chromosome 10 (10q22-q24:7 cM and 10q25.1:17 cM) and one on 10p, suggesting that at least three tumor suppressor genes associated with prostate cancer are present on this chromosome. We observed loss of heterozygosity more frequently in tumors from fatal cases (stage D, 8/16, 50%) than in localized tumors (stage B, 0/16, 0%; P = 0.001 or stage B + C, 5/30, 17%; P = 0.02 Fisher's exact test). All metastatic tissues showed allelic loss at one or more loci on 10q. In five of the nine patients from whom DNAs were available from both metastatic and primary tumors, the primary cancer foci had no detectable abnormality of chromosome 10, while the metastatic foci showed allelic loss on chromosome 10. These results suggested that inactivation of one or more tumor suppressor genes on chromosome 10 plays an important role in late stages of prostate cancer.
Size and Density of Fibrin Fibers from Turbidity (1978)

In agreement with earlier observations that the angular dependence of light scattering by fibrin gels obeys the theory for light scattering by very long and thin rigid rodlike particles (intensity proportional to the square of half the scattering angle), we find that the turbidity, tau, of the less opaque gels varies as the inverse third power of the wavelength, lambda. Mass-length ratios of the fibers calculated from these two measurements closely agree. For fibrin gels containing fibers with a very high mass-length ratio (of which we had not been able to obtain interpretable scattering data), the turbidity is found not quite to vary as 1/lambda3. For these opaque gels, the fiber diameter is no longer negligible with respect to the wavelength. It is shown how the radius of gyration of the fiber cross section (and therefore the radius of cylindrical fibers) can be obtained from the ratio of slope and intercept of a plot of 1/tau lambda3 vs. 1/lambra2. The square of the radius of the fibers is found to be proportional to the mass-length ratio. The density of the fibers is calculated to be 0.28. This corresponds to a ratio of fiber volume to volume of protein contained in the fiber of 5.0.
Genomic Structures and Chromosomal Location of p91, a Novel Murine Regulatory Receptor Family (1998)

Recently, we found a novel murine cell-surface glycoprotein, designated as p91, expressed mainly in myeloid cells such as macrophages and mast cells. The molecule has six immunoglobulin-like extracellular domains, a transmembrane segment, and a cytoplasmic tail containing four immunoreceptor tyrosine-based inhibition motif (ITIM) or ITIM-like sequences, resembling the structural features of human killer-cell inhibitory receptors (KIR). Here we show that p91 comprises a polymorphic gene family, harboring one potent inhibitory-type p91 and at least two other p91 genes. Tyrosine-phosphorylated, but not nonphosphorylated, synthetic peptides matching the third ITIM and the fourth ITIM-like sequences, respectively, found in the cytoplasmic portion of p91A, the sole inhibitory-type p91, were associated with the tyrosine phosphatases, SHP-1 and SHP-2. In addition, the phosphotyrosyl peptide matching the third ITIM sequence also bound the inositol 5-phosphatase, SHIP. These results support the notion that p91A may function as an inhibitory cell-surface molecule against cell activation. The p91 genes were shown to be clustered in the proximal region of mouse chromosome 7, a syntenic position of human chromosome 19 where the genes for the KIR family are found. A human cDNA clone cross-hybridizing to a murine p91 probe was isolated from a human spleen cDNA library, and was found to code for a molecule quite similar to members of the immunoglobulin-like transcript (or ILT) family. The gene was found to be located on human chromosome 19q13.3-13.4. These results establish the existence of a novel set of potent regulatory receptors in mouse and man, similar but different from the KIR family.
Retinoic Acid Induces Autophagosome Maturation Through Redistribution of the Cation-Independent Mannose-6-Phosphate Receptor (2010)

Retinoic acids (RAs) have diverse biologic effects and regulate several cellular functions. Here, we investigated the role of RA on autophagy by studying its effects on autophagosome (AUT) maturation, as well as on upstream regulators of autophagosome biogenesis. Our studies, based on the use of pH-sensitive fluorescent reporter markers, suggested that RA promotes AUT acidification and maturation. By using competitive inhibitors and specific agonists, we demonstrated that this effect is not mediated by the classic RAR and RXR receptors. RA did not affect the levels of upstream regulators of autophagy, such as Beclin-1, phospho-mTOR, and phospho-Akt1, but induced redistribution of both endogenous cation-independent mannose-6-phosphate receptor CIMPR and transiently transfected GFP and RFP full-length CIMPR fusion proteins from the trans-Golgi region to acidified AUT structures. Those structures were found to be amphisomes (acidified AUTs) and not autophagolysosomes. The critical role of CIMPR in AUT maturation was further demonstrated by siRNA-mediated silencing of endogenous CIMPR. Transient CIMPR knockdown resulted in remarkable accumulation of nonacidified AUTs, a process that could not be reversed with RA. Our results suggest that RA induces AUT acidification and maturation, a process critical in the cellular autophagic mechanism.
Matrix metalloproteinase 9 (92-kDa gelatinase/type IV collagenase) from HT 1080 human fibrosarcoma cells. Purification and activation of the precursor and enzymic properties. (1992)

Matrix metalloproteinase 9 (MMP-9) has been purified as an inactive zymogen of M(r) 92,000 (proMMP-9) from the culture medium of HT 1080 human fibrosarcoma cells. The NH2-terminal sequence of proMMP-9 is Ala-Pro-Arg-Gln-Arg-Gln-Ser-Thr-Leu-Val-Leu-Phe-Pro, which is identical to that of the 92-kDa type IV collagenase/gelatinase. The zymogen can be activated by 4-aminophenylmercuric acetate, yielding an intermediate form of M(r) 83,000 and an active species of M(r) 67,000, the second of which has a new NH2 terminus of Met-Arg-Thr-Pro-Arg-(Cys)-Gly-Val-Pro-Asp-Leu-Gly-Arg-Phe-Gln-Thr- Phe-Glu. Immunoblot analyses demonstrate that this activation process is achieved by sequential processing of both NH2- and COOH-terminal peptides. TIMP-1 complexed with proMMP-9 inhibits the conversion of the intermediate form to the active species of M(r) 67,000. The proenzyme is fully activated by cathepsin G, trypsin, alpha-chymotrypsin, and MMP-3 (stromelysin 1) but not by plasmin, leukocyte elastase, plasma kallikrein, thrombin, or MMP-1 (tissue collagenase). During the activation by MMP-3, proMMP-9 is converted to an active species of M(r) 64,000 that lacks both NH2- and COOH-terminal peptides. In addition, HOCl partially activates the zymogen by reacting with an intermediate species of M(r) 83,000. The enzyme degrades type I gelatin rapidly and also cleaves native collagens including alpha 2 chain of type I collagen, collagen types III, IV, and V at undenaturing temperatures. These results indicate that MMP-9 has different activation mechanisms and substrate specificity from those of MMP-2 (72-kDa gelatinase/type IV collagenase).
Clinical relationship of extrapyramidal symptoms and tardive dyskinesia. (1994)

The author reviews the relationship between extrapyramidal syndromes (EPS) such as dystonia, akathisia and parkinsonism, and tardive dyskinesia (TD), characterized clinically by late-onset repetitive movements. While the pathophysiological mechanisms are unclear, neuroleptic-induced EPS have been shown to be associated with a higher risk of TD. The appearance of EPS, however, has not been shown to predict the occurrence of TD. It has been hypothesized that dopamine hypofunction resulting in EPS may lead to the development of dopamine receptor supersensitivity, thereby increasing the TD risk. If this theory can be validated in the clinical setting, atypical neuroleptics (for example, clozapine, risperidone) with a lower EPS liability may result in a lower incidence of TD.
Disorders of the Red Blood Cells (2011)

Trustworthy guidance spanning every aspect of adolescent health care. Unlike other adolescent medicine references, the all-new AAP Textbook of Adolescent Care is an action-oriented working tool expressly built for efficient, on-target clinical problem-solving. Broad scope - Nearly 200 chapters cover physical growth and development, examination and laboratory screening, sexual development, puberty, obesity, sleep disorders, adolescent dermatology and much more. Clear management guidelines - Provides step-by-step recommendations: What to do, How to do it; When to admit, When to treat, When to refer. Evidence-based approach - Treat patients and counsel parents with high confidence. Excellent study reference - for the pediatric or internal medicine boards. Integrated companion resources - Use with complementary AAP resources: AAP Textbook of Pediatric Care, Tools for Practice, and Pediatric Care Online.
Antifungal agents commonly used in the superficial and mucosal candidiasis treatment: mode of action and resistance development (2013)

Recent progress in medical sciences and therapy resulted in an increased number of immunocompromised individuals. Candida albicans is the leading opportunistic fungal pathogen causing infections in humans, ranging from superficial mucosal lesions to disseminated or bloodstream candidiasis. Superficial candidiasis not always presents a risk to the life of the infected host, however it significantly lowers the quality of life. Superficial Candida infections are difficult to treat and their frequency of occurrence is currently rising. To implement successful treatment doctors should be up to date with better understanding of C. albicans resistance mechanisms. Despite high frequency of Candida infections there is a limited number of antimycotics available for therapy. This review focuses on current understanding of the mode of action and resistance mechanisms to conventional and emerging antifungal agents for treatment of superficial and mucosal candidiasis.
Progress and development of small molecule HCV antivirals. (2004)

Hepatitis C virus (HCV) is a disease that has a growing impact worldwide. A combination therapy comprising interferon-alpha (IFNalpha) and ribavirin represents the current standard treatment for chronic HCV infection, although it has demonstrated limited success and causes some serious side effects. Promising alternative approaches toward the control of HCV infection, and the development of new antiviral agents, include the use of NS3/4A serine protease and NS5B polymerase inhibitors. Successful proof-of-concept clinical trials of the NS3/4A protease inhibitor BILN-2061 have confirmed the usefulness of a peptidomimetic product-based approach, providing impetus for the generation of improved molecules. Preclinical results from the development of HCV polymerase inhibitors, both nucleoside and non-nucleoside, are promising. This review provides an overview of recent progress in these areas, and discusses the potential of various approaches toward small molecule HCV antivirals.