gebhart/patrepeval huggingface dataset:
Comparison of Gene Expression of Umbilical Cord Vein and Bone Marrow–Derived Mesenchymal Stem Cells (2004)

Mesenchymal stem cells (MSCs) give origin to the marrow stromal environment that supports hematopoiesis. These cells present a wide range of differentiation potentials and a complex relationship with hematopoietic stem cells (HSCs) and endothelial cells. In addition to bone marrow (BM), MSCs can be obtained from other sites in the adult or the fetus. We isolate MSCs from the umbilical cord (UC) veins that are morphologically and immunophenotpically similar to MSCs obtained from the BM. In culture, these cells are capable of differentiating in vitro into adipocytes, osteoblasts, and condrocytes. The gene expression profiles of BM-MSCs and of UC-MSCs were compared by serial analysis of gene expression, then validated by reverse transcription polymerase chain reaction of selected genes. The two lineages shared almost all of the first thousand most expressed transcripts, including vimentin, galectin 1, osteonectin, collagens, transgelins, annexin A2, and MMP2. Nevertheless, a set of genes related to antimicrobial activity and to osteogenesis was more expressed in BM-MSCs, whereas higher expression in UC-MSCs was observed for genes that participate in pathways related to matrix remodeling via metalloproteinases and angiogenesis. Finally, cultured endothelial cells, CD34+ HSCs, MSCs, blood leukocytes, and bulk BM clustered together, separated from seven other normal nonhematopoietic tissues, on the basis of shared expressed genes. MSCs isolated from UC veins are functionally similar to BM-MSCs, but differentially expressed genes may reflect differences related to their sites of origin: BM-MSCs would be more committed to osteogenesis, whereas UC-MSCs would be more committed to angiogenesis.
Efficient Palladium-Catalyzed Synthesis of Aminopyridyl Phosphonates from Bromopyridines and Diethyl Phosphite (2008)

International audience
RNA Secondary Structure Analysis Using RNAstructure (2014)

Abstract RNAstructure is a user‐friendly program for the prediction and analysis of RNA secondary structure. It is available as a Web server, as a program with a graphical user interface, or as a set of command‐line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the Web server or the graphical user interface) and prediction of high‐affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface). Curr. Protoc. Bioinform . 46:12.6.1‐12.6.25. © 2014 by John Wiley &amp; Sons, Inc.
The H7N9 Influenza Virus in China — Changes since SARS (2013)

Ten years after the emergence in China of the severe acute respiratory syndrome, an avian influenza A (H7N9) virus has emerged there, causing substantial disease. But China is now better prepared to address emerging infectious diseases and potential pandemics.
Methods in nitric oxide research (1996)

This book covers the methodologies associated with the chemistry, biochemistry, pharmacology, molecular biology, and therapeutic applications of nitric oxide (NO). In addition, specific methods for the preparation and handling of NO solutions and related NO donors are discussed, together with other procedures such as characterizing enzyme systems associated with NO metabolism.
Forms of Market Orientation and Business Performance in China (2006)

China is going through a rapid transition phase from the old centrally planned economy to an increasingly open market economy.This paper examines whether the market orientation (MO) concept originally developed in the West can also be applied to China.It investigates the extent of the market orientation practice among Chinese firms and its effect on business performance.Three different forms ofMO, namely Underdeveloped Orientation, Fragmented Orientation, and Comprehensive Orientation, were found to be practised by 331 Chinese companies operating in the residential property development sector in Guangzhou, China.The three forms ofMO were found to have significantly different levels of business performance and have distinct organisational characteristics.
Spontaneous atopic dermatitis in mice expressing an inducible thymic stromal lymphopoietin transgene specifically in the skin (2005)

The cytokine thymic stromal lymphopoietin (TSLP) has recently been implicated in the pathogenesis of atopic dermatitis (AD) and other allergic diseases in humans. To further characterize its role in this disease process, transgenic mice were generated that express a keratinocyte-specific, tetracycline-inducible TSLP transgene. Skin-specific overexpression of TSLP resulted in an AD-like phenotype, with the development of eczematous lesions containing inflammatory dermal cellular infiltrates, a dramatic increase in Th2 CD4+ T cells expressing cutaneous homing receptors, and elevated serum levels of IgE. These transgenic mice demonstrate that TSLP can initiate a cascade of allergic inflammation in the skin and provide a valuable animal model for future study of this common disease.
Association of HLA-DRB1*0401 Allele with Chronic Pancreatitis (2003)

This study supports a role of HLA-DRB1*0401 as a susceptibility factor for patients with CP. HLA DRB1*0401 contains the 70QKRAA74 amino acid sequence, which is also expressed by several human pathogens, including Epstein-Barr virus. T cells may be triggered in the pancreatic tissue upon exposure to foreign peptides similar enough to cross-react and to break immunologic tolerance.
The Protective Dose of the Potent GPIIb/IIIa Antagonist SC-54701A Is Reduced When Used in Combination With Aspirin and Heparin in a Canine Model of Coronary Artery Thrombosis (1996)

SCa has dose-dependent antithrombotic efficacy and inhibits ex vivo platelet aggregation. ASA, heparin, or saline was ineffective in this model. SCa (0.5X) plus ASA and heparin maximized the antithrombotic effect of this lower dose of SCa.
Overcoming the poor short wavelength spectral response of CdS/CdTe photovoltaic modules via luminescence down‐shifting: ray‐tracing simulations (2006)

Abstract The short‐wavelength response of cadmium sulfide/cadmium telluride (CdS/CdTe) photovoltaic (PV) modules can be improved by the application of a luminescent down‐shifting (LDS) layer to the PV module. The LDS layer contains a mixture of fluorescent organic dyes that are able to absorb short‐wavelength light of λ &lt; 540 nm, for which the PV module exhibited low external quantum efficiency (EQE), and re‐emit it at a longer wavelength (λ &gt; 540 nm), where the solar cell EQE is high. Ray‐tracing simulations indicate that a mixed LDS layer containing three dyes could lead to an increase in the short‐circuit current density from J sc = 19.8 mA/cm 2 to J sc = 22.9 mA/cm 2 for a CdS/CdTe PV module. This corresponds to an increase in conversion efficiency from 9.6% to 11.2%. This indicates that a relative increase in the performance of a production CdS/CdTe PV module of nearly 17% can be expected via the application of LDS layers, possibly without any making any alterations to the solar cell itself. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Abscisic acid deficiency in the tomato mutant high‐pigment 3 leading to increased plastid number and higher fruit lycopene content (2007)

Carotenoids are present in most tissues of higher plants where they play a variety of essential roles. To study the regulation of carotenoid biosynthesis, we have isolated novel mutations in tomato (Solanum lycopersicum) with altered pigmentation of fruit or flowers. Here we describe the isolation and analysis of a tomato mutant, high-pigment 3 (hp3), that accumulates 30% more carotenoids in the mature fruit. Higher concentrations of carotenoids and chlorophyll were also measured in leaves and the pericarp of green fruit. The mutation in hp3 had occurred in the gene for zeaxanthin epoxidase (Zep), which converts zeaxanthin to violaxanthin. Consequently, leaves of the mutant lack violaxanthin and neoxanthin, and flowers contain only minute quantities of these xanthophylls. The concentration in the hp3 mutant of abscisic acid (ABA), which is derived from xanthophylls, is 75% lower than the normal level, making hp3 an ABA-deficient mutant. The plastid compartment size in fruit cells is at least twofold larger in hp3 plants compared with the wild-type. The transcript level in the green fruit of FtsZ, which encodes a tubulin-like protein involved in plastid division, is 60% higher in hp3 than in the wild-type, suggesting that increased plastid division is responsible for this phenomenon. Elevated fruit pigmentation and plastid compartment size were also observed in the ABA-deficient mutants flacca and sitiens. Taken together, these results suggest that ABA deficiency in the tomato mutant hp3 leads to enlargement of the plastid compartment size, probably by increasing plastid division, thus enabling greater biosynthesis and a higher storage capacity of the pigments.
Increased Tissue Factor Expression Is Associated with Reduced Survival in Non–Small Cell Lung Cancer and with Mutations of TP53 and PTEN (2009)

These results provide clear evidence that combined oncogene events affecting TSG dramatically increase TF gene expression in lung tumors. Moreover, this study suggests that TF gene expression could be used as a prognostic marker in NSCLC.
LTE-advanced 8×8 MIMO measurements in an indoor scenario (2012)

The potential link performance gains obtained with up to 8×8 MIMO transmissions as standardized in 3GPP LTE Release 10 have been evaluated in an indoor measurement campaign using a testbed implementation. For well-separated antennas, the results show increasing downlink throughput when increasing the number of transmit and receive antennas, up to a median throughput of 335 Mbps for an 8×8 MIMO configuration on a 20 MHz carrier. A similar and only slightly smaller throughput is achieved when using a compact UE array of a size that is more reasonable for a consumer device implementation.
Immunity to cancer: attack and escape in T lymphocyte–tumor cell interaction (2002)

Tumor cells may express antigens which are recognized in a form of HLA/peptide complexes by T cells. The frequency at which different antigens are seen by T cells of melanoma patients and healthy donors was evaluated by human leukocyte antigen (HLA)/peptide tetramer technology which stains T cells bearing the specific receptor for a given epitope. By this technique, it was found that the majority of metastatic melanoma patients can recognize differentiation antigens (particularly Melan-A/MART-1), whereas such a recognition is scanty in the early phase of the disease and in healthy subjects. Despite the presence of melanoma-specific T cells infiltrating tumor lesions, tumor rejection rarely occurs. Among the different mechanisms of such inefficient antitumor response, this review discusses the possible anti-T-cell counterattack mediated by FasL-positive tumor cells, and shows that FasL is located in the cytoplasm of melanoma cells and is transported in the tumor microenvironment through the release of melanosomes. Additionally, mechanisms of suboptimal T cell activation through tumor cell expression of peptide analogs with antagonist activity are described, together with the possibility of overcoming such anergy induction by the usage of optimized tumor epitopes. Down-modulation of HLA expression by target tumor cells and its multiple mechanisms is also considered. Finally, we discuss the role of inducible nitric oxide synthases in determining the inhibition of apoptosis in melanoma cells, which can make such tumor cells resistant to the T-cell attack.
The effect of Arg-Gly-Asp-containing peptides on fibrinogen and von Willebrand factor binding to platelets. (1985)

The Arg-Gly-Asp sequence resides in the cell attachment region of fibronectin. Arg-Gly-Asp-containing peptides support fibroblast attachment, inhibit fibroblast adhesion to fibronectin, and inhibit fibronectin binding to thrombin-stimulated platelets. In view of the similarities between the binding of fibronectin, fibrinogen, and von Willebrand factor to stimulated platelets, we have examined the effects of Arg-Gly-Asp-containing peptides on the interaction of these latter two adhesive proteins with platelets. Gly-Arg-Gly-Asp-Ser-Pro was used as a prototype peptide, and this hexapeptide inhibited fibrinogen binding to ADP and thrombin-stimulated platelets in the 10-200 microM range. The inhibition exceeded 90% at high concentrations of peptide and was observed in the presence of either calcium or magnesium. Platelet aggregation was also inhibited by the peptide in this dose range. The hexapeptide inhibited fibrinogen binding to platelets with receptors fixed in an exposed state, indicating direct interference with the ligand-platelet interaction. The peptide was 1/2 to 1/3rd as potent in inhibiting fibrinogen as fibronectin binding to platelets, but fibrinogen and von Willebrand factor binding were inhibited to an identical extent. Conservative amino acid substitutions for the arginine, glycine, or aspartic acid markedly reduced inhibitory activity and the Asp-Gly-Arg sequence was inactive. These results indicate that Arg-Gly-Asp-containing peptides can inhibit the binding of the three adhesive proteins to stimulated platelets, establishing a basic common feature between the interaction of these molecules with platelets.
Spinal Cord Regeneration (2001)

The past 20 years has seen the emergence of many exciting and promising experimental therapeutic strategies to promote regeneration of the injured spinal cord in laboratory animals. A greater understanding of the pathophysiologic mechanisms that contribute to the initial and secondary cord injury may facilitate the development of neuroprotective strategies that preserve axonal function and prevent apoptotic cell death, thus optimizing neurologic function. Neurotrophic factors have been used to augment the poor intrinsic regenerative capacity of central nervous system neurons, and the need for sophisticated delivery of such trophic agents has stimulated the application of gene therapy in this context. In addition to augmenting the neuronal capacity to regenerate axons, many researchers are developing strategies to overcome the inhibitory environment into which these axons must grow. Characterizing the inhibitory elements of the glial scar at the site of injury and of myelin in the distal tracts is therefore a focus of intense scientific interest. To this effect, a number of strategies have also been developed to bridge the injury site and facilitate axonal growth across the lesion with a variety of cellular substrates. These include fetal tissue transplants, stem cells, Schwann cells, and olfactory ensheathing cells. With the collaboration of basic scientists and clinicians, it is hoped that these experimental strategies coupled with a greater understanding of the neurobiology of spinal cord injury will be translatable to the clinical setting in the near future.
Theory of edge detection (1980)

A theory of edge detection is presented. The analysis proceeds in two parts. (1) Intensity changes, which occur in a natural image over a wide range of scales, are detected separately at different scales. An appropriate filter for this purpose at a given scale is found to be the second derivative of a Gaussian, and it is shown that, provided some simple conditions are satisfied, these primary filters need not be orientation-dependent. Thus, intensity changes at a given scale are best detected by finding the zero values of delta 2G(x,y)*I(x,y) for image I, where G(x,y) is a two-dimensional Gaussian distribution and delta 2 is the Laplacian. The intensity changes thus discovered in each of the channels are then represented by oriented primitives called zero-crossing segments, and evidence is given that this representation is complete. (2) Intensity changes in images arise from surface discontinuities or from reflectance or illumination boundaries, and these all have the property that they are spatially. Because of this, the zero-crossing segments from the different channels are not independent, and rules are deduced for combining them into a description of the image. This description is called the raw primal sketch. The theory explains several basic psychophysical findings, and the operation of forming oriented zero-crossing segments from the output of centre-surround delta 2G filters acting on the image forms the basis for a physiological model of simple cells (see Marr & Ullman 1979).
Mapping of complex regulatory elements by pufferfish/zebrafish transgenesis (2001)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Microbial bionanotechnology : biological self-assembly systems and biopolymer-based nanostructures (2006)

Internationally acknowledged experts provide a survey of the most striking and successful approaches for the production of biogenic nanodevices using microorganisms. Entire chapters are dedicated to the biotechnological production of tailor-made biopolymer-based self-assembled nanostructures such as biopolyester, cyanophycin inclusions and alginates, which can be processed into nanoparticles. Other chapters summarise recent developments in protein- and DNA-based nanodevice production. The book demonstrates the diversity of biological nanostructures, the implied design space and the enormous potential for applications in medicine, biotechnology, drug delivery and biocomputing.
Identification and characterization of enhancer agonist human cytotoxic T-cell epitopes of the human papillomavirus type 16 (HPV16) E6/E7 (2017)

Human papillomavirus (HPV) is associated with the etiology of cervical carcinoma, head and neck squamous cell carcinoma, and several other cancer types. Vaccines directed against HPV virus-like particles and coat proteins have been extremely successful in the prevention of cervical cancer through the activation of host HPV-specific antibody responses; however, HPV-associated cancers remain a major public health problem. The development of a therapeutic vaccine will require the generation of T-cell responses directed against early HPV proteins (E6/E7) expressed in HPV-infected tumor cells. Clinical studies using various vaccine platforms have demonstrated that both HPV-specific human T cells can be generated and patient benefit can be achieved. However, no HPV therapeutic vaccine has been approved by the Food and Drug Administration to date. One method of enhancing the potential efficacy of a therapeutic vaccine is the generation of agonist epitopes. We report the first description of enhancer cytotoxic T lymphocyte agonist epitopes for HPV E6 and E7. While the in silico algorithm revealed six epitopes with potentially improved binding to human leukocyte antigen-A2 allele (HLA-A2)-Class I, 5/6 demonstrated enhanced binding to HLA-Class I in cell-based assays and only 3/6 had a greater ability to activate HPV-specific T cells which could lyse tumor cells expressing native HPV, compared to their native epitope counterparts. These agonist epitopes have potential for use in a range of HPV therapeutic vaccine platforms and for use in HPV-specific adoptive T- or natural killer-cell platforms.
Botulinum Toxin Type A as a Therapeutic Agent against Headache and Related Disorders (2015)

Botulinum neurotoxin A (BoNT/A) is a toxin produced by the naturally-occurring Clostridium botulinum that causes botulism. The potential of BoNT/A as a useful medical intervention was discovered by scientists developing a vaccine to protect against botulism. They found that, when injected into a muscle, BoNT/A causes a flaccid paralysis. Following this discovery, BoNT/A has been used for many years in the treatment of conditions of pathological muscle hyperactivity, like dystonias and spasticities. In parallel, the toxin has become a "glamour" drug due to its power to ward off facial wrinkles, particularly frontal, due to the activity of the mimic muscles. After the discovery that the drug also appeared to have a preventive effect on headache, scientists spent many efforts to study the potentially-therapeutic action of BoNT/A against pain. BoNT/A is effective at reducing pain in a number of disease states, including cervical dystonia, neuropathic pain, lower back pain, spasticity, myofascial pain and bladder pain. In 2010, regulatory approval for the treatment of chronic migraine with BoNT/A was given, notwithstanding the fact that the mechanism of action is still not completely elucidated. In the present review, we summarize experimental evidence that may help to clarify the mechanisms of action of BoNT/A in relation to the alleviation of headache pain, with particular emphasis on preclinical studies, both in animals and humans. Moreover, we summarize the latest clinical trials that show evidence on headache conditions that may obtain benefits from therapy with BoNT/A.
In vitro activities of 12 orally administered antimicrobial agents against four species of bacterial respiratory pathogens from U.S. Medical Centers in 1992 and 1993 (1994)

Clinical isolates of Haemophilus influenzae, Streptococcus pneumoniae, Streptococcus pyogenes, and Moraxella catarrhalis were gathered from 19 different clinical laboratories throughout the continental United States. The in vitro activities of 12 orally administered antimicrobial agents were compared by broth microdilution tests with 3,151 bacterial isolates. Among 890 H. influenzae isolates, 30% were capable of producing beta-lactamase enzymes (12 to 41% in different medical centers). Most of the 619 beta-lactamase-negative H. influenzae strains were susceptible to ampicillicin (MIC, < or = 1.0 micrograms/ml): 5 strains were intermediate in susceptibility (MIC, 2.0 micrograms/ml) and 1 strain was ampilicillin resistant (MIC, 4.0 micrograms/ml). Ninety-two percent of 698 M. catarrhalis strains were beta-lactamase positive. Of 799 S. pneumoniae isolates, 15% were intermediate in susceptibility to penicillin and 7% were resistant to penicillin. The prevalence of penicillin-susceptible pneumococci in different institutions ranged from 63 to 95%. Only 1% of 764 S. pyogenes isolates were resistant to the macrolides, but 5% of S. pneumoniae isolates were macrolide resistant. Only 71% of 58 penicillin-resistant S. pneumoniae isolates were erythromycin susceptible, whereas 97% of the 622 penicillin-susceptible strains were erythromycin susceptible. Penicillin-resistant pneumococci were also relatively resistant to the cephalosporins and amoxicillin. Penicillin-susceptible pneumococci were susceptible to amoxicillin-clavulanic acid (MIC for 90% of isolates tested [MIC90], < or = 0.12/0.06 microgram/ml), cefixime (MIC90, 0.25 microgram/ml), cefuroxime axetil (MIC90, < or = 0.5 microgram/ml), cefprozil (MIC90, < or = 0.5 micrograms/ml), cefaclor (MIC90, 0.5 microgram/ml), and loracarbef (MIC90, 1.0 microgram/ml). Most strains of the other species remained susceptible to the study drugs other than amoxicillin.