gebhart/patrepeval huggingface dataset:
Air Muscle Controller Design in the Distributed Macro-Mini (DM2) Actuation Approach (2007)

Recently, on the base of distributed macro-mini actuation approach (DM <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), a new robotic manipulator with hybrid actuation, air muscles-DC motor, has been developed. Among existing actuators, the hybrid actuation employs air muscles because they represent an advantageous tradeoff of performance and safety, due to their power/weight ratio and inherent compliance. The air muscles, however, are limited in bandwidth and their behavior is highly nonlinear. In order to overcome these limitations, the paper presents a torque control strategy based on a pair of differentially connected force-controlled air muscles. This controller was implemented and evaluated on a single joint testbed, first by itself and then as macro component into the Macro-Mini control strategy.
An Unsupervised Self-Organizing Neural Network for Automatic Semiconductor Wafer Defect Inspection (2006)

Semiconductor wafer defect inspection is an important process before die packaging. The defective regions are usually identified through visual judgment with the aid of a scanning electron microscope. Dozens of people visually check wafers and hand-mark their defective regions. By this means, potential misjudgment may be introduced due to human fatigue. In addition, the process can incur significant personnel costs. Prior work has proposed automated post-sawing wafer defect inspection that is based on supervised neural networks. Since it requires learned patterns specific to each application, its disadvantage is the lack of product flexibility. Self-Organizing Neural Networks (SONNs) have been proven to have the capabilities of unsupervised auto-clustering. In this paper, automated wafer inspection based on a self-organizing neural network is proposed. Based on real-world data, experimental results show that the proposed method successfully identifies the defective regions on wafers with good performances.
Self-Calibrating Camera-Assisted Presentation Interface (2000)

This paper presents a self-calibrating camera-assisted presentation interface that enables the user to control presentations using a laser pointer. The setup system consists of a computer connected to an LCD projector and a consumer-level digital camera aimed at the presentation screen. Although the locations, orientations and optical parameters of the camera and projector are unknown, the projector-camera calibrates itself by inferring the mapping between pixels in the camera image to pixels in the presentation slide. The camera is subsequently used to detect the position of the pointing device (such as a laser pointer dot) on the screen, allowing the laser pointer to emulate the pointing actions of a mouse. The user may then select active regions in the presentation, or even draw on the projected image. Additionally, arbitrary distortions due to projector placement are negated, allowing the projector (and camera) to be placed anywhere in the presentation room --- for instance, at the side rather than the center of the room. This solution works with standard hardware, but could easily be incorporated into the next generation of LCD projector systems.
The expanding role of aerosols in systemic drug delivery, gene therapy and vaccination: an update (2014)

Until the late 1990s, aerosol therapy consisted of beta2-adrenergic agonists, anti-cholinergics, steroidal and non-steroidal agents, mucolytics and antibiotics that were used to treat patients with asthma, COPD and cystic fibrosis. Since then, inhalation therapy has matured to include drugs that: (1) are designed to treat diseases outside the lung and whose target is the systemic circulation (systemic drug delivery); (2) deliver nucleic acids that lead to permanent expression of a gene construct, or protein coding sequence, in a population of cells (gene therapy); and (3) provide needle-free immunization against disease (aerosolized vaccination). During the evolution of these advanced applications, it was also necessary to develop new devices that provided increased dosing efficiency and less loss during delivery. This review will present an update on the success of each of these new applications and their devices. The early promise of aerosolized systemic drug delivery and its outlook for future success will be highlighted. In addition, the challenges to aerosolized gene therapy and the need for appropriate gene vectors will be discussed. Finally, progress in the development of aerosolized vaccination will be presented. The continued expansion of the role of aerosol therapy in the future will depend on: (1) improving the bioavailability of systemically delivered drugs; (2) developing gene therapy vectors that can efficiently penetrate the mucus barrier and cell membrane, navigate the cell cytoplasm and efficiently transfer DNA material to the cell nucleus; (3) improving delivery of gene vectors and vaccines to infants; and (4) developing formulations that are safe for acute and chronic administrations.
Crystallization and Preliminary X-ray Analysis of a Trimeric Form of Human Mannose Binding Protein (1994)

A trimeric form of the carbohydrate recognition domain of human mannose binding protein has been crystallized in two different forms. The first form crystallizes with symmetry consistent with space group P2(1)2(1)2(1) and a = 61 A; b = 144 A; c = 107 A with presumably two trimers in the asymmetric unit. The second form crystallizes with symmetry consistent with space group P321 and a = b = 77 A; c = 58 A and one monomer per asymmetric unit. The molecular and crystallographic 3-folds must be coincident in this crystal form.
Introducing Structural Diversity in Oligonucleotides via Photolabile, Convertible C5-Substituted Nucleotides (1999)

Chemically synthesized oligonucleotides are functionalized at defined sites while in their protected form on solid-phase supports via the incorporation of nucleotides containing masked alkyl carboxylic acids or alkylamines. The reactive functional groups are selectively revealed upon 365 nm irradiation of the appropriate o-nitrobenzyl based protecting group. For the photolabile nucleotide that reveals alkylamines, a combination of analytical methods revealed that very high yields (≥94%) of the oligonucleotide containing a single reactive functional group were obtained by using photolysis conditions that do not damage the biopolymer. Either functionalized nucleotide is efficiently coupled to the corresponding reaction partner via PyBOP mediated amide bond formation. Isolated yields of the conjugated oligonucleotides are ≥90%. This method is compatible with introducing multiple modified sites sequentially and is amenable to the synthesis of libraries of oligonucleotides in a combinatorial fashion containing nonnative nucleotides while bound to their solid supports.
Heparan sulphate proteoglycans interact with neurocan and promote neurite outgrowth from cerebellar granule cells (2004)

We found that neurocan, a major brain chondroitin sulphate proteoglycan, interacts with HSPGs (heparan sulphate proteoglycans) such as syndecan-3 and glypican-1. Binding of these HSPGs to neurocan was prevented by treatment of the HSPGs with heparitinases I and II, but not by treatment of neurocan with chondroitinase ABC. Scatchard plot analysis indicated that neurocan has two binding sites for these HSPGs with different affinities. It is known that neurocan in the rodent brain is proteolytically processed with aging into N- and C-terminal fragments. When a mixture of whole neurocan and N- and C-terminal fragments prepared from neonatal mouse brains or recombinant N- and C-terminal fragments was applied to a heparin column, the whole molecule and both the N- and C-terminal fragments bound to heparin. A centrifugation cell adhesion assay indicated that both the N- and C-terminal neurocan fragments could interact with these HSPGs expressed on the cell surface. To examine the biological significance of the HSPG-neurocan interaction, cerebellar granule cells expressing these HSPGs were cultured on the recombinant neurocan substrate. A significant increase in the rate of neurite outgrowth was observed on the wells coated with the C-terminal neurocan fragment, but not with the N-terminal one. Neurite outgrowth-promoting activity was inhibited by pretreatment of neurocan substrate with heparin or the addition of heparitinase I to culture medium. These results suggest that HSPGs such as syndecan-3 and glypican-1 serve as the cell-surface receptor of neurocan, and that the interaction of these HSPGs with neurocan through its C-terminal domain is involved in the promotion of neurite outgrowth.
The human kidney low affinity Na+/glucose cotransporter SGLT2. Delineation of the major renal reabsorptive mechanism for D-glucose. (1994)

The major reabsorptive mechanism for D-glucose in the kidney is known to involve a low affinity high capacity Na+/glucose cotransporter, which is located in the early proximal convoluted tubule segment S1, and which has a Na+ to glucose coupling ratio of 1:1. Here we provide the first molecular evidence for this renal D-glucose reabsorptive mechanism. We report the characterization of a previously cloned human kidney cDNA that codes for a protein with 59% identity to the high affinity Na+/glucose cotransporter (SGLT1). Using expression studies with Xenopus laevis oocytes we demonstrate that this protein (termed SGLT2) mediates saturable Na(+)-dependent and phlorizin-sensitive transport of D-glucose and alpha-methyl-D-glucopyranoside (alpha MeGlc) with Km values of 1.6 mM for alpha MeGlc and approximately 250 to 300 mM for Na+, consistent with low affinity Na+/glucose cotransport. In contrast to SGLT1, SGLT2 does not transport D-galactose. By comparing the initial rate of [14C]-alpha MeGlc uptake with the Na(+)-influx calculated from alpha MeGlc-evoked inward currents, we show that the Na+ to glucose coupling ratio of SGLT2 is 1:1. Using combined in situ hybridization and immunocytochemistry with tubule segment specific marker antibodies, we demonstrate an extremely high level of SGLT2 message in proximal tubule S1 segments. This level of expression was also evident on Northern blots and likely confers the high capacity of this glucose transport system. We conclude that SGLT2 has properties characteristic of the renal low affinity high capacity Na+/glucose cotransporter as previously reported for perfused tubule preparations and brush border membrane vesicles. Knowledge of the structural and functional properties of this major renal Na+/glucose reabsorptive mechanism will advance our understanding of the pathophysiology of renal diseases such as familial renal glycosuria and diabetic renal disorders.
Hypothyroidism Impairs Colonic Motility and Function. An Experimental Study in the Rat (1992)

Hypothyroidism (HT) may be associated with either megacolon or severe constipation that mimics Hirschsprung's disease. The exact nature of this relationship is unclear. This report evaluates colonic motility in experimental HT. HT was produced by a total thyroidectomy in 20 male Sprague-Dawley rats (200-300 g). Ten of the HT rats were given thyroxin (30 micrograms/kg/day i.p. for 4 weeks) for a replacement study (RS). Ten sham operated rats (SH) and 50 unoperated rats (UN) were studied as controls. HT was documented at 4 weeks following total thyroidectomy by measuring serum T3, T4 uptake, and TSH. At four to 6 weeks the animals were evaluated for several studies concerning colonic motility. Normal weight gain was significantly impaired under HT. In addition, daily stool volume as well as the number of fecal pellets were significantly reduced in HT. A barium enema showed a dilated colon in HT with an increase of recto-colonic ratio. Anal canal pressure was relatively low in HT. HT rats had a decreased frequency of rhythmic colonic activity (cycle/min) (HT: 10.22 +/- 2.16 vs. UN: 18.09 +/- 4.79, SH: 15.88 +/- 3.92, p less than 0.001). RS rats showed a recovery of rhythmic frequency (15.56 +/- 4.46, p less than 0.001). A positive recto-anal reflex was seen in all UN and SH rats, but only 40% in HT and 80% in RS. The effect of isoproterenol on anal canal pressure was significantly less in HT. Colonic transit at 4 hours was considerably slower in HT (HT: 29.0 +/- 21.0% vs. US: 60.4 +/- 18.3%, SH: 58.7 +/- 14.8%, p less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and opioid antagonist potencies of naltrexamine bivalent ligands with conformationally restricted spacers (1986)

Bivalent ligands 1-4 with naltrexamine pharmacophores and spacers of different lengths containing a fumaryl moiety were synthesized and evaluated for mu and kappa opioid antagonist activity on the electrically stimulated guinea pig ileal longitudinal muscle (GPI). The fumaryl moiety was incorporated into the spacer in order to determine the effect of conformational restriction of the spacer on the relationship between spacer length and opioid antagonist potency. While it was found that the fumaryl and succinyl series (11) possessed a very similar structure-potency profile with respect to antagonism at mu opioid receptors, the interaction of these two series at kappa receptors differed substantially from one another. This difference was manifested by the longer spacer requirement for peak kappa antagonist potency in the fumaryl relative to the succinyl series. It is concluded that the conformational restriction imposed by the fumaryl group in a short spacer (n = 0) prevents effective interaction of both pharmacophores with vicinal recognition sites of the kappa receptor system; as the spacer is lengthened (n = 2) and becomes more flexible, the simultaneous occupation of vicinal recognition sites occurs with greater facility.
The Best of Both Worlds: Combining Ranked List and Clustering, (1999)

Abstract : An information retrieval system arranges retrieved documents into a list and ranks them in the order they are expected to be relevant. The ranked list is a well-known and widely accepted technique for information presentation for the task of finding relevant documents as quick as possible. Clustering is also a well-known and successful method for grouping similar documents together - in particular, for grouping relevant documents. In this paper we present a system that combines the ranked list with a clustering approach, accepts a modest amount of user feedback, and yields an approach that exceeds the retrieval effectiveness of a traditional ranked list, with and without relevance feedback.
Bovine Papilloma Virus Transcription: Polyadenylated RNA Species and Assessment of the Direction of Transcription (1982)

The bovine papilloma virus type 1 (BPV-1)-specific RNA species were identified in virus-induced bovine warts, hamster tumors, and transformed hamster and mouse cells. In each case two major species were present (1.1 and 1.3 kilobases [kb]). Also two species of 1.6 and 1.8 kb appearing in variable amounts were found. Only in the keratinized periphery of the warts, where virus replication takes place, was it possible to reveal an additional 2-kb RNA species. In this tissue, however, the 1.6-kb species was not detected. The basal part of a bovine wart contained an additional minor, 2.9-kb, BPV-1-specific RNA sequence. By hybridization with purified defined BPV-1 DNA fragments it was shown that most of the coding sequences of the 2-kb species were transcribed from a region between 0.02 and 0.19 map units. The majority of the coding sequences of the smaller species in transformed cells were located in the region between 0.31 and 0.61 map units. The putative 5' ends mapped between 0.72 and 0.96 map units. Oligodeoxythymidylic acid-primed [(32)P]cDNA was synthesized from various RNA preparations to generate probes for the detection of 3' termini of the polyadenylated BPV-1 RNAs. By hybridization across the BPV-1 genome only one signal between the map positions 0.30 and 0.40 was obtained when RNA from transformed cells and from a tumor was used as a template. In contrast, RNA from the periphery of a wart led to the detection of an additional signal which was confined to the region between 0.96 and 1.00 map units. From the arrangement of both the 3' termini and the coding areas along the viral genome it appears that several RNA species are transcribed from one DNA strand.
Reduction of GnRH and infertility in the R6/2 mouse model of Huntington's disease (2005)

Reductions in testosterone and luteinizing hormone levels and reduced sexual functions have been reported in Huntington's disease (HD) patients. Atrophy of the reproductive organs and loss of fertility have also been observed in the R6/2 mouse, which is currently the most studied transgenic model of HD. In an effort to define the cause of infertility we studied the expression of gonadotropin-releasing hormone (GnRH) in the medial septum, diagonal band of Broca and hypothalamus of R6/2 male mice during sexual maturation. We found a progressive reduction in the numbers of GnRH-immunoreactive neurons in the analysed brain areas of R6/2 mice starting at 5 weeks of age and becoming statistically significant with only 10% of the neurons remaining by 9 weeks of age. Atrophy of testes and seminal vesicles combined with a significant reduction in serum and testicular testosterone levels were detected in 12-week-old R6/2mice. These results suggest that infertility in the R6/2 males is due either to death of GnRH neurons or to a reduction in GnRH expression leading to a downstream impairment of the gonadotropic hormones. Gonadotropic hormone replacement did not mitigate weight loss or restore motor function in R6/2 males.
Analysis of afferent, central, and efferent components of the baroreceptor reflex in mice (2002)

Studies of genetically modified mice provide a powerful approach to investigate consequences of altered gene expression in physiological and pathological states. The goal of the present study was to characterize afferent, central, and efferent components of the baroreceptor reflex in anesthetized Webster 4 mice. Baroreflex and baroreceptor afferent functions were characterized by measuring changes in renal sympathetic nerve activity (RSNA) and aortic depressor nerve activity (ADNA) in response to nitroprusside- and phenylephrine-induced changes in arterial pressure. The data were fit to a sigmoidal logistic function curve. Baroreflex diastolic pressure threshold (P(th)), the pressure at 50% inhibition of RSNA (P(mid)), and baroreflex gain (maximum slope) averaged 74 +/- 5 mmHg, 101 +/- 3 mmHg, and 2.30 +/- 0.54%/mmHg, respectively (n = 6). The P(th), P(mid), and gain for the diastolic pressure-ADNA relation (baroreceptor afferents) were similar to that observed for the overall reflex averaging 79 +/- 9 mmHg, 101 +/- 4 mmHg, and 2.92 +/- 0.53%/mmHg, respectively (n = 5). The central nervous system mediation of the baroreflex and the chronotropic responsiveness of the heart to vagal efferent activity were independently assessed by recording responses to electrical stimulation of the left ADN and the peripheral end of the right vagus nerve, respectively. Both ADN and vagal efferent stimulation induced frequency-dependent decreases in heart rate and arterial pressure. The heart rate response to ADN stimulation was nearly abolished in mice anesthetized with pentobarbital sodium (n = 4) compared with mice anesthetized with ketamine-acepromazine (n = 4), whereas the response to vagal efferent stimulation was equivalent under both types of anesthesia. Application of these techniques to studies of genetically manipulated mice can be used to identify molecular mechanisms of baroreflex function and to localize altered function to afferent, central, or efferent sites.
Role of Zymogen and Activated Factor X as Scaffolds for the Inhibition of the Blood Coagulation Factor VIIa-Tissue Factor Complex by Recombinant Nematode Anticoagulant Protein c2 (2001)

Recombinant nematode anticoagulant protein c2 (rNAPc2) is a potent, factor Xa (fXa)-dependent small protein inhibitor of factor VIIa-tissue factor (fVIIa.TF), which binds to a site on fXa that is distinct from the catalytic center (exo-site). In the present study, the role of other fX derivatives in presenting rNAPc2 to fVIIa.TF is investigated. Catalytically active and active site blocked fXa, as well as a plasma-derived and an activation-resistant mutant of zymogen fX bound to rNAPc2 with comparable affinities (K(D) = 1-10 nm), and similarly supported the inhibition of fVIIa.TF (K(i)* = approximately 10 pm). The roles of phospholipid membrane composition in the inhibition of fVIIa.TF by rNAPc2 were investigated using TF that was either detergent-solubilized (TF(S)), or reconstituted into membranes, containing phosphatidylcholine (TF(PC)) or a mixture of phosphatidylcholine and phosphatidylserine (TF(PCPS)). In the absence of the fX derivative, inhibition of fVIIa.TF was similar for all three conditions (K(i) approximately 1 microm), whereas the addition of the fX derivative increased the respective inhibition by 35-, 150-, or 100,000-fold for TF(S), TF(PC), and TF(PCPS). The removal of the gamma-carboxyglutamic acid-containing domain from the fX derivative did not affect the binding to rNAPc2, but abolished the effect of factor Xa as a scaffold for the inhibition of fVIIa.TF by rNAPc2. The overall anticoagulant potency of rNAPc2, therefore, results from a coordinated recognition of an exo-site on fX/fXa and of the active site of fVIIa, both of which are properly positioned in the ternary fVIIa.TF.fX(a) complex assembled on an appropriate phospholipid surface.
Complete Genomic Sequence and Comparative Analysis ofthe Tumorigenic Poxvirus Yaba Monkey TumorVirus (2003)

The Yatapoxvirus genus of poxviruses is comprised of Yaba monkey tumor virus (YMTV), Tanapox virus, and Yaba-like disease virus (YLDV), which all have the ability to infect primates, including humans. Unlike other poxviruses, YMTV induces formation of focalized histiocytomas upon infection. To gain a greater understanding of the Yatapoxvirus genus and the unique tumor formation properties of YMTV, we sequenced the 134,721-bp genome of YMTV. The genome of YMTV encodes at least 140 open reading frames, all of which are also found as orthologs in the closely related YLDV. However, 13 open reading frames found in YLDV are completely absent from YMTV. Common to both YLDV and YMTV are the unusually large noncoding regions between many open reading frames. To determine whether any of these noncoding regions might be functionally significant, we carried out a comparative analysis between the putative noncoding regions of YMTV and similar noncoding regions from other poxviruses. This approach identified three new gene poxvirus families, defined as orthologs of YMTV23.5L, YMTV28.5L, and YMTV120.5L, which are highly conserved in virtually all poxvirus species. Furthermore, the comparative analysis also revealed a 40-bp nucleotide sequence at approximately 14,700 bases from the left terminus that was 100% identical in the comparable intergene site within members of the Yatapoxvirus, Suipoxvirus, and Capripoxvirus genera and 95% conserved in the Leporipoxvirus genus. This conserved sequence was shown to function as a poxvirus late promoter element in transfected and infected cells, but other functions, such as an involvement in viral replication or packaging, cannot be excluded. Finally, we summarize the predicted immunomodulatory protein repertoire in the Yatapoxvirus genus as a whole.