gebhart/patrepeval huggingface dataset:
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia (2009)

The transcription factor Hypoxia-inducible factor 1 (HIF-1) plays a central role in the transcriptional response to oxygen flux. To gain insight into the molecular pathways regulated by HIF-1, it is essential to identify the downstream-target genes. We report here a strategy to identify HIF-1-target genes based on an integrative genomic approach combining computational strategies and experimental validation. To identify HIF-1-target genes microarrays data sets were used to rank genes based on their differential response to hypoxia. The proximal promoters of these genes were then analyzed for the presence of conserved HIF-1-binding sites. Genes were scored and ranked based on their response to hypoxia and their HIF-binding site score. Using this strategy we recovered 41% of the previously confirmed HIF-1-target genes that responded to hypoxia in the microarrays and provide a catalogue of predicted HIF-1 targets. We present experimental validation for ANKRD37 as a novel HIF-1-target gene. Together these analyses demonstrate the potential to recover novel HIF-1-target genes and the discovery of mammalian-regulatory elements operative in the context of microarray data sets.
Recombinant hydrophilic region of murine retroviral protein p15E inhibits stimulated T-lymphocyte proliferation. (1987)

Retroviral envelope protein p15E and antigenically related proteins have been implicated as potential mediators of immune dysfunction associated with retroviral infections and with neoplasia. Due to its extreme hydrophobicity, purified p15E has not been available in a nondenatured form or in sufficient quantities for detailed studies on the mechanisms of its immunosuppressive effects. Therefore, a plasmid was constructed to direct the synthesis in Escherichia coli of the major hydrophilic region of murine p15E. The purified recombinant p15E derivative, soluble under physiological conditions, inhibited by up to 60% (EC50 = 7.5 nM) the anti-CD3-driven proliferation of human T lymphocytes but had no effect on the proliferation of the transformed T-cell line Jurkat. The recombinant protein also inhibited, by up to an average of 92% (EC50 = 2.1 microM), the proliferation of the murine T-cell line CTLL-2. These data (i) provide direct evidence that a retroviral envelope protein can itself inhibit lymphoproliferative function and (ii) map the inhibitory activity to a specific region of p15E. The availability of soluble, recombinant p15E should facilitate studies of the pathogenesis of the immunosuppression accompanying retroviral infections and neoplastic diseases.
Resonance energy transfer measurements between substrate binding sites within the large (Klenow) fragment of Escherichia coli DNA polymerase I (1989)

Resonance energy transfer was used to determine separation distances between fluorescent derivatives of substrates for Klenow fragment and a unique sulfhydryl, cysteine 907, on the enzyme. Fluorescent derivatives of duplex DNA, deoxynucleotide triphosphates (dNTP), and deoxynucleotide monophosphates (dNMP), modified with aminonaphthalenesulfonates (ANS), served as energy-transfer donors to the fluorophore used to modify cysteine 907, 4-[N-[(iodoacetoxy)ethyl]-N-methylamino]-7-nitrobenz-2-oxa-1,3-diazole (IANBD). The labeling of cysteine 907 with NBD caused no decrease in the enzyme's polymerase activity, suggesting that the probe did not significantly alter the conformation of the enzyme. The efficiency of singlet-singlet resonance energy transfer was determined from the quantum yield of the donor in the presence and absence of acceptor. By Förster's theory, the measured distances between cysteine 907 and binding sites for duplex DNA, dNTP, and dNMP were 25-39, 19-28, and 17-26 A, respectively. As the fluorophores, attached to the substrates via a tether arm, are separated from the substrates by approximately 12 A, the distances measured between binding sites are subject to this uncertainty. To measure the separation between binding sites for duplex DNA and dNMP, and to reduce the uncertainty introduced by the tether arm, two experiments were carried out. In the first, duplex DNA was labeled with the acceptor fluorophore NBD and used with the donor ANS-modified dNMP to yield a measured distance separating these two sites of 19-28 A.(ABSTRACT TRUNCATED AT 250 WORDS)
Updates in the treatment of ocular allergies (2010)

Allergic diseases have greatly increased in industrialized countries. About 30% of people suffer from allergic symptoms and 40%-80% of them have symptoms in the eyes. Atopic conjunctivitis can be divided into seasonal allergic conjunctivitis (SAC) and perennial allergic conjunctivitis (PAC). The treatment of SAC is simple; antihistamines, anti-inflammatory agents, or chromoglycate. In severe cases of SAC, subcutaneous or sublingual immunotherapy is helpful. PAC needs longer therapy, often year round, with mast cell stabilizers, antihistamines, and sometimes local steroids. Atopic keratoconjunctivitis is a more severe disease showing chronic blepharitis often connected with severe keratitis. It needs, in many cases, continuous treatment of the lid eczema and keratoconjunctivitis. Blepharitis is treated with tacrolimus or pimecrolimus ointment. Conjunctivitis additionally needs corticosteroids and, if needed, cyclosporine A (CsA) drops are administered for longer periods. Basic conjunctival treatment is with mast cell-stabilizing agents and in addition, antihistamines are administered. Vernal keratoconjunctivitis is another chronic and serious allergic disease that mainly affects children and young people. It is a long-lasting disease which commonly subsides in puberty. It demands intensive therapy often for many years to avoid serious complicating corneal ulcers. Treatment is mast cell-stabilizing drops and additionally antihistamines. In relapses, corticosteroids are needed. When the use of corticosteroids is continuous, CsA drops should be used, and in relapses, corticosteroids should be used additionally. Nonallergic eosinophilic conjunctivitis (NAEC) is a less known, but rather common, ocular disease. It affects mostly middle-aged and older women. The eye symptoms of NAEC are largely similar to those seen in chronic allergic conjunctivitis. Basic therapy is mast cell-stabilizing drops. Eosinophilic inflammation needs additional corticosteroids. In severe cases, CsA drops are recommended. Antihistamines should be avoided. It is important to recognize the different forms of allergic ocular diseases and to start the treatment early and intensively enough to avoid chronicity of the disease and accompanying tissue destruction.
Cutting Edge: IFN-γ Regulates the Induction and Expansion of IL-17-Producing CD4 T Cells during Mycobacterial Infection (2006)

T cell responses are important to the control of infection but are deleterious if not regulated. IFN-gamma-deficient mice infected with mycobacteria exhibit enhanced accumulation of activated effector T cells and neutrophils within granulomatous lesions. These cells do not control bacterial growth and compromise the integrity of the infected tissue. We show that IFN-gamma-deficient mice have increased numbers of IL-17-producing T cells following infection with Mycobacterium bovis bacille Calmette Guérin. Furthermore, exogenous IFN-gamma increases IL-12 and decreases IL-23 production by bacille Calmette Guérin-infected bone marrow-derived dendritic cells and reduces the frequency of IL-17-producing T cells induced by these bone marrow-derived dendritic cells. These data support the hypothesis that, during mycobacterial infection, both IFN-gamma- and IL-17-producing T cells are induced, but that IFN-gamma serves to limit the IL-17-producing T cell population. This counterregulation pathway may be an important factor in limiting mycobacterially associated immune-mediated pathology.
Evolutionary paths of streptococcal and staphylococcal superantigens (2012)

Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and staphylococcal SAgs.
Bone Mineral Density and the Risk of Alzheimer Disease (2005)

Low femoral neck BMD was associated with approximately 2 times the risk of AD and all-cause dementia in women but not men, suggesting the possibility that cumulative estrogen exposure may influence the risk of developing AD. Additional studies are needed to confirm this correlation.
A cluster of fourteen genes from enteropathogenic Escherichia coli is sufficient for the biogenesis of a type IV pilus (1996)

Enteropathogenic Escherichia coli (EPEC) adhere to epithelial cells in microcolonies, a pattern termed localized adherence (LA). LA is dependent upon the presence of 50-70 MDa plasmids, termed EPEC adherence factor (EAF) plasmids. Expression of an EAF plasmid-encoded type IV fimbria, the bundle-forming pilus (BFP), is associated with the LA phenotype. TnphoA insertions in bfpA, the gene encoding the major structural subunit of the BFP, abolish LA. While bfpA::TnphoA mutants cannot be complemented for LA by plasmids carrying the bfpA gene alone in trans, this work shows that they can be complemented by plasmids carrying the bfpA gene, as well as approximately 10 kb of downstream sequence, suggesting that such mutations have polar effects on downstream genes. The identification and characterization of a cluster of 13 genes immediately downstream of bfpA are described. The introduction into a laboratory Escherichia coli strain of a plasmid containing these 14 bfp gene cluster genes, along with pJPN14, a plasmid containing another fragment derived from the EAF plasmid, confers LA ability and BFP biogenesis. However, when a mutation is introduced into the last gene of the bfp cluster, neither LA nor BFP biogenesis is conferred. This work also provides evidence to show that the fragment cloned in pJPN14 encodes a factor(s) which results in increased levels of the pilin protein. Finally, it is shown that expression of the 14 genes in the bfp cluster from an IPTG-inducible promoter, in the absence of pJPN14, is sufficient to reconstitute BFP biogenesis in a laboratory E. coli strain, but is insufficient for LA. This is the first report demonstrating the reconstitution of a type IV pilus in a laboratory E. coli strain with a defined set of genes. The BFP system should prove to be a useful model for studying the molecular mechanisms of type IV pilus biogenesis.
Epidemic viral pneumonia (2010)

The severe acute respiratory syndrome outbreak was too short to allow management protocols to be tested in a research environment. The current 2009 influenza A (H1N1) pandemic is fortunately not associated with as high a mortality rate as the avian influenza A (H5N1), another potential pandemic candidate virus. Prior pandemic planning as well as research planning has allowed a rapid response to this outbreak, with a significant amount of literature generated in a few months. Other common seasonal viruses, such as respiratory syncytial virus and parainfluenza, as well as previously poorly recognized viruses such as hantavirus, have the ability to cause significant respiratory morbidity and mortality.
What Drives Codon Choices in Human Genes? (1996)

Synonymous codon usage is biased and the bias seems to be different in different organisms. Factors with proposed roles in causing codon bias include degree and timing of gene expression, codon – anticodon inter actions, transcription and translation rate and fidelity, codon context, and global and local G + C content. We offer a new perspective and new methods for elucidating codon choices applied especially to the human genome. We present data supporting the thesis that codon choices for human genes are largely a consequence of two factors: (1) amino acid constraints, (2) maintaining DNA structures dependent on base-step con-formational tendencies consistent with the organism's genome signature that is determined by genome-wide processes of DNA modification, replication and repair. The related codon signature defined as the dinucleotide relative abundances at the distinct codon positions {1, 2}, {2, 3}, and {3, 4} (4=1 of the next codon) accommodates both the global genome signature and amino acid constraints. In human genes, codon positions {2, 3} and {3, 4} containing the silent site have similar codon signatures reflecting DNA symmetry. Strong CG and TA dinucleotide underrepresen tation is observed at all codon positions as well as in non-coding regions. Estimates of synonymous codon usage based on codon signatures are in excellent agreement with the actual codon usage in human and general vertebrate genes. These properties are largely independent of the isochore compartment (G + C content), gene size, and transcriptional and translational constraints. We hypothesize that major influences on codon usage in human genes result from residue preferences and diresidue associations in proteins coupled to biases on the DNA level, related to replication and repair processes and/or DNA structural requirements.
Prodrugs for Amines (2008)

The purpose of this work is to review the published strategies for the production of prodrugs of amines. The review is divided in two main groups of approaches: those that rely on enzymatic activation and those that take advantage of physiological chemical conditions for release of the drugs. A compilation of the most important approaches is presented in the form of a table, where the main advantages and disadvantages of each strategy are also referred.
Joint transmit and receive optimization for high data rate wireless communication using multiple antennas (2003)

We propose a joint transmit and receive optimization scheme for the multi-input multi-output (MIMO) spatial multiplexing system (also known as BLAST) in a narrowband wireless channel. The optimum solution is found using the minimum mean square error criterion subject to average transmitter power constraint. The transmit and receive filters are shown to decouple the MIMO channel into parallel sub-chanhels. The optimum power allocation policy on these sub-channels is derived.
Therapeutic Potential of Angiostatin in Diabetic Nephropathy (2006)

Angiostatin is a proteolytic fragment of plasminogen and a potent angiogenic inhibitor. Previous studies have shown that angiostatin inhibits retinal neovascularization and reduces retinal vascular permeability in diabetic retinopathy. Here, it is reported for the first time that angiostatin is also implicated in diabetic nephropathy (DN). Angiostatin levels are dramatically decreased in the kidney of streptozotocin-induced diabetic rats. Consistently, diabetic kidneys also showed decreased expression and proteolytic activities of matrix metalloproteinase-2, an enzyme that releases angiostatin from plasminogen. Adenovirus-mediated delivery of angiostatin significantly alleviated albuminuria and attenuated the glomerular hypertrophy in diabetic rats. Moreover, angiostatin treatment downregulated the expression of vascular endothelial growth factor and TGF-beta1, two major pathogenic factors of DN, in diabetic kidneys. In cultured human mesangial cells, angiostatin blocked the overexpression of vascular endothelial growth factor and TGF-beta1 that were induced by high glucose while increasing the levels of pigment epithelium-derived factor, an endogenous inhibitor of DN. Moreover, angiostatin effectively inhibited the high-glucose-and TGF-beta1-induced overproduction of proinflammatory factors and extracellular matrix proteins via blockade of the Smad signaling pathway. These findings suggest that the decrease of angiostatin levels in diabetic kidney may contribute to the pathologic changes such as inflammation and fibrosis in DN. Therefore, angiostatin has therapeutic potential in DN as a result of its anti-inflammatory and antifibrosis activities.
Stability and Rate Capability of Al Substituted Lithium-Rich High-Manganese Content Oxide Materials for Li-Ion Batteries (2011)

The structures, electrochemical properties and thermal stability of Al-substituted lithium-excess oxides, Li1.2Ni0.16 Mn0.56Co0.08−yAlyO2 (y = 0, 0.024, 0.048, 0.08), are reported, and compared to the stoichiometric compounds, LiNizMnzCo1−2zO2. A solid solution was found up to at least y = 0.06. Aluminum substitution improves the poor thermal stability while preserving the high energy density of lithium-excess oxides. However, these high manganese compositions are inferior to the lithium stoichiometric materials, LiNizMnzCo1−2zO2 (z = 0.333, 0.4), in terms of both power and thermal stability.
Fall in C-Peptide During First 2 Years From Diagnosis (2012)

Interpretation of clinical trials to alter the decline in β-cell function after diagnosis of type 1 diabetes depends on a robust understanding of the natural history of disease. Combining data from the Type 1 Diabetes TrialNet studies, we describe the natural history of β-cell function from shortly after diagnosis through 2 years post study randomization, assess the degree of variability between patients, and investigate factors that may be related to C-peptide preservation or loss. We found that 93% of individuals have detectable C-peptide 2 years from diagnosis. In 11% of subjects, there was no significant fall from baseline by 2 years. There was a biphasic decline in C-peptide; the C-peptide slope was -0.0245 pmol/mL/month (95% CI -0.0271 to -0.0215) through the first 12 months and -0.0079 (-0.0113 to -0.0050) from 12 to 24 months (P < 0.001). This pattern of fall in C-peptide over time has implications for understanding trial results in which effects of therapy are most pronounced early and raises the possibility that there are time-dependent differences in pathophysiology. The robust data on the C-peptide obtained under clinical trial conditions should be used in planning and interpretation of clinical trials.
Complex Interaction of the Sleep-Wake Cycle and Circadian Phase Modulates Mood in Healthy Subjects (1997)

These results indicate that, in healthy young subjects, subjective mood is influenced by a complex and nonadditive interaction of circadian phase and duration of prior wakefulness. The nature of this interaction is such that moderate changes in the timing of the sleep-wake cycle may have profound effects on subsequent mood.
Sox2 regulatory sequences direct expression of a β-geo transgene to telencephalic neural stem cells and precursors of the mouse embryo, revealing regionalization of gene expression in CNS stem cells (2000)

Sox2 is one of the earliest known transcription factors expressed in the developing neural tube. Although it is expressed throughout the early neuroepithelium, we show that its later expression must depend on the activity of more than one regionally restricted enhancer element. Thus, by using transgenic assays and by homologous recombination-mediated deletion, we identify a region upstream of Sox2 (-5.7 to -3.3 kb) which can not only drive expression of a (beta)-geo transgene to the developing dorsal telencephalon, but which is required to do so in the context of the endogenous gene. The critical enhancer can be further delimited to an 800 bp fragment of DNA surrounding a nuclease hypersensitive site within this region, as this is sufficient to confer telencephalic expression to a 3.3 kb fragment including the Sox2 promoter, which is otherwise inactive in the CNS. Expression of the 5.7 kb Sox2(beta)-geo transgene localizes to the neural plate and later to the telencephalic ventricular zone. We show, by in vitro clonogenic assays, that transgene-expressing (and thus G418-resistant) ventricular zone cells include cells displaying functional properties of stem cells, i.e. self-renewal and multipotentiality. We further show that the majority of telencephalic stem cells express the transgene, and this expression is largely maintained over two months in culture (more than 40 cell divisions) in the absence of G418 selective pressure. In contrast, stem cells grown in parallel from the spinal cord never express the transgene, and die in G418. Expression of endogenous telencephalic genes was similarly observed in long-term cultures derived from the dorsal telencephalon, but not in spinal cord-derived cultures. Thus, neural stem cells of the midgestation embryo are endowed with region-specific gene expression (at least with respect to some networks of transcription factors, such as that driving telencephalic expression of the Sox2 transgene), which can be inherited through multiple divisions outside the embryonic environment.
TILLING to detect induced mutations in soybean (2008)

The development of four independent populations with considerable mutation density, together with an additional method for screening closely related targets, indicates that soybean is a suitable organism for high-throughput mutation discovery even with its extensively duplicated genome.
The Physiology of Willpower: Linking Blood Glucose to Self-Control (2007)

Past research indicates that self-control relies on some sort of limited energy source. This review suggests that blood glucose is one important part of the energy source of self-control. Acts of self-control deplete relatively large amounts of glucose. Self-control failures are more likely when glucose is low or cannot be mobilized effectively to the brain (i.e., when insulin is low or insensitive). Restoring glucose to a sufficient level typically improves self-control. Numerous self-control behaviors fit this pattern, including controlling attention, regulating emotions, quitting smoking, coping with stress, resisting impulsivity, and refraining from criminal and aggressive behavior. Alcohol reduces glucose throughout the brain and body and likewise impairs many forms of self-control. Furthermore, self-control failure is most likely during times of the day when glucose is used least effectively. Self-control thus appears highly susceptible to glucose. Self-control benefits numerous social and interpersonal processes. Glucose might therefore be related to a broad range of social behavior.
Sector informal : una forma de utilizar el trabajo como consecuencia de la manera de producir y no viceversa: a propósito del artículo de Portes y Benton (1988)

Portes y Beton presentan una interesante hipotesis su articulo Desarrollo industrial y absorcion laboral: una reinterpretacion,1 con la que pretenden explicar la importancia y permanencia del sector informal. Segun ellos, con esta hipotesis se ofrece respuesta a dos interrogantes. La primera es por que los sectores modernos no han absorbido un mayor segmento de la fuerza de trabajo. La segunda es la aparente paradoja entre la incapacidad del sector industrial para asegurar empleo y la continua migracion de grandes contingentes de trabajadores a las ciudades (p. 117). Para los autores la explicacion esta en los diferentes modos de absorcion y utilizacion laboral las economias industrializadas (p. 120). 2 Esto implica, a su juicio, que aquellos que la perspectiva economica ortodoxa considera como subutilizados el sector informal, estan efectivamente empleados por empresas del sector moderno (pp. 120 y 128). Esta relacion laboral se produce directamente como eventuales o mediante subcontratacion de produccion o comercializacion a distintas empresas informales. En definitiva, los autores proponen que ello da respuesta a las dos preguntas planteadas y que estamos presencia de un error estadistico, ya que las cifras oficia-