gebhart/patrepeval huggingface dataset:
Encoded Microcarriers For High‐Throughput Multiplexed Detection (2006)

Since the decoding of the human genome, the quest to obtain more and more molecular information from smaller and smaller samples is intensifying. Today the burden of this challenge is being borne by planar arrays, but the quality of the data provided by this approach is limited by variations in performance between different arrays. Suspension arrays of encoded microspheres provide higher quality data, but the amount of molecular information that can be acquired with them is limited by the number of codes that can be distinguished in the same sample. New methods of preparing encoded particles promise to alleviate this problem, but in the face of a growing number of new technologies it is sometimes difficult to decide which, if any, will succeed. Herein we appraise these new forms of encoded particle critically, and ask if they can deliver the necessary multiplexing power and whether they will perform well in multiplexed assays.
Prevention of Anastomotic Thrombosis by Botulinum Toxin A in an Animal Model (2008)

Botulinum toxin type A was successful in preventing thrombosis within this model. Its ability to decrease vasospasm and thrombosis may have applications for improving free flap survival in select patients.
Solubilization of the platelet plasma membrane serotonin transporter in an active form. (1980)

The activity of the serotonin transporter of platelet plasma membrane may be assessed by its ability to bind [N-methyl-3H]imipramine, even in the presence of detergents which disrupt the membrane and inactivate serotonin transport. Of the 21 detergents which were tested for their ability to solubilize the transporter in an active form, some, such as Triton X-100, inactivate imipramine-binding activity in a manner which is difficult or impossible to reverse, while inactivation by others, such as cholate, is readily reversed by gel filtration. Of the detergents which do not inactivate imipramine binding, most, such as the Tween series, also fail to solubilize significant amounts of the transporter. Of all the detergents tested, only one, digitonin, solubilized specific imipramine-binding activity. Imipramine binds to the digitonin-solubilized transporter with slightly reduced affinity, but in all other respects binding to intact and digitonin-solubilized membranes is identical. Thus, binding is, in both cases, saturable and Na+-dependent, and is reversed by serotonin. Furthermore, inhibitors of serotonin transport but not of serotonin-mediated platelet aggregation block imipramine binding to the soluble preparation. Sodium-dependent binding to the soluble extract is insensitive to K+, suggesting that separate sites on the serotonin transporter mediate the effects of effects of Na+ and K+.
Design Optimization of a Cartesian Parallel Manipulator (2003)

This paper introduces a 3-DOF translational parallel manipulator called Cartesian Parallel Manipulator (CPM). The manipulator consists of a moving platform that is connected to a fixed base by three limbs. Each limb is made up of one prismatic and three revolute joints and all joint axes are parallel to one another. In this way, each limb provides two rotational constraints to the moving platform and the combined effects of the three limbs lead to an over-constrained mechanism with three translational degrees of freedom. The manipulator behaves like a conventional X-Y-Z Cartesian machine due to the orthogonal arrangement of the three limbs. Two actuation methods are analyzed. However, the rotary actuation method is discarded because of the existence of singularities within the workspace. For the linear actuation method, there exists a one-to-one correspondence between the input and output displacements of the manipulator. The effects of misalignment of linear actuators on the motion of the moving platform are discussed. Each limb structure is exposed to a bending moment induced by external forces exerted on the moving platform. In order to minimize the deflection at the joints caused by the bending moment, a method to maximize the stiffness is suggested. A numerical example of the optimal design is presented.
Steady-State Throughput and Scheduling Analysis of Multicluster Tools: A Decomposition Approach (2008)

Cluster tools are widely used as semiconductor manufacturing equipment. While throughput analysis and scheduling of single-cluster tools have been well-studied, research work on multicluster tools is still at an early stage. In this paper, we analyze steady-state throughput and scheduling of multicluster tools. We consider the case where all wafers follow the same visit flow within a multicluster tool. We propose a decomposition method that reduces a multicluster tool problem to multiple independent single-cluster tool problems. We then apply the existing and extended results of throughput and scheduling analysis for each single-cluster tool. Computation of lower-bound cycle time (fundamental period) is presented. Optimality conditions and robot schedules that realize such lower-bound values are then provided using ldquopullrdquo and ldquoswaprdquo strategies for single-blade and double-blade robots, respectively. For an -cluster tool, we present lower-bound cycle time computation and robot scheduling algorithms. The impact of buffer/process modules on throughput and robot schedules is also studied. A chemical vapor deposition tool is used as an example of multicluster tools to illustrate the decomposition method and algorithms. The numerical and experimental results demonstrate that the proposed decomposition approach provides a powerful method to analyze the throughput and robot schedules of multicluster tools.
APPENDIX A The SV40 Nucleotide Sequence (1980)

The SV system is based on the SV40 DNA sequence reported by Fiers et al. (1978), with further corrections as modifed by Fiers (van Heuverswyn and Fiers 1979). The sequence therefore contains 5243 nucleotides. In agreement with Fiers et al. (1978), the 27-base palindrome at the Bgl I recognition site is taken as the reference origin of the SV system. The centermost nucleotide in the palindrome is defined as nucleotide 0/5243. The entire genome is numbered in a clockwise sense from the reference origin, from nucleotide 1 to nucleotide 5243 (5′ – 3′). This clockwise sense is the same sense as the Eco RI map unit direction, as the Weissman sequence (Reddy et al. 1978b), and as the late RNA sense only of the Fiers sequence. Fiers’ suggestion of providing a separate additional numbering system in the sense of the early RNA is not adopted here. The nucleotide sequence of the strand in the sense of the late and early RNAs is presented in Sections 1 and 2, respectively. Additional data about nucleotide and dinucleotide frequencies accompany each sequence 3. Conversion between the SV Numbering System and Coordinates Used by Others We introduce the following abbreviations: SV = SV numbering FE = Fiers “early sense” numbers (Fiers et al. 1978) FL = Fiers “late sense” numbers (Fiers et al. 1978) mu = Eco RI map units W = Weissman numbers (Reddy et al. 1978) Due to numerous differences between the original Fiers and Weissman sequences and the one used here, conversion between the three...
Identification of hemoglobin‐α and ‐β subunits as potential serum biomarkers for the diagnosis and prognosis of ovarian cancer (2005)

The development of new biomarkers for ovarian cancer is clearly necessary for the improved detection and monitoring of the disease. Surface enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF-MS) can be employed in the identification of differentially expressed proteins in cancer cells. The objective of this study was, then, to identify potential diagnostic serological biomarkers for ovarian cancer. We performed protein expression difference analyses of 45 serum samples using SELDI protein chip array. Forty-five sera obtained from ovarian cancer patients (n=35) and normal healthy females (n=10), were profiled on the surface of SELDI protein chip. The candidate biomarkers were purified by CM-Sepharose, and their N-terminal amino sequence was determined. The amounts of hemoglobin (Hb) in cancer patient's sera versus that of normal sera were measured by ELISA. Nine sera proteins that were found to be significantly differentially expressed (P<0.05) between the sera of ovarian cancer patients and that of normal healthy females were selected using the WCX2 array. The most distinctive polypeptide peaks detected in the ovarian cancer samples were at 15.1 and 15.8 kDa and these two peaks were identified as the hemoglobin-alpha (Hb-alpha) and -beta (Hb-beta) chain, respectively. ELISA indicated that the sensitivity for intact Hb level was 77% in sera obtained from ovarian cancer patients, as compared with normal healthy female sera. In conclusion, two ovarian cancer biomarker proteins were discovered and identified as Hb-alpha and Hb-beta. Hb levels were significantly different in ovarian cancer serum samples and those obtained from normal healthy females, as determined by ELISA. Additional studies are required to further validate Hb-alpha and Hb-beta biomarkers.
Expression of the Wilms' tumor suppressor gene WT1 during mouse embryogenesis. (1993)

WT1 is a Wilms' tumor suppressor gene that maps to human chromosome 11p13 and encodes a putative transcription factor implicated in controlling normal urogenital development. Sporadic homozygous mutations in WT1 result in the development of Wilms' tumor (nephroblastoma), and heterozygous germline mutations can give rise to a phenotype which includes nephropathy and urogenital abnormalities (the Denys-Drash syndrome). Thus, inappropriate expression of WT1 results in developmental abnormalities affecting the urogenital system. To better define the temporal and spatial distribution of WT1 expression during embryogenesis, we have used in situ mRNA hybridization and immunohistochemistry to examine WT1 expression in murine embryos during the period prior to and throughout active organogenesis. Prior to embryological day 9.5 (E9.5), WT1 mRNA expression is absent in the embryo proper but is strongly expressed in the maternal uterus. During the initiation of organogenesis on E10.5, WT1 mRNA is localized within the pronephric and mesonephric tissues. By E11.5, the nephrogenic cord, urogenital ridge, and condensing metanephric tissue show intense WT1 hybridization signals, and increasingly centripetal expression of WT1 in the kidney correlates with renal differentiation from days E11.5 through E16.5. The stromal cell components in the developing gonad show expression of WT1 by E10.5, whereas in the remaining organs examined, WT1 expression is restricted to the uterus, spleen, abdominal wall musculature, and mesothelial lining of organs within the thoracic and abdominal cavities. Interestingly, there is also WT1 expression in the central nervous system which localizes to the ependymal layer of the ventral aspect of the spinal cord.(ABSTRACT TRUNCATED AT 250 WORDS)
Functionality and substrate specificity of human box H/ACA guide RNAs (2008)

A large number of box H/ACA RNAs have been identified in human cells, and have been predicted to account for nearly all pseudouridylation sites in human rRNAs. However, the function of these mammalian H/ACA RNAs in directing pseudouridylation has been verified experimentally in only two cases. In this study, we used three in vitro reconstitution systems, including yeast and mammalian systems, to test the function of seven H/ACA RNAs guiding16 pseudouridylation sites. Our results verified 12 of these sites; four predictions were incorrect. Further analyses indicated that three components, including the stability of the hairpin structure harboring the pseudouridylation pocket, the stability of guide sequence-target RNA base-pairing interaction, and the distance between the target uridine and the box H or ACA, were critical for the guide function, as changes in these components were sufficient to alter the functionality and specificity of the pseudouridylation pocket. The dynamic functional changes in response to changes in these three important components were further tested in vivo, and the results were completely consistent with the in vitro results. Finally, we compared our results with predictions made by two computer programs, as well as predictions made by human experts using visual inspection. We found that the predictions of one program (snoGPS) agreed with our experimental results with 100% sensitivity (12/12) and 75% specificity (3/4).
Turning a surface superrepellent even to completely wetting liquids (2014)

Superhydrophobic and superoleophobic surfaces have so far been made by roughening a hydrophobic material. However, no surfaces were able to repel extremely-low-energy liquids such as fluorinated solvents, which completely wet even the most hydrophobic material. We show how roughness alone, if made of a specific doubly reentrant structure that enables very low liquid-solid contact fraction, can render the surface of any material superrepellent. Starting from a completely wettable material (silica), we micro- and nanostructure its surface to make it superomniphobic and bounce off all available liquids, including perfluorohexane. The same superomniphobicity is further confirmed with identical surfaces of a metal and a polymer. Free of any hydrophobic coating, the superomniphobic silica surface also withstands temperatures over 1000°C and resists biofouling.
JAK2V617F: prevalence in a large Chinese hospital population (2006)

Recently, the JAK2(V617F) mutation was found in patients with myeloproliferative disorders (MPDs), including most with polycythemia vera (PV). The mutant JAK2 has increased kinase activity, and it was shown to be pathogenic in mouse models. Herein, we analyzed blood samples randomly collected from a clinical laboratory. Surprisingly, as many as 37 samples from a total of 3935 were found positive for the JAK2 mutation. However, only one of these samples had blood test results indicative for probable PV, but several had nonhematologic diseases. On average, samples with the mutation had normal red cell counts but significantly higher white blood cell and platelet counts, although most were within the normal range. The data suggest that the JAK2(V617F) mutation is apparently much more common than MPDs. Its occurrence may be a prelude to full blood cell abnormalities and other diseases, but it cannot by itself diagnose MPDs.
Treatment of mature port wine stains with the PhotoDerm VL (1999)

Port wine stains (PWS) are congenital vascular naevi. Their presence is the cause of significant psychological morbidity due to their cosmetic appearance. The flashlamp-pumped dye laser (FPDL) is considered to be the treatment of choice for PWS. However, there is a recognized morbidity related to the use of the FPDL. The PhotoDerm VL is a broad spectrum, non-coherent, intense pulsed light source which has been shown to be an effective tool in the treatment of a number of vascular lesions including PWS. Our strategy was to assess the effectiveness of the PhotoDerm VL in the treatment of mature PWS in three fair skinned subjects. Three patients with mature PWS were recruited. They were treated at 6-weekly intervals with the PhotoDerm VL machine using predetermined parameters and assessed at each visit prior to treatment. In all three patients there was at least a 50% improvement in the clinical appearance of the lesions as assessed by both operator and patient. No complications were reported. Further treatments in two patients, however, failed to produce any further clinical improvement. We conclude that the PhotoDerm VL appears to be a promising treatment for PWS with no post-operative complications. However, a comparative study with the FPDL needs to be undertaken to determine the most effective therapy option for patients with this disfiguring cutaneous lesion.
In Vitro Selection of High-Affinity DNA Ligands for Human IgE Using Capillary Electrophoresis (2004)

Aptamers with high affinity for IgE were selected using capillary electrophoresis to demonstrate the compatibility of this technique with SELEX. The high selectivity and efficiency of CE gave rise to a very high rate of enrichment, allowing high-affinity, high-selectivity aptamers to be obtained in only four rounds of selection. Decreasing the number of rounds shortens the selection procedure from the 4-6 weeks typical of SELEX to several days. The use of "bulk" dissociation constant measurements was introduced as a method for assessing the DNA pool after each round of selection. The average dissociation constant of the sequences in the DNA pool for IgE after four rounds of selection was 29 nM. The distribution of the dissociation constants for the sequences in the pool was very narrow with a standard deviation of only 6 nM. All of the sequences assessed exhibited high specificity for human IgE when compared with human IgG or mouse IgE.
Topics on the Na+/Ca2+ Exchanger: Pharmacological Characterization of Na+/Ca2+ Exchanger Inhibitors (2006)

Using the whole-cell voltage clamp, we examined acute effects of various agents on Na(+)/Ca(2+) exchange current (I(NCX)) in guinea-pig cardiac ventricular cells and transfected cells. Among the antiarrhythmic drugs, amiodarone, bepridil, dronedarone, cibenzoline, azimilide, and aprindine inhibited I(NCX) in a concentration-dependent manner. We also investigated the effects on NCX of 2,3-buanedione monoxim (BDM) and selective NCX inhibitors such as KB-R7943, SEA0400, and SN-6. The presence of trypsin in the pipette solution attenuated the inhibitory effects on NCX of amiodarone, bepridil, and BDM, suggesting that these drugs inhibit NCX from the cytosolic side. In contrast, the trypsin-insensitive NCX inhibitors were aprindine, azimilide, dronedarone, cibenzoline, KB-R7943, SEA0400, and SN-6. KB-R7943, SEA0400, and SN-6 suppressed the uni-directional outward I(NCX) more potently than the uni-directional inward I(NCX). The mechanism of this mode-dependency is unknown, but is suggested to be related to intracellular Na(+) concentration.
ABCdb: an ABC transporter database. (2000)

We present the first release of a database devoted to the ATP-binding cassette (ABC) protein domains (ABCdb). The ABC proteins are involved in a wide variety of physiological processes in Archea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across the membranes. In bacteria, ABC transporters are involved in the uptake of a wide range of molecules and in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cells, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families and suggests that they have diverged from common ancestral forms. In this release, ABCdb includes the inventory and assembly of the ABC transporter systems of completely sequenced genomes. In addition to the protein entries, the database comprises information on functional domains, sequence motifs, predicted trans-membrane segments, and signal peptides. It also includes a classification in sub-families of the ABC systems as well as a classification of the different partners of the systems. Evolutionary trees and specific sequence patterns are provided for each sub-family. The database is endowed with a powerful query system and it was interfaced with blastP2 program for similarity searches. ABCdb has been developed in the ACeDB format, a database system developed by Jean Thierry-Mieg and Richard Durbin. ABCdb can be accessed via the World Wide Web (http://ir2lcb.cnrs-mrs.fr/ABCdb/).
Novel Transcriptional Regulatory Signals in the Adeno-Associated Virus Terminal Repeat A/D Junction Element (2000)

Adeno-associated virus (AAV) type 2 vectors transfer stable, long-term gene expression to diverse cell types in vivo. Many gene therapy applications require the control of long-term transgene expression, and AAV vectors, similar to other gene transfer systems, are being evaluated for delivery of regulated gene expression cassettes. Previously, we (R. P. Haberman, T. J. McCown, and R. J. Samulski, Gene Ther. 5:1604-1611, 1998) demonstrated the use of the tetracycline-responsive system for long-term regulated expression in rat brains. In that study, we also observed residual expression in the "off" state both in vitro and in vivo, suggesting that the human cytomegalovirus (CMV) major immediate-early minimal promoter or other cis-acting elements (AAV terminal repeats [TR]) were contributing to this activity. In the present study, we identify that the AAV TR, minus the tetracycline-responsive minimal CMV promoter, will initiate mRNA expression from vector templates. Using deletion analysis and specific PCR-derived TR reporter gene templates, we mapped this activity to a 37-nucleotide stretch in the A/D elements of the TR. Although the mRNA derived from the TR is generated from a non-TATA box element, the use of mutant templates failed to identify function of canonical initiator sequences as previously described. Finally, we demonstrated the presence of green fluorescent protein expression both in vitro and in vivo in brain by using recombinant virus carrying only the TR element. Since the AAV terminal repeat is a necessary component of all recombinant AAV vectors, this TR transcriptional activity may interfere with all regulated expression cassettes and may be a problem in the development of novel TR split gene vectors currently being considered for genes too large to be packaged.
A radical approach to cancer. (2002)

Reactive oxygen species are known to be potentially dangerous, but are also needed for signal-transduction pathways. Tumor cells have relatively low amounts of superoxide dismutase (SOD), which quenches superoxide anion (O2(-*)), and as a result of a higher level of aerobic metabolism, higher concentrations of O2(-*) , compared to normal cells. But this may not be true of all tumor cells. Some tumor cells have relatively higher amounts of vitamin E, a potent anti-oxidant, and a higher level of anaerobic metabolism, resulting in a balance that is tilted more towards higher anti-oxidant capacity. In both instances of higher aerobic and anaerobic metabolism methods designed to augment free radical generation in tumor cells can cause their death. It is suggested that free radicals and lipid peroxides suppress the expression of Bcl-2, activate caspases and shorten telomere, and thus inducing apoptosis of tumor cells. Ionizing radiation, anthracyclines, bleomycin and cytokines produce free radicals and thus are useful as anti-cancer agents. But they also produce many side-effects. 2-methoxyoestradiol and polyunsaturated fatty acids (PUFAs) inhibit SODs and cause an increase of O2(-*) in tumor cells leading to their death. In addition, PUFAs (especially gamma-linolenic acid), 2-methoxyoestradiol and thalidomide may possess anti-angiogenic activity. This suggests that free radicals can suppress angiogenesis. Limited clinical studies done with gamma-linolenic acid showed that it can regress human brain gliomas without any significant side-effects. Thus, PUFAs, thalidomide and 2-methoxyoestradiol or their derivatives may offer a new radical approach to the treatment of cancer.
Podocyte-Specific Sialylation-Deficient Mice Serve as a Model for Human FSGS (2019)

Loss of cell-surface sialylation in mice resulted in disturbance of podocyte homeostasis and FSGS development. Impaired podocyte adhesion to the glomerular basement membrane most likely contributed to disease development. Our data support the notion that loss of sialylation might be part of the complex process causing FSGS. Sialylation, such as through a Sia supplementation therapy, might provide a new therapeutic strategy to cure or delay FSGS and potentially other glomerulopathies.