gebhart/patrepeval huggingface dataset:
Nanoelectrode-Gated Detection of Individual Molecules with Potential for Rapid DNA Sequencing (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
β amyloid fragments derived from activated platelets deposit in cerebrovascular endothelium: Usage of a novel blood brain barrier endothelial cell model system (2000)

Amyloid precursor protein (A betaPP) processing results in generation of amyloid beta peptide (A beta) which deposits in the brain parenchyma and cerebrovasculature of patients with Alzheimer's disease (AD). Evidence that the vascular deposits derive in part from A betaPP fragments originating from activated platelets includes findings that individuals who have had multiple small strokes have a higher prevalence of AD compared to individuals who have taken anti-platelet drugs. Thus, determination of whether platelet A betaPP fragments are capable of traversing the blood-brain barrier (BBB) is critical. We have established that activated platelets from patients with AD retain more surface transmembrane-bound A betaPP (mA betaPP) than control platelets. We report here that this mA betaPP can be cleaved to A beta-containing fragments which pass through a novel BBB model system. This model utilizes human BBB endothelial cells (BEC) isolated from brains of patients with AD. These BEC, after exposure to activated platelets which have been surface-labeled with fluorescein and express surface-retained mA betaPP, cleave fluorescein-tagged surface proteins, including mA betaPP, resulting in passage to the BEC layer The data confirm that BEC contribute to processing of platelet-derived mA betaPP and show that the processing yields A beta containing fragments which could potentially contribute to cerebrovascular A beta deposition.
Adaptive Cache Decay using Formal Feedback Control (2002)

This paper argues that adaptive techniques in processor architecture should be designed using formal feedback-control theory. We use the derivation of a controller for cache decay---a technique for leakage-energy savings---to illustrate the process of formal feedback-control design and to show the benefits of feedback control. Control theory provides a powerful framework that simplifies the task of designing an adaptive system. It provides well-known control designs that are easy to tune for performance and stability. Open-loop adaptation, on the other hand, is vulnerable to unacceptable behaviors when presented with workloads or conditions that were not anticipated at design time. In contrast, feedback control responds to unanticipated behaviors and provides robust operation in cases where open-loop designs fail. Since interest in adaptivity only continues to grow, the need for feedback control techniques and formal design techniques can only grow accordingly. Although our work so far leaves several open questions---especially the question of how best to choose the control setpoint---we hope that this paper will demonstrate the value of formal feedback control and provide guidelines for its general application in architecture research.
A novel detection and recognition system for Chinese traffic signs (2013)

In this paper, a novel detection and recognition system using an on-board single camera for Chinese traffic signs is proposed. First of all, image preprocessing method using white balance is adopted to weaken the effect of illumination changes. In the detection stage, sign candidates within Regions of Interest (ROIs) are detected by the combination of color and shape information. Then the uniform rotation-invariant Local Binary Patterns (LBP) and Support Vector Machine (SVM) are applied for the recognition stage. We have conducted lots of experiments in real road scenes and the results show that our system has high accuracy and good performance in clustered backgrounds.
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome (2020)

The complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generate a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs), many (485 MAGs, 73%) of which are linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota; i.e., more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows more accurate prediction of functional profiles of communities than predictions based on 16S rRNA amplicons alone. Accompanying iMGMC, we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC, together with MAG collections, will enhance the resolution of numerous existing and future sequencing-based studies.
WebIQ: Learning from the Web to Match Deep-Web Query Interfaces (2006)

Integrating Deep Web sources requires highly accurate semantic matches between the attributes of the source query interfaces. These matches are usually established by comparing the similarities of the attributes’ labels and instances. However, attributes on query interfaces often have no or very few data instances. The pervasive lack of instances seriously reduces the accuracy of current matching techniques. To address this problem, we describe WebIQ, a solution that learns from both the Surface Web and the Deep Web to automatically discover instances for interface attributes. WebIQ extends question answering techniques commonly used in the AI community for this purpose. We describe how to incorporate WebIQ into current interface matching systems. Extensive experiments over five realworld domains show the utility ofWebIQ. In particular, the results show that acquired instances help improve matching accuracy from 89.5% F-1 to 97.5%, at only a modest runtime overhead.
Apicomplexan autophagy and modulation of autophagy in parasite-infected host cells (2017)

Apicomplexan parasites are responsible for a number of important human pathologies. Obviously, as Eukaryotes they share a number of cellular features and pathways with their respective host cells. One of them is autophagy, a process involved in the degradation of the cell's own components. These intracellular parasites nonetheless seem to present a number of original features compared to their very evolutionarily distant host cells. In mammals and other metazoans, autophagy has been identified as an important contributor to the defence against microbial pathogens. Thus, host autophagy also likely plays a key role in the control of apicomplexan parasites, although its potential manipulation and subversion by intracellular parasites creates a complex interplay in the regulation of host and parasite autophagy. In this mini-review, we summarise current knowledge on autophagy in both parasites and their host cells, in the context of infection by three Apicomplexa: Plasmodium, Toxoplasma, and Theileria.
Increased Plasma Concentration of Brain-Derived Neurotrophic Factor With Electroconvulsive Therapy (2007)

This is the first report of an increase in plasma BDNF concentration in patients receiving ECT. These preliminary results encourage further investigation of a neurotrophic mechanism for the antidepressant effect of ECT.
Design of an Electrochemical Cell Making Syngas (CO+H[sub 2]) from CO[sub 2] and H[sub 2]O Reduction at Room Temperature (2007)

An electrolysis-cell design for simultaneous electrochemical reduction of and to make syngas at room temperature was developed, based on a technology very close to that of proton-exchange-membrane fuel cells (PEMFC), i.e., based on the use of gas-diffusion electrodes so as to achieve high current densities. While a configuration involving a proton-exchange membrane (Nafion) as electrolyte was shown to be unfavorable for reduction, a modified configuration based on the insertion of a pH-buffer layer (aqueous ) between the silver-based cathode catalyst layer and the Nafion membrane allows for a great enhancement of the cathode selectivity for reduction to CO [ca. at a potential of vs SCE (saturated-calomel reference electrode)]. A ratio of , suitable for methanol synthesis, is obtained at a potential of ca. vs SCE and a total current density of ca. . An issue that has been identified is the change in product selectivity upon long-term electrolysis. Results obtained with two other cell designs are also presented and compared.
Insights into the Biosynthesis of the Lantibiotic Mutacin 1140 (2016)

The rise of antibiotic-resistant bacteria poses a large problem for healthcare systems across the world. This problem is further exacerbated by the lack of development in new types of antibiotics. The CDC has identified antibiotic development as one of the key solutions in combating antibiotic resistance. Lantibiotics, a class of posttranslationally modified (PTM) peptide antibiotics, are promising candidates for antibiotic development. Lantibiotics are characterized by the presence of lanthionine rings and dehydrated residues. Mutacin 1140, produced by Streptococcus mutans JH1140, is a lantibiotic which has shown promising activity against a variety of Gram-positive pathogens. Although lantibiotics, such as mutacin 1140 show promise, they are still hampered by the lack of development. Furthering the understanding of lantibiotic biosynthesis is crucial for promoting the development of lantibiotics. \n\nLantibiotic biosynthesis requires a leader peptide for efficient posttranslational modification, which is then cleaved off to produce the full lantibiotic. A novel four amino acid EDLF motif was found to be important for biosynthesis in Mutacin 1140. Additionally, I have shown that a second cleavage occurs 8 amino acids upstream of the defined MutP cleavage site, and that this cleavage event is dependent upon position and not sequence. I sought to determine the importance of different PTM’s in the formation for the coordination of PTMs and transport of mutacin 1140. Deletion of the lanthionine rings show that lanthionine ring formation affects other PTM’s, and that it is important for transport out of the cytoplasm. \n\nThe role of the unique S-[(Z)-2-aminovinyl]-D-cysteine (AviCys) residue found in mutacin 1140 is poorly understood. Removal of the C-terminal carboxyl group increases the antibiotic's affinity to its molecular target lipid II. A carboxyl variant of mutacin 1140 does not affect the other PTM’s and is important for activity. This variant is agreeable to the chemical addition of a wide variety of substrates, producing novel variants of mutacin 1140 with restored activity class of lantibiotics that can be screened for improvements in drug development. The advancements made in understanding the mutacin 1140 biosynthesis pathway will help in developing mutacin 1140 as a tool to help combat the problem of antibiotic resistance.
Investigation of multistage linear region drain current degradation and gate-oxide breakdown under hot-carrier stress in BCD HV PMOS (2011)

Hot-carrier injection (HCI) at maximum gate current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) stress condition for BCD HVPMOS has been studied. It is found that HCI not only causes linear region drain current degradation and minimizes the operation window, but also degrades the gate oxide (GOX) and may result in GOX breakdown. A multistage I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Dlin</sub> degradation behavior has been observed during HCI stress, which is associated with two competing mechanisms, i.e., interface-state (N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> ) generation and electron trapping caused by hot electrons originated from impact ionization. HCI leads to the gate oxide breakdown even at very low e-field of ~1.5MV/cm across the GOX. TCAD simulation results by placing N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</sub> and negative charges at different location of the device also support a multistage I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Dlin</sub> degradation. It is found that both initial I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> and bulk current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">B</sub> ) are well correlated with GOX time-dependent-dielectric-breakdown (TDDB). In addition, better TDDB has been observed at higher temperature compared to lower temperature, which verifies that GOX breakdown is associated with HCI.
Cytokine, Chemokine, and Costimulatory Molecule Modulation to Enhance Efficacy of HIV Vaccines (2003)

Understanding key intervention points in developing immune responses may allow the rational inclusion of biological adjuvants into vaccines that could potentiate the immune response both quantitatively and qualitatively and enhance effective memory responses. Cytokine and chemokine combinations can potentially help target antigen to the appropriate antigen presenting cell and initiate maturation of these presenting cells, attract cells expressing different chemokine receptors, steer cellular immune responses toward Th1 and CD8 CTL, and enhance systemic and mucosal IgG and secretory IgA antibodies and determine their isotype balance. Animal protection studies suggest that synergistic combinations of cytokines and immunomodulating molecules may be required to protect from a viral challenge. For example, GM-CSF has been shown to be synergistic with IL-12 or CD40 ligand for induction of CTL and for antiviral protection, and the triple combination of GM-CSF, IL-12, and TNF alpha appears to induce the most effective protection in some mouse models. Chemokine-antigen fusions have also been shown to enhance immunogenicity of the antigen. Combinations of costimulatory molecules have been found to be synergistic when incorporated in a vaccine. Combined use of newer more potent vaccine constructs, containing codon optimized epitopes, relevant CpG motifs, cytokines, costimulatory molecules and chemokines, used in heterologous prime-boost strategies with viral vector vaccines or recombinant proteins, might afford the most potent vaccine approaches yet developed. In this review we will discuss the application and delivery of cytokines, costimulatory molecules, and chemokines toward improving current vaccine strategies.
Acetabulum Fractures (1980)

Twenty-two years of experience in this field allow us to say that a perfect open reduction is the method of choice to treat displaced acetabular fractures. But difficult cases require experience. Late follow-up of hips treated by open reduction and internal fixation supports the contention that a satisfactory outcome can be expected if the fracture reduction is perfect. The converse applies, and in some instances it would have been better to accept the result which might have been obtained by conservative methods. The type of fracture dictates the choice of approach, but the indication for operative treatment as well as the result of acetabular fracture treatment is the degree of congruence achieved between the acetabulum and the femoral head. Incongruence may be total, partial or apparent. Total incongruence is seen in both persistent posterior or central dislocation in which, on all three standard radiographs, the fragments of the acetabulum are seen separated from the femoral head. The situation may exist from the moment of trauma or following attempts at reduction. In all instances, operative treatment is indicated. With partial incongruence, the femoral head lies well centered beneath an undisplaced fragment of roof, but other fragments of articular surface remain displaced. A very good clinical result cannot be expected in more than 55% of hips left in this state, and neglecting operative complications, the same can be expected following conservative management. A small degree of incongruence can be accepted but one of the difficulties lies in determining the size of the fragment "roof" left in situ. Certainly, congruency seen on one standard radiograph and not in the others must not be accepted, and surgical treatment is indicated. With apparent congruence, the fragments of shattered acetabulum have regrouped around a displaced femoral head and exhibit a fair degree of congruence in this displaced position. Examples like this can often be treated conservatively because while surgery may achieve a better true congruence, this cannot be guaranteed and will be accompanied by the risks of operation. Further, the result could be worse. In nine acetabular fractures, it has been possible to achieve an apparent congruence by reconstituting displaced acetabular fragments around the femoral head but accepting the overall displacement. Seven of these obtained very good clinical results but it should be emphasized that the need to resort to this approach has been very infrequent.
An agent-based market platform for Smart Grids (2010)

The trend towards renewable, decentralized, and highly fluctuating energy suppliers (e.g. photovoltaic, wind power, CHP) introduces a tremendous burden on the stability of future power grids. By adding sophisticated ICT and intelligent devices, various Smart Grid initiatives work on concepts for intelligent power meters, peak load reductions, efficient balancing mechanisms, etc. As in the Smart Grid scenario data is inherently distributed over different, often non-cooperative parties, mechanisms for efficient coordination of the suppliers, consumers and intermediators is required in order to ensure global functioning of the power grid. In this paper, a highly flexible market platform is introduced for coordinating self-interested energy agents representing power suppliers, customers and prosumers. These energy agents implement a generic bidding strategy that can be governed by local policies. These policies declaratively represent user preferences or constraints of the devices controlled by the agent. Efficient coordination between the agents is realized through a market mechanism that incentivizes the agents to reveal their policies truthfully to the market. By knowing the agent's policies, an efficient solution for the overall system can be determined. As proof of concept implementation the market platform D'ACCORD is presented that supports various market structures ranging from a single local energy exchange to a hierarchical energy market structure (e.g. as proposed in [10]).
Management, Leadership and Change: Views from Rectors, Vice-Rectors and Academic Staff in Vietnamese Higher Education Institutions (2014)

Recent changes in the Vietnamese Higher Education system have mandated more autonomy for institutions, thereby highlighting the importance of leaders and managers with suitable experience and expertise. Rectors/Vice-Rectors and Academic staff in Vietnamese Higher Education institutions were surveyed to determine their satisfaction with leadership and management. Academic staff reported significantly lower mean ratings of satisfaction than Rectors/Vice-Rectors. Academic staff were also questioned about the value they place on autonomy and control over their working life. A large majority of Academic staff supported more autonomy and control over their working life. Results suggest a pressing need to augment leadership and managerial expertise at the institutional level in Vietnam, to develop skills in decision making and to move from reactive to proactive leadership. Change from an authoritarian hierarchical culture focused on management to a reciprocal culture focused on distributed leadership requires a cultural change in the way Higher Education institutions are managed and led in Vietnam.
RNA toxicity in non‐coding repeat expansion disorders (2019)

Several neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia (SCA) are caused by non-coding nucleotide repeat expansions. Different pathogenic mechanisms may underlie these non-coding repeat expansion disorders. While gain-of-function mechanisms, such as toxicity associated with expression of repeat RNA or toxicity associated with repeat-associated non-ATG (RAN) products, are most frequently connected with these disorders, loss-of-function mechanisms have also been implicated. We review the different pathways that have been linked to non-coding repeat expansion disorders such as C9ORF72-linked ALS/frontotemporal dementia (FTD), myotonic dystrophy, fragile X tremor/ataxia syndrome (FXTAS), SCA, and Huntington's disease-like 2. We discuss modes of RNA toxicity focusing on the identity and the interacting partners of the toxic RNA species. Using the C9ORF72 ALS/FTD paradigm, we further explore the efforts and different methods used to disentangle RNA vs. RAN toxicity. Overall, we conclude that there is ample evidence for a role of RNA toxicity in non-coding repeat expansion diseases.
The <i>yl</i> Gene of Maize Codes for Phytoene Synthase (1996)

The cloned y1 locus of maize was sequenced and found to encode phytoene synthase. Different "wild-type" alleles of the locus were found to differ by the insertion of transposable elements in their promoter and polyA addition regions, and by the length of a CCA tandem repeat series, without any obvious effect on function of the gene. A dominant Y1 ("wild-type") allele was observed to be expressed at highest levels in the seedling but also in the embryo and endosperm. The Mu3 transposable element insertion responsible for a pastel allele of y1, which gives lowered levels of carotenoids in the endosperm of kernels and seedlings grown at high temperatures, was located in the 5' end of the gene. Although the size of the transcript from this y1 mutation suggests that the Mu3 element provides the promoter for this allele, leaf tissue in this mutant line contained approximately normal amounts of y1 mRNA. A recessive allele of y1, which conditions normal levels of carotenoids in the embryo and seedling, but almost no carotenoids in the endosperm, was found to accumulate normal amounts of y1 mRNA in the seedling and embryo, while y1 transcripts were not detected in the endosperm.
Cytoplasmic HuR expression correlates with poor outcome and with cyclooxygenase 2 expression in serous ovarian carcinoma. (2003)

Cyclooxygenase-2 (COX-2) expression has been shown to associate with poor prognosis in ovarian cancer, and an mRNA stability protein HuR has been shown to enhance expression of COX-2 in tissue culture conditions. We found cytoplasmic immunoreactivity for HuR protein in 52% (233 of 445) of serous-type ovarian carcinoma specimens, and it associated with high COX-2 expression (P = 0.0045) and with clinicopathological variables, including poor prognosis (P < 0.0001) and high grade (P < 0.0001). In ovarian cancer cells in vitro, a small interfering RNA against HuR and leptomycin B, an inhibitor of nucleocytoplasmic translocation of HuR, inhibited COX-2 expression. Our results show that cytoplasmic HuR expression associates with poor outcome in ovarian cancer, and one plausible explanation for this finding may be related to the ability of HuR to induce COX-2 expression.