gebhart/patrepeval huggingface dataset:
Cargo-activated ATPase activity of kinesin. (1995)

We have measured the ATPase activity of squid optic lobe kinesin bound to polystyrene beads in the presence of microtubules. We find that there is a substantial increase (> 10-fold) in the microtubule-activated ATPase activity for bead-bound kinesin over free kinesin. We tentatively attribute such cargo-activated ATPase activity to the presence of a self-inhibited form of kinesin in solution, which becomes activated when bound to a bead in the presence of alpha-casein. Further experiments are underway to unravel this phenomenon and, in addition, to associate the traveling distance of beads with the observed ATPase rate to determine the average number of ATP consumed per kinesin-bead per micron of travel along microtubule.
A Fast Image Super-Resolution Algorithm Using an Adaptive Wiener Filter (2007)

A computationally simple super-resolution algorithm using a type of adaptive Wiener filter is proposed. The algorithm produces an improved resolution image from a sequence of low-resolution (LR) video frames with overlapping field of view. The algorithm uses subpixel registration to position each LR pixel value on a common spatial grid that is referenced to the average position of the input frames. The positions of the LR pixels are not quantized to a finite grid as with some previous techniques. The output high-resolution (HR) pixels are obtained using a weighted sum of LR pixels in a local moving window. Using a statistical model, the weights for each HR pixel are designed to minimize the mean squared error and they depend on the relative positions of the surrounding LR pixels. Thus, these weights adapt spatially and temporally to changing distributions of LR pixels due to varying motion. Both a global and spatially varying statistical model are considered here. Since the weights adapt with distribution of LR pixels, it is quite robust and will not become unstable when an unfavorable distribution of LR pixels is observed. For translational motion, the algorithm has a low computational complexity and may be readily suitable for real-time and/or near real-time processing applications. With other motion models, the computational complexity goes up significantly. However, regardless of the motion model, the algorithm lends itself to parallel implementation. The efficacy of the proposed algorithm is demonstrated here in a number of experimental results using simulated and real video sequences. A computational analysis is also presented.
Analyzing Highly Volatile Driving Trips Taken by Alternative Fuel Vehicles (2018)

Volatile driving, characterized by fluctuations in speed and accelerations and aggressive lane changing/merging, is known to contribute to transportation crashes. To fully understand driving volatility with the intention of reducing it, the objective of this study is to identify its key correlates, while focusing on highly volatile trips. First, a measure of driving volatility based on vehicle speed is applied to trip data collected in the California Household Travel Survey during 2012-2013. Specifically, the trips containing driving cycles (N=62839 trips) were analyzed to obtain driving volatility. Second, correlations of volatility with the trip, vehicle, and person level variables were quantified using Ordinary Least Squares and quantile regression models. The results of the 90th percentile regression (which distinguishes the 10% highly volatile trips from the rest) show that trips taken by pickup trucks, hatchbacks, convertibles, and minivans are less volatile when compared to the trips taken by sedans. Moreover, longer trips have less driving volatility. In addition, younger drivers are more volatile drivers than old ones. Overall, the results of this study are reasonable and beneficial in identifying correlates of driving volatility, especially in terms of understanding factors that differentiate highly volatile trips from other trips. Reductions in driving volatility have positive implications for transportation safety. From a methodological standpoint, this study is an example of how to extract useful (volatility) information from raw vehicle speed data and use it to calm down drivers and ultimately improve transportation safety.
Remarkable Remission Rate and Long-Term Efficacy of Upfront Metronomic Chemotherapy in Elderly and Frail Patients, with Diffuse Large B-Cell Lymphoma (2022)

The upfront treatment of very elderly and frail patients with diffuse large B-cell lymphoma (DLBCL) is still a matter of debate. Herein, we report results of the metronomic all-oral DEVEC [prednisolone/deltacortene®, vinorelbine (VNR), etoposide (ETO), cyclophosphamide] combined with i.v. rituximab (R). This schedule was administered as a first line therapy in 22 elderly/frail DLBCL subjects (median age = 84.5 years). In 17/22 (77%) patients, the Elderly-IPI-score was high. After a median follow-up of 24 months, 15 patients had died: seven (50%) for causes unrelated to DLBCL or its treatment, six (40%) for progression, and two (13%) for multiorgan failure. Six treatment-pertinent serious-adverse-events occurred. At the end of induction, 14/22 (64%) achieved complete remission; overall survival and event-free survival at 24 months were both 54% (95% CI = 32−72%), while the time to progression was 74% (95% CI = 48−88%). Furthermore, antiproliferative and proapoptotic assays were performed on DLBCL/OCI-LY3 cell-line using metronomic VNR and ETO and their combination. Both metronomic VNR and ETO had concentration-dependent antiproliferative (IC50 = 0.036 ± 0.01 nM and 7.9 ± 3.6 nM, respectively), and proapoptotic activities in DLBCL cells. Co-administration of the two drugs showed a strong synergism (combination index < 1 and dose reduction index > 1) against cell proliferation and survival. This low-dose schedule seems to compare favourably with intravenous-CHEMO protocols used in the same subset. Indeed, the high synergism shown by metronomic VRN+ETO in in vitro studies, explains the remarkable clinical responses and it allows significant dose reductions.
Herpes Zoster in African Patients: An Early Manifestation of HIV Infection (1988)

During a 3-month period, 131 cases of herpes zoster were diagnosed in Kigali, Rwanda. There were 46 female and 85 male patients. Mean age was 29 years (range 1-66). An unusually high proportion of patients presented with cranial and sacral nerve localisation of their cutaneous lesions. 55/131 patients (42%) had involvement of more than one dermatome. None of the patients had an underlying condition known to favour herpes zoster. 120/131 (92%) had antibodies to HIV detected by an immunoenzymatic assay (EIA) and indirect immunofluorescence. 92/125 adult patients (74%) had no sign or symptom related to HIV infection other than herpes zoster. This study suggests that herpes zoster in Central Africa is an early and readily detectable manifestation of HIV-induced immunosuppression.
Substrate-Directed Growth of N-Heteropolycyclic Molecules on a Metal Surface (2016)

N-Heteropolycyclic compounds are promising organic n-channel semiconductors for applications in field effect transistors. The adsorption behavior of these molecules on inorganic substrates is of great interest, since it affects the transport properties. Utilizing high-resolution electron energy-loss spectroscopy (HREELS) and density functional theory (DFT), we determined the adsorption geometry of three different N-heteropolycyclic molecules as a function of coverage on Au(111). All three π-conjugated aromatic molecules adopt a planar geometry with respect to the substrate in both the monolayer (ML) and thin films (up to 10 ML). Contrary, in their crystal structure the molecules are tilted up to 82° between the molecular planes in neighboring stacks. Electronic HREELS and DFT calculations allowed the determination of the optical gaps of the molecules which are unaffected by the nitrogen substitution of the polycyclic aromatic hydrocarbons, while the frontier orbitals of the N-heteropolycyclic compounds are stabilized. The present study provides important aspects such as adsorption and electronic properties which are essential for designing organic-molecules-based electronic devices.
Effects of estradiol on transcriptional profiles in atherosclerotic iliac arteries in ovariectomized cynomolgus macaques (2013)

Estradiol treatment of monkeys with established atherosclerosis affected iliac artery gene expression, suggesting changes in the cellular composition of lesions. Moreover, it is probable that the presence of atherosclerotic plaque affected the gene expression responses of arteries to estrogen.
Diode Laser Stabilization for Coherent Driving of Rare Earth Ions (2005)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text V. Crozatier, F. de Seze, F. Bretenaker, I. Lorgeré, and J. Le Gouët, "Diode Laser Stabilization for Coherent Driving of Rare Earth Ions," in Advanced Solid-State Photonics, Technical Digest (Optical Society of America, 2005), paper MB36. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Co‐Catalyzed Intramolecular S‐N Bond Formation in Water for 1,2‐Benzisothiazol‐3(2H)‐ones and 1,2,4‐Thiadiazoles Synthesis (2018)

An efficient and versatile Co‐catalyzed intramolecular S‐N bond formation in water to synthesize 1,2‐benzisothiazol‐3( 2H )‐one and 1,2,4‐thiadiazoles derivatives in good to excellent yields was developed. The transformation showed great tolerance with a broad range of substituents. The mother liquor was able to be recycled 6 times with minor loss in product yield.
[Expression of GP5-M fusion protein of porcine reproductive and respiratory syndrone virus (PRRSV) and establishment of ELISA diagnose based on the recombinant fusion protein]. (2005)

The cDNA fragment encoding the truncated GP5 and the full-length M protein of Porcine Reproductive and Respiratory Syndrone Virus (PRRSV) were orderly fused to the downstream of glutathione S-transferase (GST) of pGEX-KG expression vector, resulting in the fusion expression plasmid pKG-56. After transformed into E. coli BL21 (DE3) and induced by IPTG, the results of SDS-PAGE showed that the GST-GP5-M fusion protein was expressed in high level. Western-blot was performed to confirm that the expressed fusion protein could specifically react with antiserum against PRRSV. The fusion protein was further purified and used as an antigen to establish a novel PRRSV ELISA diagnose assay (P56-ELISA). Comparison between P56-ELISA and the abroad kit IDEXX-ELISA showed the two methods had 94.1 percent agreement by detecting 205 serum samples, indicating that the indirect P56-ELISA was specific and sensitive. The correlation between virus neutralization antibody of the infected pigs (not convalescent pigs) and antibody response to the fusion protein GP5-M was further studied. The regression function analysis suggested that there was no significant correlation between ELISA antibody response (OD630 nm) to the fusion protein GP5-M in clinical serum and their specific neutralizing titers.
The Activation Function-1 of Estrogen Receptor Alpha Prevents Arterial Neointima Development Through a Direct Effect on Smooth Muscle Cells (2015)

Altogether, ERαAF1-mediated nuclear action is both necessary and sufficient to inhibit postinjury arterial VSMC proliferation, whereas membrane ERα largely regulates the endothelial functions of E2. This highlights the exquisite cell/tissue-specific actions of the ERα subfunctions and helps to delineate the spectrum of action of selective ER modulators.
An adaptive cooperative scheme to ensure connectivity of consumer devices for infotainment services (2014)

A scheme for improving connectivity between an infrastructure and consumer devices is proposed for infotainment services based on the IEEE 802.11p/WAVE standard. The connectivity can be improved with the adaptive cooperation of consumer devices even in fast moving environments.
Lossless watermarking of categorical attributes for verifying medical data base integrity (2011)

In this article, we propose a new lossless or reversible watermarking approach that allows the embedding of a message within categorical data of relational database. The reversibility property of our scheme is achieved by adapting the well known histogram shifting modulation. Based on this algorithm we derive a system for verifying the integrity of the database content, it means detecting addition, removal or modification of any t-uples or attributes. Such a content integrity check is independent of the manner the database is stored or structured. We illustrate the overall capability of our method and its constraints of deployment considering one medical database of inpatient hospital stay records. Especially, we reversibly watermark ICD-10 diagnostic codes.
Strong influence of vertebrate host phylogeny on gut archaeal diversity (2020)

Abstract Commonly used 16S rRNA gene primers miss much of the archaeal diversity present in the vertebrate gut, leaving open the question of which archaea are host associated, the specificities of such associations, and the major factors influencing archaeal diversity. We applied 16S rRNA amplicon sequencing with Archaea-targeting primers to a dataset of 311 fecal/gut samples spanning 5 taxonomic classes (Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii) and obtained from mainly wild individuals (76% were wild). We obtained sufficient archaeal sequence data from 185 samples comprising 110 species that span all 5 classes. We provide evidence for novel Archaea-host associations, including Bathyarchaeia and Methanothermobacter — the latter of which was prevalent among Aves and enriched in higher body temperatures. Host phylogeny more strongly explained archaeal diversity than diet, while specific taxa were associated with each factor. Co-phylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last command ancestors of mammals and all host species. Archaea-Bacteria interactions seem to have a limited effect on archaeal diversity. These findings substantially expand on the paradigm of Archaea-vertebrate associations and the factors that explain those associations. Significance Archaea play key roles in the vertebrate gut such as promoting bacterial fermentation via consumption of waste products. Moreover, gut-inhabiting methanogenic Archaea in livestock are a substantial source of greenhouse gas production. Still, much is not known of the archaeal diversity in most vertebrates, especially since 16S rRNA sequence surveys often miss much of the archaeal diversity that is present. By applying Archaea-targeted gut microbiome sequencing to a large collection of diverse vertebrates, we reveal new Archaea-host associations such as a high prevalence of Methanothermobacter in birds. We also show that host evolutionary history explains archaeal diversity better than diet, and certain genera in one particular class of Archaea (Methanobacteria) were likely pervasive in the ancestral vertebrate gut.
Vertical-cavity saturable absorber intensity modulator (2004)

We demonstrate a vertical-cavity intensity modulator exploiting optical pumping of a semiconductor saturable absorber mirror. The device reflection is modulated by means of a control beam generated by a laser integrated within the modulator structure.
Ontology based metadata management in medical domains (2008)

In medical research, one of major challenges is to archive, access, and analyse various heterogeneous databases containing patient information gathered from a large volume of data over a long period of time. The main objective of this paper is (1) to examine how the use of metadata and ontologies can support the management and integration of clinical research databases and (2) to present our ontology-based metadata management system developed for the Cardiovascular Research Department at MAHI. Using the concept of web services, our system is globally accessible. The system is currently deployed on the existing medical information system at Mid America Heart Institute (MAHI) and used for clinical research.
T-cell receptor (TCR) usage in Lewis rat experimental autoimmune encephalomyelitis: TCR beta-chain-variable-region V beta 8.2-positive T cells are not essential for induction and course of disease. (1995)

Predominant usage of V beta 8.2 gene segments, encoding a T-cell receptor (TCR) beta chain variable region, has been reported for pathogenic Lewis rat T cells reactive to myelin basic protein (MBP). However, up to 75% of the alpha/beta T cells in a panel of MBP-specific T-cell lines did not display TCR V beta 8.2, V beta 8.5, V beta 10, or V beta 16 elements. To further investigate TCR usage, we sorted the T-cell lines for V beta 8.2- and V beta 10-positive T cells or depleted the lines of cells with these TCRs. V beta 8.2-positive T cells and one of the depleted T-cell lines strongly reacted against the MBP peptide MBP-(68-88). The depleted T-cell line caused marked experimental autoimmune encephalomyelitis (EAE) even in Lewis rats in which endogenous V beta 8.2-positive T cells had been eliminated by neonatal treatment with anti-V beta 8.2 monoclonal antibodies. T-cell hybridomas generated from this line predominantly used V beta 3 TCR genes coexpressed with TCR V alpha 2 transcripts, which were also used by V beta 8.2-positive T cells. Furthermore, V beta 10-positive T cells reactive to MBP-(44-67) were encephalitogenic when injected immediately after positive selection. After induction of EAE by sorted V beta 8.2- or V beta 10-positive T-cell lines, immunocytochemical analysis of the spinal cord tissue showed a predominance of the injected TCR or of nontypable alpha/beta T cells after injection of the depleted line. Our results demonstrate heterogeneity of TCR beta-chain usage even for a single autoantigen in an inbred strain. Moreover, V beta 8.2-positive T cells are not essential for the induction and progression of adoptive-transfer EAE.
Evaluation of an early‐stage innovation for full‐thickness excision of benign colonic polyps using the IDEAL framework (2019)

The FLEX procedure is still under development. Early data demonstrate that it is safe for excision of selected benign polyps. Modifications to transcolonic suture delivery are now required and there is a need for wider adoption before more definitive evaluation can be performed.
Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg–Carbon Bond Cleavage and Metal Binding Specificity (2016)

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.
Class IIa HDACs – new insights into their functions in physiology and pathology (2014)

HDAC4, 5, 7 and 9 constitute the class IIa histone deacetylases (HDACs) within the large family of protein deacetylases. Class IIa HDACs have unique features that distinguish them from other HDACs. They contain an N-terminal domain that is required for their interaction with tissue-specific transcription factors and recruitment to their target genes. The N-terminal domain on class IIa HDACs also bears conserved serine residues that undergo signal-dependent phosphorylation, which brings about nuclear export of the enzymes and de-repression of their targets. One of the most important aspects of class IIa HDACs is their expression in specific tissues and organs within the organism, where they have crucial roles in development and differentiation processes. This review brings up to date our knowledge of the physiological and pathological functions of class IIa HDACs, focusing in particular on the most recent discoveries from in vivo studies of mouse model systems.
Supplemental Figure 2 from Attenuated <i>Toxoplasma gondii</i> Stimulates Immunity to Pancreatic Cancer by Manipulation of Myeloid Cell Populations (2023)

&lt;p&gt;Distal presence of &lt;i&gt;CPS&lt;/i&gt; and FACS data for CD80/86 activation.&lt;/p&gt;
Inelastic neutron scattering, lattice dynamics, and high-pressure phase stability of zircon-structured lanthanide orthophosphates (2010)

Inelastic neutron-scattering experiments and lattice-dynamical calculations are reported on a series of rare-earth orthophosphates $R{\text{PO}}_{4}$ ($R=\text{Tm}$, Er, Ho, and Tb). The experimental phonon spectra for the compounds are in good agreement with our model calculations. The lattice-dynamical model is found useful for the calculation of various thermodynamic properties such as the lattice specific heat, thermal expansion, and equation of state of these compounds. The $R{\text{PO}}_{4}$ compounds are known to transform to the scheelite (body-centered tetragonal, $I{4}_{1}/a$) or monoclinic phase $(P{2}_{1}/n)$ at high pressures. Our calculations show that while the scheelite phase stabilizes at high pressure due to its lower volume, the monoclinic phase may occur as an intermediate phase depending on the ionic size of the $R$ atom. The latter phase is stabilized at higher temperature (at high pressure) due to its high vibrational entropy. A pressure-temperature phase diagram is proposed.
The selective 5-lipoxygenase inhibitor A63162 reduces PC3 proliferation and initiates morphologic changes consistent with secretion. (1994)

We examined the effect of A63162 (Abbott), a selective inhibitor of 5-lipoxygenase on human prostate (PC3) cell proliferation. Within 5 min DNA synthesis was reversibly inhibited by 40 microM A63162, without altered cellular attachment or uptake of trypan blue. After 72 Hr, cells continued to be attached and exclude dye, were reduced in number and their histology was altered. Many treated cells were larger, more pleomorphic, with nuclear and cytoplasmic ultrastructural changes consistent with preparation for secretion. Some cells contained moderately swollen, distorted mitochondria. ETYA, a less selective inhibitor of 5-lipoxygenase that also inhibits cell replication, acutely reduced O2 uptake by 40%, but A63162 did not. The retention of the supravital mitochondrial dye, rhodamine 123 was increased by ETYA at 4 hr, but not after 24 hr; retention was not altered by A63162. Although the mechanism by which A63162 reversibly inhibits PC3 proliferation and initiates preparation for secretion is not identified, additional studies should further define its role in these events.