gebhart/patrepeval huggingface dataset:
Three-Dimensional Models for β-Adrenergic Receptor Complexes with Agonists and Antagonists (2003)

Molecular modeling methods have been used to construct three-dimensional models for agonist and antagonist complexes with beta-adrenergic receptors. The recent rhodopsin crystal structure was used as a template in standard homology modeling methods. The rhodopsin-based homology models were assessed for agreement with experimental results for beta-adrenergic receptors, and compared with receptor models developed using de novo modeling techniques. While the de novo and homology-derived receptor models are generally quite similar, there are some localized structural differences that impact the putative ligand-binding site significantly. The de novo receptor models appear to provide much better agreement with experimental data, particularly for receptor complexes with agonist ligands. The de novo receptor models also yield some interesting and testable hypotheses for the structural basis of beta-adrenergic receptor subtype ligand selectivity.
Fine mapping of Xq11.1‐q21.33 and mutation screening of RPS6KA6, ZNF711, ACSL4, DLG3, and IL1RAPL2 for autism spectrum disorders (ASD) (2011)

About 80% of cases with autism express intellectual disability. Both in autism and in mental retardation without autism the majority of the cases are males, suggesting a X-chromosomal effect. In fact, some molecular evidence has been obtained for a common genetic background for autism spectrum disorders (ASD) and X-linked mental retardation (XLMR). In several genome-wide scans (GWS), evidence for linkage at X-chromosome has been reported including the GWS of Finnish ASD families with the highest multipoint lod score (MLS) of 2.75 obtained close to DXS7132 at Xq11.1. To further dissect the relationship between autism and genes implicated in XLMR, we have fine-mapped Xq11.1-q21.33 and analyzed five candidate genes in the region. We refined the region using 26 microsatellite markers and linkage analysis in 99 Finnish families with ASD. The most significant evidence for linkage was observed at DXS1225 on Xq21.1 with a nonparametric multipoint NPL(all) value of 3.43 (P = 0.0004). We sequenced the coding regions and splice sites of RPS6KA6 and ZNF711 residing at the peak region in 42 male patients from families contributing to the linkage. We also analyzed ACSL4 and DLG3, which have previously been known to cause XLMR and IL1RAPL2, a homologous gene for IL1RAPL1 that is mutated in autism and XLMR. A total of six novel and 11 known single nucleotide polymorphisms were identified. Further studies are warranted to analyze the candidate genes at Xq11.1-q21.33.
Plane-Wave Decomposition of Acoustical Scenes Via Spherical and Cylindrical Microphone Arrays (2009)

Spherical and cylindrical microphone arrays offer a number of attractive properties such as direction-independent acoustic behavior and ability to reconstruct the sound field in the vicinity of the array. Beamforming and scene analysis for such arrays is typically done using sound field representation in terms of orthogonal basis functions (spherical/cylindrical harmonics). In this paper, an alternative sound field representation in terms of plane waves is described, and a method for estimating it directly from measurements at microphones is proposed. It is shown that representing a field as a collection of plane waves arriving from various directions simplifies source localization, beamforming, and spatial audio playback. A comparison of the new method with the well-known spherical harmonics based beamforming algorithm is done, and it is shown that both algorithms can be expressed in the same framework but with weights computed differently. It is also shown that the proposed method can be extended to cylindrical arrays. A number of features important for the design and operation of spherical microphone arrays in real applications are revealed. Results indicate that it is possible to reconstruct the sound scene up to order p with p2 microphones spherical array.
Spider-silk-like shape memory polymer fiber for vibration damping (2014)

In this study, the static and dynamic properties of shape memory polyurethane (SMPU) fiber are reported and compared to those of spider dragline silk. Although the polymeric fiber has a lower strength compared to spider dragline silks (0.2–0.3 GPa versus 1.1 GPa), it possesses much higher toughness (276–289 MJ m−3 versus 160 MJ m−3), due to its excellent extensibility. The dynamic mechanical tests reveal that SMPU fiber has a high damping capacity (tan δ = 0.10–0.35) which is comparable to or even higher than that of spider silks (tan δ = 0.15). In addition, we found that, different programming methods change the shape memory and damping properties of the fiber in different ways and cold-drawing programming is more advocated in structural applications. These results suggest that the SMPU fiber has similar vibration damping and mechanical properties as spider silk, and may find applications in lightweight engineering structures.
Cytochrome Components of Plant Microsomes (1975)

The electron transport components of the microsomal fraction of cauliflower buds and mung bean hypocotyls were investigated using split-beam and dual wavelength spectrophotometry under a variety of reducing conditions. Cauliflower microsomes were found to contain an ascorbate-reducible component, termed cytochrome b-559.5 [E'0 = +135 +/- 20 mV; lambdamax (reduced minus oxidised) = 559.5, 527 and 429 nm at 23 degrees C], cytochrome b5 [E'0 = -20 +/- 20 mV; lambdamax (reduced minus oxidised) = 556, 526 and 425 nm at 23 degrees C], cytochromes P-450 and P-420. On the basis of binding studies with ethyl isocyanide, degradation of cytochrome P-450 to P-420, redox potential, aniline binding, and relative rates of reduction by NADPH and NADH, it is suggested that the cytochrome P-450 system is analogous to that mammalian microsomes. Other components, reducible only by dithionite, may also be present. Mung bean microsomes were found to contain an ascorbate-reducible component, termed cytochrome b-562 [E'0 = +120 +/- 20 mV; lambdamax (reduced minus oxidised) = 562, 528 and 430 nm at 23 degrees C], cytochrome b5, and a low potential component which was reducible only by sodium dithionite. No cytochrome P-450 or P-420 could be detected. A general method of analysis of the cytochromes was developed and applied to the microsomes from a variety of plant sources. The results indicate that large variations, both in type and amount of components, occur between the microsomes from different plant materials.
A new type of cohesin domain that specifically binds the dockerin domain of the Clostridium thermocellum cellulosome-integrating protein CipA (1996)

The cellulosome-integrating protein CipA, which serves as a scaffolding protein for the cellulolytic complex produced by Clostridium thermocellum, comprises a COOH-terminal duplicated segment termed the dockerin domain. This paper reports the cloning and sequencing of a gene, termed sdbA (for scaffoldin dockerin binding), encoding a protein which specifically binds the dockerin domain of CipA. The sequenced fragment comprises an open reading frame of 1,893 nucleotides encoding a 631-amino-acid polypeptide, termed SdbA, with a calculated molecular mass of 68,577 kDa. SAA comprises an NH2-terminal leader peptide followed by three distinct regions. The NH2-terminal region is similar to the NH2-terminal repeats of C. thermocellum OlpB and ORF2p. The central region is rich in lysine and harbors a motif present in Streptococcus M proteins. The COOH-terminal region consists of a triplicated sequence present in several bacterial cell surface proteins. The NH2-terminal region of SdbA and a fusion protein carrying the first NH2-terminal repeat of OlpB were shown to bind the dockerin domain of CipA. Thus, a new type of cohesin domain, which is present in one, two, and four copies in SdbA, ORF2p, and OlpB, respectively, can be defined. Since OlpB and most likely SdbA and ORF2p are located in the cell envelope, the three proteins probably participate in anchoring CipA (and the cellulosome) to the cell surface.
On Triazoles. VI. The acylation of 5‐amino‐1,2,4‐triazoles (1987)

Abstract The isomeric and tautomeric structure of I and II type monoacylated 5‐amino‐1,2,4‐triazole derivatives was studied with the help of their ir, uv, pmr and cmr spectra as well as model compounds prepared for this purpose. It was stated that the structure of the I type ring‐acylated derivatives is 2o and those of their II type isomers is 5a .
Paxos made live (2007)

We describe our experience in building a fault-tolerant data-base using the Paxos consensus algorithm. Despite the existing literature in the field, building such a database proved to be non-trivial. We describe selected algorithmic and engineering problems encountered, and the solutions we found for them. Our measurements indicate that we have built a competitive system.
1423: PDE5 Dysregulation in Penile Erectile Tissue: Mechanism of Priapism (2004)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 11, 2004, 8:00 am - 12:00 pm1 Apr 20041423: PDE5 Dysregulation in Penile Erectile Tissue: Mechanism of Priapism Trinity J. Bivalacqua, Hunter C. Champion, Eiki Takimoto, David Kass, and Arthur L. Burnett Trinity J. BivalacquaTrinity J. Bivalacqua More articles by this author , Hunter C. ChampionHunter C. Champion More articles by this author , Eiki TakimotoEiki Takimoto More articles by this author , David KassDavid Kass More articles by this author , and Arthur L. BurnettArthur L. Burnett More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38648-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1423: PDE5 Dysregulation in Penile Erectile Tissue: Mechanism of Priapism." The Journal of Urology, 171(4S), p. 375 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 375 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Trinity J. Bivalacqua More articles by this author Hunter C. Champion More articles by this author Eiki Takimoto More articles by this author David Kass More articles by this author Arthur L. Burnett More articles by this author Expand All Advertisement PDF downloadLoading ...
COMPOSITE MATERIALS PREPARED BY PHENOL RESIN COATING ON NATURAL FLAKE GRAPHITE AND THEIR USE AND PERFORMANCE AS CARBON ANODE MATERIALS IN LITHIUM ION SECONDARY BATTERIES (2002)

To improve charging discharging property of graphite and its compatibility with electrolyte solutions, the natural flake graphite(NFG) is coated with phenol resin first, and then carbonized under different carbonization conditions in inert gas. With metal lithium as the opposite electrode and the composite materials as carbon anode materials in lithium ion secondary batteries, the charging discharging behavior of the composite materials is studied. The elemental composition and the true density of some composite materials are analyzed, and the composite materials are also characterized by X ray diffraction technique.
MANF Is Indispensable for the Proliferation and Survival of Pancreatic β Cells (2014)

All forms of diabetes mellitus (DM) are characterized by the loss of functional pancreatic β cell mass, leading to insufficient insulin secretion. Thus, identification of novel approaches to protect and restore β cells is essential for the development of DM therapies. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-stress-inducible protein, but its physiological role in mammals has remained obscure. We generated MANF-deficient mice that strikingly develop severe diabetes due to progressive postnatal reduction of β cell mass, caused by decreased proliferation and increased apoptosis. Additionally, we show that lack of MANF in vivo in mouse leads to chronic unfolded protein response (UPR) activation in pancreatic islets. Importantly, MANF protein enhanced β cell proliferation in vitro and overexpression of MANF in the pancreas of diabetic mice enhanced β cell regeneration. We demonstrate that MANF specifically promotes β cell proliferation and survival, thereby constituting a therapeutic candidate for β cell protection and regeneration.
A survey of design techniques for system-level dynamic power management (2000)

Dynamic power management (DPM) is a design methodology for dynamically reconfiguring systems to provide the requested services and performance levels with a minimum number of active components or a minimum load on such components. DPM encompasses a set of techniques that achieves energy-efficient computation by selectively turning off (or reducing the performance of) system components when they are idle (or partially unexploited). In this paper, we survey several approaches to system-level dynamic power management. We first describe how systems employ power-manageable components and how the use of dynamic reconfiguration can impact the overall power consumption. We then analyze DPM implementation issues in electronic systems, and we survey recent initiatives in standardizing the hardware/software interface to enable software-controlled power management of hardware components.
No difference in stem cell somatic mutation between the background mucosa of right- and left-sided sporadic colorectal carcinomas (1998)

Epidemiological, morphological, and molecular differences exist between carcinomas of the right and left sides of the large bowel. To investigate whether this is reflected in differences in somatic mutation frequency in the background mucosa, mutation of the neutral O-acetyltransferase gene (oat) was quantified in histologically normal resection margins from 20 informative (heterozygous) patients with caecal or ascending colon cancer (11 males, median age 75 years) and 20 with sigmoid colon or rectal cancer (10 males, median age 70 years). Mutant discordant crypts lacking O-acetyltransferase activity were visualized by mPAS staining and classified as wholly or partially involved by the mutant phenotype; median frequencies (x10(-4) were compared (Mann-Whitney U-test) after assessing a sample of more than 10,000 crypts per case. No significant difference was found between the frequencies of wholly involved mPAS-positive crypts in background mucosa of left- and right-sided cancers (p = 0.4569), indicating that tumours on both sides of the colon are associated with similar levels of lifetime-accumulated stem cell mutational load. However, partially involved mPAS-positive crypts were significantly more frequent in mucosa from left-sided cancers (p < 0.04), indicating increased mutational activity during the previous 12 months. Analysis of mucosa proximal and distal to left-sided cancers showed that this increase was due to a statistically higher frequency of partially involved crypts in proximal mucosa, which probably resulted from the obstructive effects of the tumour causing increased exposure of the proximal mucosa to luminal carcinogens and/or epithelial regeneration in response to low-grade inflammation or ischaemia. The findings indicate that although left-sided colonic cancer is commoner than right-sided cancer in the British population, carcinomas on both sides of the large bowel arise in a background of similar levels of stem cell mutational activity.
Immunosuppressive Cyclolignans (1996)

The immunosuppressive activity of several lactonic, nonlactonic, and heterocycle-fused cyclolignans has been demonstrated for the first time by use of a T-cell-mediated immune response. Of the compounds tested, 4'-demethyldeoxypodophyllotoxin (8), beta-apopicropodophyllin (6), and the isoxazoline-fused cyclolignan 15 are the most potent with respect to their suppression of activated splenocytes.
Selective displacement of nuclear proteins by antitumor drugs having affinity for nucleic acids. (1989)

The nuclear chromatin binding sites of the antitumor drugs mitoxantrone, ametantrone, doxorubicin, mithramycin, and actinomycin D and the intercalating ligand ethidium were studied by polyacrylamide gel electrophoresis of the proteins released from rat liver nuclei in the presence and absence of these drugs in buffer of low ionic strength (10 mM NaCl). At 25-50 microM free ligand concentration, each drug produced a specific and reproducible pattern of extractable proteins of different molecular weight by (i) releasing new proteins, (ii) altering the quantity of particular extracted proteins, and/or (iii) selectively entrapping other proteins in the nuclei. Ethidium, up to 100 microM, did not affect release of proteins from the nuclei. These results indicate that each ligand either has different binding site(s) in chromatin or modulates chromatin structure in a specific way by changing the affinity of different sets of proteins for their respective binding sites, resulting in their selective extraction or entrapment. The lack of effect of ethidium indicates that intercalation of the ligand to DNA, per se, does not alter the release of nuclear proteins. If patterns of nuclear proteins selectively released or retained by antitumor drugs are found to correlate with biological activity, this type of analysis may be helpful in new drug design and screening.
CD38 expression distinguishes two groups of B-cell chronic lymphocytic leukemias with different responses to anti-IgM antibodies and propensity to apoptosis (1996)

The expression of CD38 by B cells chronic lymphocytic leukemia (B-CLL) was studied in 20 untreated patients. The cells expressed abundant CD38 (relative fluorescence intensity range, 6 to 15) in 6 cases (group I patients), whereas CD38 expression was low to absent (relative fluorescence intensity range, 0 to 3) in the remaining cases (group II patients). Exposure of the cells from group I patients to goat antihuman mu chain antibodies (Ga mu-ab) resulted in the elevation of intracellular free Ca2+ concentration([Ca2+]i) followed by apoptosis. In contrast, exposure of group II cells to Ga mu-ab was not followed by increased levels of [Ca2+]i, programmed cell death or cell proliferation. No differences in the expression of surface IgM were noted in the two groups of B-CLL cells. Normal peripheral blood B cells, which expressed low to absent CD38, were capable of mobilizing [Ca2+]i and of proliferating after exposure to Ga mu-ab. The collected data suggest that, although group I B-CLL cells were able to transduce the signals delivered by IgM crosslinking, this pathway was severely impaired in group II B-CLL cells. However, unlike that observed in normal circulating B cells, stimulation of group I cells with Ga mu-ab resulted in apoptosis rather than proliferation. CD38 did not appear to be directly involved in [Ca2+]i mobilization induced by Ga mu-ab in group I B-CLL cells because their exposure to anti-CD38 monoclonal antibodies failed to cause [Ca2+]i mobilization or to block the [Ca2+]i response induced by Ga mu-ab. These data indicate that CD38 expression identified a particular subset of B-CLL cells with defined functional properties, including the propensity to undergo apoptosis.
Task Compatibility of Manipulator Postures (1988)

In performing a manipulation task, humans tend to adopt arm postures that most effectively utilize the motion and strength capabilities of the arm. Selecting arm postures that are compatible with the task requirements has become almost instinctive to humans. By mimicking this approach in robotic manipulation, we can exploit the full capability of a manipu lator in performing a task. An index is proposed for measur ing the compatibility of manipulator postures with respect to a generalized task description. The manipulator is viewed as a mechanical transformer, with joint space velocity and force as input and task space velocity and force as output. Optimi zation of the index corresponds to matching the velocity and force transmission characteristics to the task requirements. The applications of this index to manipulator redundancy utilization and workspace design are also discussed.
Biology, detection, and clinical implications of circulating tumor cells (2014)

Cancer metastasis is the main cause of cancer-related death, and dissemination of tumor cells through the blood circulation is an important intermediate step that also exemplifies the switch from localized to systemic disease. Early detection and characterization of circulating tumor cells (CTCs) is therefore important as a general strategy to monitor and prevent the development of overt metastatic disease. Furthermore, sequential analysis of CTCs can provide clinically relevant information on the effectiveness and progression of systemic therapies (e.g., chemo-, hormonal, or targeted therapies with antibodies or small inhibitors). Although many advances have been made regarding the detection and molecular characterization of CTCs, several challenges still exist that limit the current use of this important diagnostic approach. In this review, we discuss the biology of tumor cell dissemination, technical advances, as well as the challenges and potential clinical implications of CTC detection and characterization.
Sacral Neuromodulation in Women With Idiopathic Detrusor Overactivity Incontinence: Decreased Overactivity but Unchanged Bladder Contraction Strength and Urethral Resistance During Voiding (2006)

Our study confirmed the depressant effect of sacral (S3) nerve neuromodulation on detrusor overactivity. No effect on urethral resistance and bladder contraction strength during voiding could be demonstrated using volume independent parameters.
Comparison of intracerebral inoculation and osmotic blood-brain barrier disruption for delivery of adenovirus, herpesvirus, and iron oxide particles to normal rat brain. (1995)

Delivery of adenovirus, herpes simplex virus (HSV), and paramagnetic monocrystalline iron oxide nanoparticles (MION) to rat brain (n = 64) was assessed after intracerebral inoculation or osmotic disruption of the blood-brain barrier (BBB). After intracerebral inoculation, the area of distribution was 7.93 +/- 0.43 mm2 (n = 9) for MION and 9.17 +/- 1.27 mm2 (n = 9) for replication-defective adenovirus. The replication-compromised HSV RH105 spread to 14.00 +/- 0.87 mm2 (n = 8), but also had a large necrotic center (3.54 +/- 0.47 mm2). No infection was detected when virus was administered intra-arterially without hyperosmotic mannitol. After osmotic BBB disruption, delivery of the viruses and MIONs was detected throughout the disrupted cerebral cortex. Positive staining was found in 4 to 845 cells/100 microns thick coronal brain section (n = 7) after adenovirus administration, and in 13 to 197 cells/section (n = 8) after HSV administration. Cells of glial morphology were more frequently stained after administration of adenovirus, whereas neuronal cells were preferentially stained after delivery of both HSV vectors and MION. In a preliminary test of vector delivery in the feline, MION was detected throughout the white matter tracts after inoculation into normal cat brain. Thus MION may be a tool for use in vivo, to monitor the delivery of virus to the central nervous system. Additionally, BBB disruption may be an effective method to globally deliver recombinant viruses to the CNS.
Effects of Cache Coherency in Multiprocessors (1982)

In many commercial multiprocessor systems, each processor accesses the memory through a private cache. One problem that could limit the extensibility of the system and its performance is the enforcement of cache coherence. A mechanism must exist which prevents the existence of several different copies of the same data block in different private caches. In this paper, we present an in-depth analysis of the effects of cache coherency in multiprocessors. A novel analytical model for the program behavior of a multitasked system is introduced. The model includes the behavior of each process and the interactions between processes with regard to the sharing of data blocks. An approximation is developed to derive the main effects of the cache coherency contributing to degradations in system performance.