gebhart/patrepeval huggingface dataset:
Conformal contact and pattern stability of stamps used for soft lithography (2000)

Patterning in soft lithography techniques such as microcontact printing or light-coupling mask lithography is mediated by surface topographical patterns of elastomeric stamps: intimate contact with the substrate is achieved locally at the protruding areas, whereas a gap remains between the substrate and recessed zones. This principle challenges the properties of the stamp, especially when printing high-resolution or extreme aspect-ratio patterns with high accuracy. On the one hand, the stamp must be soft enough to enable conformal contact with the substrate, which means that it must adapt elastically without leaving voids created by the natural roughness of the substrate. On the other hand, a precise definition of micropatterns requires a rigid material. In this article, we analyze the conditions of elasticity, roughness, and energy of adhesion to establish conformal contact between an elastomer and the target surface. Furthermore, we address questions of replication accuracy and evaluate local elastic deformation induced by normal forces using model calculations for simple pattern geometries. Pressure applied during contact leads to a sagging or collapse of the unsupported areas. We discuss implications on both material and pattern design that allow spontaneous propagation of conformal contact while inhibiting the spreading of collapse.
Brassicaceae INDEHISCENT genes specify valve margin cell fate and repress replum formation (2010)

Members of the Brassicaceae family, including Arabidopsis thaliana and oilseed rape (Brassica napus), produce dry fruits that open upon maturity along a specialised tissue called the valve margin. Proper development of the valve margin in Arabidopsis is dependent on the INDEHISCENT (IND) gene, the role of which in genetic and hormonal regulation has been thoroughly characterised. Here we perform phylogenetic comparison of IND genes in Arabidopsis and Brassica to identify conserved regulatory sequences that are responsible for specific expression at the valve margin. In addition we have taken a comparative development approach to demonstrate that the BraA.IND.a and BolC.IND.a genes from B. rapa and B. oleracea share identical function with Arabidopsis IND since ethyl methanesulphonate (EMS) mutant alleles and silenced transgenic lines have valve margin defects. Furthermore we show that the degree of these defects can be fine-tuned for crop improvement. Wild-type Arabidopsis produces an outer replum composed of about six cell files at the medial region of the fruits, whereas Brassica fruits lack this tissue. A strong loss-of-function braA.ind.a mutant gained outer replum tissue in addition to its defect in valve margin development. An enlargement of replum size was also observed in the Arabidopsis ind mutant suggesting a general role of Brassicaceae IND genes in preventing valve margin cells from adopting replum identity.
Macrophage foam cells from experimental atheroma constitutively produce matrix-degrading proteinases. (1995)

Monocyte-derived foam cells figure prominently in rupture-prone regions of atherosclerotic plaques. Peripheral blood monocytes in culture can produce certain enzymes that degrade extracellular matrix, known as matrix metalloproteinases (MMPs). Lipid-laden macrophages may thus contribute to weakening of extracellular matrix of rupture-prone atherosclerotic plaques. However, the spectrum and regulation of MMP production by foam cells remain unknown. To investigate this issue, we isolated lipid-laden macrophages from rabbit aortic lesions produced by a combination of hypercholesterolemia and balloon injury. Freshly isolated aortic macrophage foam cells, identified using cell-specific antibodies, contained immunoreactive stromelysin and interstitial collagenase, whereas alveolar macrophages isolated from the lungs of same rabbits did not. Macrophages from both tissue sources released gelatinolytic activity consistent with the 92-kDa gelatinase. In vitro, lipid-laden aortic macrophages, but not alveolar macrophages, synthesized de novo and released immunoprecipitable stromelysin and collagenase, with or without stimulation by phorbol ester or bacterial lipopolysaccharide. These stimuli caused foam cells to release additional gelatinolytic activity that migrated faster than a purified preparation of 92-kDa gelatinase in substrate-containing polyacrylamide gels, indicating activation of the 92-kDa gelatinase or induction of the 72-kDa gelatinase. Our results show that lipid-laden macrophages elaborate MMPs capable of degrading the major constituents of vascular extracellular matrix even without further stimulation. Therefore, these cells may contribute to remodeling of the extracellular matrix during atherogenesis and to the disruption of plaques often responsible for acute clinical manifestations of atherosclerosis.
Milk Production Evaluation in First Lactation Heifers (1999)

A critical evaluation of production in first lactation heifers once they reach the milking herd is important to determine the effects of the heifer rearing program.
Oligonucleotide therapeutics: clothing the emperor. (1999)

Oligonucleotides (ON) have been used in vitro, in vivo and clinically for the treatment viral infections, malignancies and inflammatory diseases. This review will focus on the application of ON-based therapeutics for hematological disease. The primary application of ONs has been as sequence specific inhibitors of gene expression, ie, antisense oligonucleotides (AS ON) and ribozymes. Based upon the unique expression of the Bcl-Abl neogene in CML cells, numerous studies have targeted this product with AS ONs and ribozymes. These studies demonstrate that ON targeting the breakpoint region selectively inhibit the proliferation of CML cells. Subsequent studies suggest that this effect may not be due to a true antisense effect of the ON. Other targets, which are being exploited for the treatment of hematological malignancies, include ON targeting c-myb gene, p53 and Bcl-2. All three have entered clinical trials and have been shown to be tolerated by patients. In addition to inhibition of gene expression, ON can be selected for sequence specific binding to proteins (aptamer). In particular an ON that binds to thrombin with high affinity is being explored as a potential anticoagulant. These early studies have identified limitations for first generation ON which may be solvable with newer ON chemistries and/or formulations. Although the technology is still nascent it continues to show promise.
Interaction between inner cell mass and trophectoderm of the mouse blastocyst : II. The fate of the polar trophectoderm (1979)

Selective labelling of polar trophectoderm cells in early mouse blastocysts has allowed the fate of polar cells to be followed during in vitro and in vivo blastocyst development. Results show that there is cell movement from polar to mural regions as blastocysts grow. This indicates that trophectoderm cells directly opposite the inner cell mass are the oldest mural cells. However, after implantation polar cells invaginate into the blastocoelic cavity and contribute to the extra-embryonic ectoderm. It is suggested that the morphogenetic changes occurring in the mouse embryo at implantation result from the maintenance of a balance between (a) regional differences in rates of cellular proliferation, and (b) mechanical constraints on the direction in which growth can occur.
Educacao e VIH/SIDA - um manual de programas de prevencao contra o VIH/SIDA (2004)

This sourcebook aims to support efforts by countries to strengthen the role of the education sector in the prevention of HIV/AIDS. It was developed in response to numerous requests for a simple forum to help countries share their practical experiences of designing and implementing programs that are targeted at school-age children. The sourcebook seeks to fulfill this role by providing concise summaries of programs, using a standard format that highlights the main elements of the programs and makes it easier to compare the programs with each other. All the programs are summarized in section two, which allows those seeking advice on program design to browse through the various options and identify those that might reward further study. The full program reports for each country are given in section three. Each program report follows the same format, so the reader can more easily find those aspects of the program that are of specific interest. The consistent design also allows for ease of comparison between programs. There are four main sections within each full program report. Part A gives an overview of the program, describing the rationale, the aims and objectives, the target audience, the components, and the main approaches. Part B describes the process from the initial needs assessment, through the development of materials and training, to the practical details of implementation. There is an attempt made to estimate unit costs, but these should be seen only as indicative, because the number of beneficiaries is often uncertain and because costs in newly implemented programs may be artificially high. Part C provides an assessment and comprises lessons learned. This section begins with comments from implementers on the challenges faced and the lessons learned, followed in a few cases by a description of any formal evaluation of the program. The final part explores the extent to which the program complies with a set of benchmarks that, on the basis of expert opinion, contribute to an effective program. Part D gives details of the organizations involved with the program, including their contact information. It lists all the materials that are available to the reader, along with an order code number.
Indenylidene Complexes of Ruthenium: Optimized Synthesis, Structure Elucidation, and Performance as Catalysts for Olefin Metathesis—Application to the Synthesis of the ADE-Ring System of Nakadomarin A (2001)

An optimized and large scale adaptable synthesis of the ruthenium phenylindenylidene complex 3 is described which employs commercially available diphenyl propargyl alcohol 5 as a stable and convenient carbene source. Previous ambiguities as to the actual structure of the complex have been ruled out by a full analysis of its NMR spectra. A series of applications to ring closing metathesis (RCM) reactions shows that complex 3 is as good as or even superior to the classical Grubbs carbene 1 in terms of yield, reaction rate, and tolerance towards polar functional groups. Complex 3 turns out to be the catalyst of choice for the synthesis of the enantiopure core segment 77 of the marine alkaloid nakadomarin A 60 comprising the ADE rings of this target. Together with a series of other examples, this particular application illustrates that catalyst 3 is particularly well suited for the cyclization of medium-sized rings by RCM. Other key steps en route to nakadomarin A are a highly selective intramolecular Michael addition setting the quaternary center at the juncture of the A and D rings and a Takai-Nozaki olefination of aldehyde 73 with CH2I2, Ti(OiPr)4 and activated zinc dust.
Fibroblast Growth Factor 21 (FGF21) Protects against High Fat Diet Induced Inflammation and Islet Hyperplasia in Pancreas (2016)

Fibroblast growth factor 21 (FGF21) is an important endocrine metabolic regulator expressed in multiple tissues including liver and adipose tissue. Although highest levels of expression are in pancreas, little is known about the function of FGF21 in this tissue. In order to understand the physiology of FGF21 in the pancreas, we analyzed its expression and regulation in both acinar and islet tissues. We found that acinar tissue express 20-fold higher levels than that observed in islets. We also observed that pancreatic FGF21 is nutritionally regulated; a marked reduction in FGF21 expression was noted with fasting while obesity is associated with 3-4 fold higher expression. Acinar and islet cells are targets of FGF21, which when systemically administered, leads to phosphorylation of the downstream target ERK 1/2 in about half of acinar cells and a small subset of islet cells. Chronic, systemic FGF21 infusion down-regulates its own expression in the pancreas. Mice lacking FGF21 develop significant islet hyperplasia and periductal lymphocytic inflammation when fed with a high fat obesogenic diet. Inflammatory infiltrates consist of TCRb+ Thy1+ T lymphocytes with increased levels of Foxp3+ regulatory T cells. Increased levels of inflammatory cells were coupled with elevated expression of cytokines such as TNFα, IFNγ and IL1β. We conclude that FGF21 acts to limit islet hyperplasia and may also prevent pancreatic inflammation.
Neuronal Activity Increases the Phosphorylation of the Transcription Factor cAMP Response Element-binding Protein (CREB) in Rat Hippocampus and Cortex (1996)

Activity-mediated gene expression is thought to play an important role in many forms of neuronal plasticities. We have used pentylenetetrazol-induced seizure that produces synchronous and sustained neuronal activity as a model to examine the mechanism(s) of gene activation. The transcription factor CREB (Ca2+/cAMP response element-binding protein) is thought to be necessary for long-term memory formation both in invertebrates and vertebrates. When phosphorylated on Ser133 either by cAMP-dependent protein kinase and/or Ca2+/calmodulin-dependent protein kinases, CREB increases transcription of genes containing the CRE (cAMP response element) sequence. Using an antibody that detects Ser133-phosphorylated CREB protein, we show that CREB phosphorylation is maximal between 3 and 8 min after the onset of seizure activity and declines slowly both in the hippocampus and the cortex. The total amount of CREB protein did not change at the time points examined. The increased phosphorylation of CREB protein is preceded by an increase in the amount of cAMP, suggestive of cAMP-dependent protein kinase activation, in the hippocampus and activation of Ca2+/calmodulin-dependent protein kinases in the cortex. Subsequent to CREB phosphorylation, the expression of the CRE-containing gene, c-fos, and the AP-1 complexes (heterodimers of Fos and Jun family members) is increased. These findings support the role of CREB-mediated gene expression in activity-dependent neuronal plasticities.
Antigenic relevance of F protein in chronic hepatitis C virus infection (2004)

The hepatitis C virus (HCV) F protein is a recently described, frameshift product of HCV core encoding sequence of genotype 1a. Its function and antigenic properties are unknown. Using enzyme-linked immunosorbent assay, we assessed the prevalence of anti-F antibodies in 154 patients chronically infected with HCV, 65 patients with other liver diseases, and 121 healthy controls. For this purpose, we expressed a highly purified HCV F recombinant protein from HCV genotype 1a in Escherichia coli. Because the F protein shares the 10 first amino acids with the core protein, the anti-HCV F response was also assessed by a F recombinant protein deleted of its 10 first amino acids [Delta(1-10)-F]. Ninety-six (62%) of the 154 HCV serum samples reacted with the complete F recombinant protein, whereas 39 (25%) showed a weaker anti-Delta(1-10)F reactivity and 150 (97%) had anti-core antibodies. No reactivity against F, Delta(1-10)F, or core was detected in any of the controls. To exclude a potential cross-reaction of anti-F antibodies with anti-core antibodies, a specific enzyme-linked immunosorbent assay was performed for anti-core antibodies. The specificity of anti-F antibodies was confirmed using an F synthetic peptide. The prevalence of anti-F antibodies did not correlate with HCV RNA serum level, genotype, or stage of liver disease. Sequence analysis from 8 anti-F-positive and 5 anti-F-negative serum samples did not reveal any particular difference potentially accounting for their respective anti-F responses. In conclusion, the F protein elicits specific antibodies in 62% of individuals chronically infected with HCV; such anti-F response does not seem to be affected by the F sequence heterogeneity.
Chemiresistive Sensor Arrays from Conductive 2D Metal–Organic Frameworks (2015)

Applications of porous metal-organic frameworks (MOFs) in electronic devices are rare, owing in large part to a lack of MOFs that display electrical conductivity. Here, we describe the use of conductive two-dimensional (2D) MOFs as a new class of materials for chemiresistive sensing of volatile organic compounds (VOCs). We demonstrate that a family of structurally analogous 2D MOFs can be used to construct a cross-reactive sensor array that allows for clear discrimination between different categories of VOCs. Experimental data show that multiple sensing mechanisms are operative with high degrees of orthogonality, establishing that the 2D MOFs used here are mechanistically unique and offer advantages relative to other known chemiresistor materials.
pppA2'p5A' blocks vesicular stomatitis virus replication in intact cells (1984)

pppA2'p5'A blocked the production of infectious vesicular stomatitis virus in HeLa cells. When this compound was present from the beginning of infection, a selective inhibitory effect was observed in viral protein synthesis. Thus, cellular translation was not affected even after 10 h of incubation with this compound, and the bulk of viral proteins was not synthesized. However, this effect was not observed with ATP, GTP, or the core A2'p5'A. The step blocked by pppA2'p5'A is located early during virus infection, but adsorption, entry, and virus uncoating seemed to be unaffected by this compound. Analysis of the antiviral spectrum of pppA2'p5'A indicated that it is active against poliovirus, encephalomyocarditis virus, and Semliki Forest virus and shows no effect against herpes simplex virus type 1 and adenovirus type 5.
Bringing gesture recognition to all devices (2014)

Existing gesture-recognition systems consume significant power and computational resources that limit how they may be used in low-end devices. We introduce AllSee, the first gesture-recognition system that can operate on a range of computing devices including those with no batteries. AllSee consumes three to four orders of magnitude lower power than state-of-the-art systems and can enable always-on gesture recognition for smartphones and tablets. It extracts gesture information from existing wireless signals (e.g., TV transmissions), but does not incur the power and computational overheads of prior wireless approaches. We build AllSee prototypes that can recognize gestures on RFID tags and power-harvesting sensors. We also integrate our hardware with an off-the-shelf Nexus S phone and demonstrate gesture recognition in through-the-pocket scenarios. Our results show that AllSee achieves classification accuracies as high as 97% over a set of eight gestures.
Cryptography against Continuous Memory Attacks (2010)

We say that a cryptographic scheme is Continuous Leakage-Resilient (CLR), if it allows users to refresh their secret keys, using only fresh local randomness, such that: 1. The scheme remains functional after any number of key refreshes, although the public key never changes. Thus, the “outside world'' is neither affected by these key refreshes, nor needs to know about their frequency. 2. The scheme remains secure even if the adversary can continuously leak arbitrary information about the current secret-key, as long as the amount of leaked information is bounded in between any two successive key refreshes. There is no bound on the total amount of information that can be leaked during the lifetime of the system. In this work, we construct a variety of practical CLR schemes, including CLR one-way relations, CLR signatures, CLR identification schemes, and CLR authenticated key agreement protocols. For each of the above, we give general constructions, and then show how to instantiate them efficiently using a well established assumption on bilinear groups, called the K-Linear assumption (for any constant K greater than or equal to 1). Our constructions are highly modular, and we develop many interesting techniques and building-blocks along the way, including: leakage-indistinguishable re-randomizable relations, homomorphic NIZKs, and leakage-of-cipher text non-malleable encryption schemes.
The Potential of Amniotic Membrane/Amnion-Derived Cells for Regeneration of Various Tissues (2007)

Regenerative medicine is a new field based on the use of stem cells to generate biological substitutes and improve tissue functions, restoring damaged tissue with high proliferability and differentiability. It is of interest as a potential alternative to complicated tissue/organ transplantation. Recently, amnion-derived cells have been reported to have multipotent differentiation ability, and these cells have attracted attention as a cell source for cell-transplantation therapy. The amnion possesses considerable advantageous characteristics: the isolated cells can differentiate into all three germ layers; they have low immunogenicity and anti-inflammatory functions; and they do not require the sacrifice of human embryos for their isolation, thus avoiding the current controversies associated with the use of human embryonic stem cells. Moreover, we developed human amniotic cell-sheets using a novel culture surface coated with a noncytotoxic, temperature-responsive elastic protein-based polymer. We also generated a "hyper-dry-amnion", which has already been applied clinically in the ophthalmological field. Compared to cryopreserved fresh amnion, "hyper-dry-amnion" is easy to handle and has started to bring good results to patients. These materials from the amnion are also expected to open a new field in tissue engineering. Thus, amnion, which had been discarded after parturition, has started to be appreciated as an attractive material in the field of regenerative medicine. In this review, the most recent and relevant clinical and experimental data about the use of amniotic membrane and cells derived from it are described.
Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity (2006)

Transfected siRNAs and miRNAs regulate numerous transcripts that have only limited complementarity to the active strand of the RNA duplex. This process reflects natural target regulation by miRNAs, but is an unintended ("off-target") consequence of siRNA-mediated silencing. Here we demonstrate that this unintended off-target silencing is widespread, and occurs in a manner reminiscent of target silencing by miRNAs. A high proportion of unintended transcripts silenced by siRNAs showed 3' UTR sequence complementarity to the seed region of the siRNA. Base mismatches within the siRNA seed region reduced the set of original off-target transcripts but generated new sets of silenced transcripts with sequence complementarity to the mismatched seed sequence. An inducible shRNA silenced a subset of transcripts that were silenced by an siRNA of the same sequence, demonstrating that unintended silencing is sequence mediated and is independent of delivery method. In all cases, off-target transcript silencing was accompanied by loss of the corresponding protein and occurred with dependence on siRNA concentration similar to that of silencing of the target transcript. Thus, short stretches of sequence complementarity to the siRNA or shRNA seed region are key to the silencing of unintended transcripts.