gebhart/patrepeval huggingface dataset:
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes (2007)

We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices. MAKER is also easily trainable: Outputs of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs. MAKER's inputs are minimal, and its outputs can be used to create a GMOD database. Its outputs can also be viewed in the Apollo Genome browser; this feature of MAKER provides an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database. As proof of principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We have also compared MAKER's performance to other published annotation pipelines. Our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging model organism genome projects for which extensive bioinformatics resources may not be readily available.
Molecular signaling in death receptor and mitochondrial pathways of apoptosis (Review) (2003)

In recent years major progress has been made in understanding the molecular steps of death receptor and mitochondrial pathway of apoptosis. Mechanisms of NF-kappaB-mediated survival (anti-apoptotic) signal have been delineated. A novel anti-apoptotic mechanism of FLIP in the recruitment of RIP and TRAF-1 and TRAF-2 to activate ERK and NF-kappaB has been defined. These are some of the recent discoveries in death receptor and mitochondrial pathways of apoptosis that have been reviewed in this article.
Biomimetic Design of an Under-Actuated Leg Exoskeleton for Load-Carrying Augmentation (2006)

Metabolic studies have shown that there is a metabolic cost associated with carrying a load. Previous work on exoskeleton design has not considered the passive dynamics of walking and has focused on fully actuated systems that are inefficient and heavy. In this thesis, an underactuated exoskeleton is presented that runs parallel to the human leg. The exoskeleton component design is based on the kinematics and kinetics of human walking. The joint components of the exoskeleton in the sagittal plane consist of a force-controllable actuator at the hip, a variable-damper mechanism at the knee, and a passive spring at the ankle. A state-machine control strategy is written based on joint angle and ground-exoskeleton force sensing. Positive non-conservative power is added at the hip during the walking cycle to help propel the mass of the human and payload forward. At the knee, the damper mechanism is turned on at heel strike as the exoskeleton leg is loaded and turned off during terminal stance to allow knee flexion. The spring at the ankle engages in controlled dorsiflexion to store energy that is later released to assist in powered plantarflexion. Kinetic and metabolic data are recorded from human subjects wearing the exoskeleton with a 75 lb. payload. These data are compared to data recorded from subjects walking without the exoskeleton. It is demonstrated that the exoskeleton transfers loads to the ground with a 90% and higher load transfer depending on the phase of gait. Further exoskeleton wearers report that the exoskeleton greatly reduces the stress on the shoulders and back. However, although a significant fraction of the payload is transferred through the exoskeleton structure, the exoskeleton is found to increase metabolic economy by 74%. By comparing distinct exoskeleton configurations, the relative effect of each exoskeleton component is determined.
Approaches to determine stoichiometry of viral assembly components (1997)

Due to the rapidity of biological reactions, it is difficult to isolate intermediates or to determine the stoichiometry of participants in intermediate reactions. Instead of determining the absolute amount of each component, this study involved the use of relative parameters, such as dilution factors, percentages probabilities, and slopes of titration curves, that can be more accurately quantified to determine the stoichiometry of components involved in bacteriophage phi29 assembly. This work takes advantage of the sensitive in vitro phage phi29 assembly system, in which 10(8) infectious virions per ml without background can be assembled from eight purified components. It provides a convenient assay for quantification of the stoichiometry of packaging components, including the viral procapsid, genomic DNA, DNA-packaging pRNA, and other structural proteins and enzymes. The presence of a procapsid binding domain and another essential functional domain within the pRNA makes it an ideal component for constructing lethal mutants for competitive procapsid binding. Two methods were used for stoichiometry determination. Method 1 was to determine the combination probability of mutant and wild-type pRNAs bound to procapsids. The probability of procapsids that possess a certain amount of mutant and a certain amount of wild-type pRNA, both with an equal binding affinity, was predicted with the binomial equation [EQUATION IN TEXT] where Z is the total number of pRNAs per procapsid, M is the number of mutant pRNAs bound to one procapsid, and (ZM) is equal to [FORMULA IN TEXT]. With various ratios of mutant to wild-type pRNA in in vitro viral assembly, the percent mutant pRNA versus the yield of virions was plotted and compared to a series of predicted curves to find a best fit. It was determined that five or six copies of pRNA were required for one DNA-packaging event, while only one mutant pRNA per procapsid was sufficient to block packaging. Method 2 involved the comparison of slopes of curves of dilution factors versus the yield of virions. Components with known stoichiometries served as standard controls. The larger the stoichiometry of the component, the more dramatic the influence of the dilution factor on the reaction. A slope of 1 indicates that one copy of the component is involved in the assembly of one virion. A slope larger than 1 would indicate multiple-copy involvement. By this method, the stoichiometry of gp11 in phi29 particles was determined to be approximately 12. These approaches are useful for the determination of the stoichiometry of functional units involved in viral assembly, be they single molecules or oligomers. However, these approaches are not suitable for the determination of exact copy numbers of individual molecules involved if the functional unit is composed of multiple subunits prior to assembly.
Protein Import into Peroxisomes and Biogenesis of the Organelle (1993)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Vision of the unseen (2011)

Digital images are everywhere—from our cell phones to the pages of our online news sites. How we choose to use digital image processing raises a surprising host of legal and ethical questions that we must address. What are the ramifications of hiding data within an innocent image? Is this an intentional security practice when used legitimately, or intentional deception? Is tampering with an image appropriate in cases where the image might affect public behavior? Does an image represent a crime, or is it simply a representation of a scene that has never existed? Before action can even be taken on the basis of a questionable image, we must detect something about the image itself. Investigators from a diverse set of fields require the best possible tools to tackle the challenges presented by the malicious use of today's digital image processing techniques. In this survey, we introduce the emerging field of digital image forensics, including the main topic areas of source camera identification, forgery detection, and steganalysis. In source camera identification, we seek to identify the particular model of a camera, or the exact camera, that produced an image. Forgery detection's goal is to establish the authenticity of an image, or to expose any potential tampering the image might have undergone. With steganalysis, the detection of hidden data within an image is performed, with a possible attempt to recover any detected data. Each of these components of digital image forensics is described in detail, along with a critical analysis of the state of the art, and recommendations for the direction of future research.
Dwarfism and early death in mice lacking C-type natriuretic peptide (2001)

Longitudinal bone growth is determined by endochondral ossification that occurs as chondrocytes in the cartilaginous growth plate undergo proliferation, hypertrophy, cell death, and osteoblastic replacement. The natriuretic peptide family consists of three structurally related endogenous ligands, atrial, brain, and C-type natriuretic peptides (ANP, BNP, and CNP), and is thought to be involved in a variety of homeostatic processes. To investigate the physiological significance of CNP in vivo, we generated mice with targeted disruption of CNP (Nppc(-/-) mice). The Nppc(-/-) mice show severe dwarfism as a result of impaired endochondral ossification. They are all viable perinatally, but less than half can survive during postnatal development. The skeletal phenotypes are histologically similar to those seen in patients with achondroplasia, the most common genetic form of human dwarfism. Targeted expression of CNP in the growth plate chondrocytes can rescue the skeletal defect of Nppc(-/-) mice and allow their prolonged survival. This study demonstrates that CNP acts locally as a positive regulator of endochondral ossification in vivo and suggests its pathophysiological and therapeutic implication in some forms of skeletal dysplasia.
Anti-IL-4 treatment of Schistosoma mansoni -infected mice inhibits development of T cells and non-B, non-T cells expressing Th2 cytokines while decreasing egg-induced hepatic fibrosis. (1994)

Increasing evidence suggests that schistosome egg granulomas are primarily Th2 cellular reactions. Mice infected with Schistosoma mansoni were treated with a neutralizing mAb against IL-4 to evaluate the role of this cytokine in the generation of parasite egg-induced cell-mediated responses and hepatic pathology. Animals treated with anti-IL-4 before egg deposition showed decreased IL-4, IL-5, and IL-10 production in response to in vitro antigenic stimulations and decreased IL-5 and IL-13 mRNA levels in the liver. As observed previously, non-B, non-T cells were a major source of IL-4 in infected mice treated with control mAb, and the diminished IL-4 response in anti-IL-4-treated animals was shown to be caused at least in part by a reduction in the number of these cells, as well as by decreased secretion of IL-4 per cell. In contrast, production of the Th1 cytokines IL-2 and IFN-gamma was elevated in anti-IL-4-treated infected mice in vitro, and the corresponding mRNAs in the liver were increased. Anti-IL-4 treatment did not consistently reduce the size of hepatic granulomas around S. mansoni eggs, but markedly inhibited granuloma formation in the lungs of the same animals after i.v. egg injection. Nevertheless, anti-IL-4-treated infected mice showed consistent and marked reductions in hepatic collagen deposition. These findings indicate that IL-4 plays a major role in the development of the Th2 response in S. mansoni-infected mice and contributes to the pathogenesis of hepatic fibrosis.
Temporally-controlled site-specific mutagenesis in the basal layer of the epidermis: comparison of the recombinase activity of the tamoxifen-inducible Cre-ERT and Cre-ERT2 recombinases (1999)

Conditional DNA excision between two LoxP sites can be achieved in the mouse using Cre-ER(T), a fusion protein between a mutated ligand binding domain of the human estrogen receptor (ER) and the Cre recombinase, the activity of which can be induced by 4-hydroxy-tamoxifen (OHT), but not natural ER ligands. We have recently characterized a new ligand-dependent recombinase, Cre-ER(T2), which was approximately 4-fold more efficiently induced by OHT than Cre-ER(T) in cultured cells. In order to compare the in vivo efficiency of these two ligand-inducible recombinases to generate temporally-controlled somatic mutations, we have engineered transgenic mice expressing a LoxP-flanked (floxed) transgene reporter and either Cre-ER(T) or Cre-ER(T2) under the control of the bovine keratin 5 promoter that is specifically active in the epidermis basal cell layer. No background recombinase activity could be detected, while recombination was induced in basal keratinocytes upon OHT administration. Interestingly, a dose-response study showed that Cre-ER(T2) was approximately 10-fold more sensitive to OHT induction than Cre-ER(T).
Early, patient-initiated treatment of herpes labialis with topical 10% acyclovir (1984)

To determine whether topical acyclovir in polyethylene glycol could reduce the severity of herpes simplex labialis if applied immediately after onset of a recurrence, 10% acyclovir in polyethylene glycol ointment or polyethylene glycol alone was prospectively dispensed to 352 patients in a double-blind, randomized trial. Sixty-nine subjects initiated treatment in the prodrome (57%) or erythema (43%) stage and were followed by clinical and virological criteria. The healing time (6.0 days), maximum lesion area (42 mm2), vesicle or ulcer formation (91%), and maximum lesion virus titer (4.8 log10 PFU) in the drug recipients were not reduced in comparison with those who received the vehicle (5.2 days, 30 mm2, 75%, and 4.5 log10 PFU, respectively). Topical acyclovir in polyethylene glycol was ineffective for the treatment of herpes labialis despite an optimum therapeutic opportunity.
Solubilization of beclomethasone dipropionate in sterically stabilized phospholipid nanomicelles (SSMs): physicochemical and in vitro evaluations (2012)

The SSM system might be an effective way of improving the therapeutic index of nebulized, poorly soluble corticosteroids.
Hydraulic Fracture Crossing Natural Fracture at Non-orthogonal Angles, A Criterion, Its Validation and Applications (2011)

Abstract Hydraulic fracturing treatments have become an indispensable part of well completion in shale gas field development. Shale formations often contain natural fractures and complex hydraulic fracture networks may form during a treatment. The complex fracture network is strongly influenced by the interaction between the hydraulic fracture and the pre-existing natural fractures. A criterion has been developed to determine whether a fracture crosses a frictional interface (pre-existing fracture) at non-orthogonal angles. This criterion is an extension of the one for orthogonal crossing originally developed by Renshaw and Pollard (1995). The dependence of crossing on the intersection angle is shown quantitatively using the extended criterion. The fracture is more likely to turn and propagate along the interface than to cross it when the angle is less than 90°. The validation of the criterion using laboratory experiments for various angles is described and discussed. When applied to laboratory experiments, good agreement between the criterion and experiments is observed for a wide range of angles. The criterion can be used to determine whether hydraulic fractures cross natural fractures under particular field conditions, and it has been incorporated in a hydraulic fracture model that simulates hydraulic fracture propagation in a natural fractured formation.
Evaluation of postoperative bupivacaine infusion for pain management after anterior cruciate ligament reconstruction (2003)

The data suggest some element of placebo benefit at median pain ratings but a protective effect of the bupivacaine at maximum pain levels.
Ovarian cancer: overview (2003)

The author overviews developments in the management of ovarian cancer and research efforts in Australia. (non-author abstract)
Correction: Spatial Distribution and Interspecific Associations of Tree Species in a Tropical Seasonal Rain Forest of China (2012)

Studying the spatial pattern and interspecific associations of plant species may provide valuable insights into processes and mechanisms that maintain species coexistence. Point pattern analysis was used to analyze the spatial distribution patterns of twenty dominant tree species, their interspecific spatial associations and changes across life stages in a 20-ha permanent plot of seasonal tropical rainforest in Xishuangbanna, China, to test mechanisms maintaining species coexistence. Torustranslation tests were used to quantify positive or negative associations of the species to topographic habitats. The results showed: (1) fourteen of the twenty tree species were negatively (or positively) associated with one or two of the topographic variables, which evidences that the niche contributes to the spatial pattern of these species. (2) Most saplings of the study species showed a significantly clumped distribution at small scales (0-10 m) which was lost at larger scales (10-30 m). ( (4) It is notable that a high number of positive small-scale interactions were found among the twenty species. For saplings, 42.6% of all combinations of species pairs showed positive associations at neighborhood scales up to five meters, but only 38.4% were negative. For poles and adults, positive associations at these distances still made up 45.5% and 29.5%, respectively. In conclusion, there is considerable evidence for the presence of positive interactions among the tree species, which suggests that species herd protection may occur in our plot. In addition, niche assembly and limited dispersal (likely) contribute to the spatial patterns of tree species in the tropical seasonal rain forest in Xishuangbanna, China.
Channel and source/drain engineering in high-performance sub-0.1 μm NMOSFETs using X-ray lithography (2002)

Channel lengths are continually scaled to smaller dimensions to improve performance and packing density. In recent years this has led to demonstrations of MOSFETs with effective channel length of 0.1 /spl mu/m and below. The key technology challenges at these linewidths include the lithography to reproducibly achieve fine dimensions, source and drain engineering to reduce device parasitics, and channel engineering to control short-channel effects. In this work, we demonstrate a high-performance NMOS technology that utilizes X-ray lithography to achieve channel lengths below 0.1 /spl mu/m; a novel cobalt salicidation (CoSi/sub 2/) technique using a titanium/cobalt laminate to achieve very low parasitic source/drain resistance; and shallow junctions and an optimized super-steep retrograde (SSR) channel profile to achieve very high transconductance devices with excellent control of short-channel effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Music and emotion: Electrophysiological correlates of the processing of pleasant and unpleasant music (2007)

Human emotion and its electrophysiological correlates are still poorly understood. The present study examined whether the valence of perceived emotions would differentially influence EEG power spectra and heart rate (HR). Pleasant and unpleasant emotions were induced by consonant and dissonant music. Unpleasant (compared to pleasant) music evoked a significant decrease of HR, replicating the pattern of HR responses previously described for the processing of emotional pictures, sounds, and films. In the EEG, pleasant (contrasted to unpleasant) music was associated with an increase of frontal midline (Fm) theta power. This effect is taken to reflect emotional processing in close interaction with attentional functions. These findings show that Fm theta is modulated by emotion more strongly than previously believed.
1,5-, 2,6- and 9,10-distyrylanthracenes as luminescent organic semiconductors (2013)

We report the synthesis, molecular and crystal structures, optoelectronic properties and organic field-effect transistor (OFET) studies of three isomeric distyrylanthracene derivatives 2,6-DPSAnt, 1,5-DPSAnt and 9,10-DPSAnt. The analysis of the structure–property relationships reveals that π-conjugation in this series is defined by two competing factors: the co-planarity of the styryl substituents (highest in 2,6-DPSAnt) and the electronic communication through the anthracene core (strongest in 9,10-DPSAnt). The charge-transport properties of the compounds, on the other hand, are primarily controlled by the solid state packing which is more efficient for the linear 2,6-DPSAnt derivative. Accordingly, the highest field-effect mobility (up to 0.75 cm2 V−1 s−1) was measured for 2,6-DPSAnt. Unexpectedly high charge mobility of 1,5-DPSAnt (up to 0.15 cm2 V−1 s−1) was attributed to excellent thin-film morphology (nearly layer-by-layer growth) and favorable molecular packing in the films, different from that found in single crystals. Unfavorable molecular packing and poor film morphology observed for 9,10-DPSAnt predictably led to no transistor properties being observed for this isomer. Both 2,6-DPSAnt and 1,5-DPSAnt afforded light-emitting transistors with green light emission area localized near an electron-injecting electrode.
Purification of Cranin, a Laminin Binding Membrane Protein (1995)

Cranin was described in 1987 as a membrane glycoprotein expressed in brain and many other tissues, which binds laminin with high affinity in a calcium-dependent manner. Dystrophin-associated glycoprotein ("dystroglycan") is a laminin-binding protein cloned in 1992 whose relation to cranin has remained uncertain. Here we describe the purification of cranin to homogeneity from sheep brain, show cranin to be a form of dystroglycan, and localize the N terminus of beta-dystroglycan to amino acid residue 654. We find that brain alpha-dystroglycan is tightly associated with membranes, and localizes to regions of synaptic contact as assessed by immunocytochemistry of rat cerebellum. Brain alpha-dystroglycan expresses high mannose/hybrid N-linked saccharides, terminal GalNAc residues, and the HNK-1 epitope. Although dystroglycan has previously been presumed to be a proteoglycan, the amino acid sequence, pI, O-sialoglycoprotease susceptibility, lectin-binding profile, and laminin-binding properties of brain dystroglycan are more typical of mucin-like proteins. Furthermore, using CHO mutant cell lines deficient in xylosyltransferase and galactosyltransferase I, which are required for glycosaminoglycan biosynthesis, it is shown that chondroitin sulfate and heparan sulfate are not critical for laminin binding, and indeed are apparently not expressed at all in dystroglycan from CHO cells.
Poly(ADP-ribose) polymerase inhibitors in Ewing sarcoma (2014)

Despite initial excitement for the potential of PARPi as single agent therapy in Ewing sarcoma, the emerging preclinical data now strongly support testing PARPi in combination with chemo/radiotherapy clinically.