gebhart/patrepeval huggingface dataset:
Fourier transform infrared spectroscopy of effluents from pulsed plasmas of 1,1,2,2-tetrafluoroethane, hexafluoropropylene oxide, and difluoromethane (1999)

Gas-phase Fourier transform infrared spectroscopy (FTIR) has been used to analyze the effluents from C2H2F4, hexafluoropropylene oxide (CF3CFOCF2, HFPO), and CH2F2 pulsed plasmas. A series of reference spectra for possible effluent species was used to identify the major species in each. The major species in pulsed C2H2F4 plasmas were found to be: C2H2F4, HF, C2F4, C2HF5, CHF3, and SiF4 (formed from free fluorine). For HFPO pulsed plasmas, the major effluents are: HFPO, CF3COF3, COF2, C2F4, C2F6, CO, CF4, and C3F8, whereas for CH2F2 pulsed plasmas, the major effluents are: CH2F2, HF, SiF4, and CHF3. Reaction sets were postulated for each precursor to account for the observed effluents, and these sets were used to explain the trends of species concentrations with pulse on and pulse off time. In each case, most of the effluent concentration trends could be traced back to competition between dissociation pathways of a particular molecule. For both C2H2F4 and CH2F2, the main reactions were the competition between CF2 production and HF elimination from the original precursor. For C2H2F4 pulsed plasmas, the competition between these pathways was found to be ∼1:1, whereas for CH2F2 pulsed plasmas, the HF elimination pathway is dominant. For HFPO, the key reactions are the three dissociation pathways of CF3COF, a main product of the initial dissociation of HFPO into CF2+CF3COF. The global warming impact of each of the pulsed plasma enhanced chemical vapor deposition processes was gauged by the million metric tons of carbon equivalent (MMTCE) metric. CH2F2 pulsed plasmas were found to have the lowest MMTCE (min=2.1×106), whereas HFPO pulsed plasmas had the highest MMTCE (max=7.7×107). For all three precursors, the MMTCE impact is reduced by decreasing the exposure to plasma excitation through increasing the off time at a fixed on time.
Joint bit-loading and power-allocation for OFDM systems based on statistical frequency-domain fading model (2003)

Orthogonal frequency division multiplexing (OFDM) modulation scheme is adopted by more and more wireless communication systems to help achieve reliable high-rate data transmission over multipath fading channels. We obtain the subcarrier fading statistics of OFDM systems operating in frequency-selective fading channels with arbitrary Rician fading parameters and inter-path correlation. This analysis leads to the discovery of practical OFDM channels with dissimilar subcarrier fading statistics. Based on the subcarrier-level statistical information, we propose an statistical bit-loading and power-allocation algorithm to maximize the overall spectral efficiency and minimize the transmission power requirement of the OFDM system while maintaining curtain target bit error rate (BER) level. Unlike its existing counterparts, our proposed algorithm adapts the transmission parameters based on the OFDM subcarrier fading statistics rather than on the instantaneous channel conditions. Results show that the proposed scheme can achieve considerable performance enhancement over non-adaptive systems.
Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation (2017)

Human Vγ9Vδ2 T cells respond to microbial infections as well as certain types of tumors. The key initiators of Vγ9Vδ2 activation are small, pyrophosphate-containing molecules called phosphoantigens (pAgs) that are present in infected cells or accumulate intracellularly in certain tumor cells. Recent studies demonstrate that initiation of the Vγ9Vδ2 T cell response begins with sensing of pAg via the intracellular domain of the butyrophilin 3A1 (BTN3A1) molecule. However, it is unknown how downstream events can ultimately lead to T cell activation. Here, using NMR spectrometry and molecular dynamics (MD) simulations, we characterize a global conformational change in the B30.2 intracellular domain of BTN3A1 induced by pAg binding. We also reveal by crystallography two distinct dimer interfaces in the BTN3A1 full-length intracellular domain, which are stable in MD simulations. These interfaces lie in close proximity to the pAg-binding pocket and contain clusters of residues that experience major changes of chemical environment upon pAg binding. This suggests that pAg binding disrupts a preexisting conformation of the BTN3A1 intracellular domain. Using a combination of biochemical, structural, and cellular approaches we demonstrate that the extracellular domains of BTN3A1 adopt a V-shaped conformation at rest, and that locking them in this resting conformation without perturbing their membrane reorganization properties diminishes pAg-induced T cell activation. Based on these results, we propose a model in which a conformational change in BTN3A1 is a key event of pAg sensing that ultimately leads to T cell activation.
Rapid 3D‐T<sub>1ρ</sub> mapping of the knee joint at 3.0T with parallel imaging (2006)

Three-dimensional spin-lattice relaxation time in the rotating frame (3D-T1rho) with parallel imaging at 3.0T was implemented on a whole-body clinical scanner. A 3D gradient-echo sequence with a self-compensating spin-lock pulse cluster was combined with generalized autocalibrating partially parallel acquisitions (GRAPPA) to acquire T1rho-weighted images. 3D-T1rho maps of an agarose phantom and three healthy subjects were constructed using an eight-channel phased-array coil without parallel imaging and with parallel imaging acceleration factors of 2 and 3, in order to assess the reproducibility of the method. The coefficient of variation (CV) of the median T1rho of the agarose phantom was 0.44%, which shows excellent reproducibility. The reproducibility of in vivo 3D-T1rho maps was also investigated in three healthy subjects. The CV of the median T1rho of the patellar cartilage varied between approximately 1.1% and 4.3%. Similarly, the CV varied between approximately 2.1-5.8%, approximately 1.4-8.7%, and approximately 1.5-4.1% for the biceps femoris and lateral and medial gastrocnemius muscles, respectively. The preliminary results demonstrate that 3D-T1rho maps can be constructed with good reproducibility using parallel imaging. 3D-T1rho with parallel imaging capability is an important clinical tool for reducing both the total acquisition time and RF energy deposition at 3T.
Relation between depression after stroke, antidepressant therapy, and functional recovery (2001)

The aim was to evaluate the effects of poststroke depression and antidepressant therapy on the improvement of motor scores and disability, to verify if the negative effects of poststroke depression on functional recovery could be counterbalanced by taking antidepressant drugs. RESULTS OBTAINED BEFORE, DURING, AND AFTER REHABILITATION: On the Barthel index, Canadian neurological scale, and Rivermead mobility index-by 49 depressed patients with stroke, who had been treated (n=25) or not treated (n=24) according to the different therapeutic approaches of their physicians, were compared with results similarly obtained by 15 non-depressed patients with stroke. Analysis was by multivariate analysis of variance for repeated measures There was a non-significant difference between the groups in their motor and functional scores, and a significant improvement on time. A significant interaction between group and time was seen. This interaction was particularly significant on the Rivermead mobility index, and was due to the fact that the recovery of non-treated depressed patients with stroke was less than the non-depressed and the depressed but treated patients with stroke. Furthermore, recovery from depression was significantly greater in treated than in non-treated depressed patients with stroke. In conclusion, poststroke depression has negative effects on functional recovery, and a pharmacological treatment of depression can counterbalance this effect.
On the convexity of piecewise-defined functions (2015)

Functions that are piecewise defined are a common sight in mathematics while convexity is a property especially desired in optimization. Suppose now a piecewise-defined function is convex on each of its defining components – when can we conclude that the entire function is convex? In this paper we provide several convenient, verifiable conditions guaranteeing convexity (or the lack thereof). Several examples are presented to illustrate our results.
Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of the Drosophila Hox Protein Ultrabithorax (2008)

During animal development, distinct tissues, organs, and appendages are specified through differential gene transcription by Hox transcription factors. However, the conserved Hox homeodomains bind DNA with high affinity yet low specificity. We have therefore explored the structure of the Drosophila melanogaster Hox protein Ultrabithorax and the impact of its nonhomeodomain regions on DNA binding properties. Computational and experimental approaches identified several conserved, intrinsically disordered regions outside the homeodomain of Ultrabithorax that impact DNA binding by the homeodomain. Full-length Ultrabithorax bound to target DNA 2.5-fold weaker than its isolated homeodomain. Using N-terminal and C-terminal deletion mutants, we demonstrate that the YPWM region and the disordered microexons (termed the I1 region) inhibit DNA binding approximately 2-fold, whereas the disordered I2 region inhibits homeodomain-DNA interaction a further approximately 40-fold. Binding is restored almost to homeodomain affinity by the mostly disordered N-terminal 174 amino acids (R region) in a length-dependent manner. Both the I2 and R regions contain portions of the activation domain, functionally linking DNA binding and transcription regulation. Given that (i) the I1 region and a portion of the R region alter homeodomain-DNA binding as a function of pH and (ii) an internal deletion within I1 increases Ultrabithorax-DNA affinity, I1 must directly impact homeodomain-DNA interaction energetics. However, I2 appears to indirectly affect DNA binding in a manner countered by the N terminus. The amino acid sequences of I2 and much of the I1 and R regions vary significantly among Ultrabithorax orthologues, potentially diversifying Hox-DNA interactions.
Induction of Mesenchymal Stem Cells from Umbilical Cord Blood into Myoctye in vitro (2005)

Objective To study the collection,culture and proliferation in vitro of mesenchymal stem cells (MSC) from canine umbilical cord blood (UCB), and to explore the possibility of differentiation of MSC into myocytes. Methods A certain amount of cord blood (5～20 mL) was collected from the hybrid pregnant canine. The mononuclear cells isolated from UCB were seeded in four different culture media: IMDM、a-MEM、DMEM and EBM-Ⅱ. The expression of surface antigens of UCB-derived MSC was detected. The MSC were treated with 5-azacytidine. After observation for 3～4 weeks continuously, then the expressions of several specific antigens of myocytes were detected. Results The canine MSC cultured in IMDM medium expanded rapidly; the cells increased two to three times in number with each passage. The cord blood could give rise to two different kinds of cells, one was the osteoclast-like, and the other fibroblast-like, and the latter expressed antigens CD29 and CD71, but did not express CD11a、CD11b and CD34. The UCB-derived MSC after being treated with 5-aza at 10 μmol/L, were elongated and connected with adjacent cells, and expressed antigen α-actin and desmin, similar to positive control group. Conclusion The UCB-derived MSC are different from the hematopoietic stem cells, and can expand largely in vitro and may differentiate into myocytes under certain circumstances.
Characterization of a Low-Cost Optical Flow Sensor When Using an External Laser as a Direct Illumination Source (2011)

In this paper, a low cost optical flow sensor is combined with an external laser device to measure surface displacements and mechanical oscillations. The measurement system is based on applying coherent light to a diffuser surface and using an optical flow sensor to analyze the reflected and transferred light to estimate the displacement of the surface or the laser spot. This work is focused on the characterization of this measurement system, which can have the optical flow sensor placed at different angles and distances from the diffuser surface. The results have shown that the displacement of the diffuser surface is badly estimated when the optical mouse sensor is placed in front of the diffuser surface (angular orientation >150°) while the highest sensitivity is obtained when the sensor is located behind the diffuser surface and on the axis of the laser source (angular orientation 0°). In this case, the coefficient of determination of the measured displacement, R(2), was very high (>0.99) with a relative error of less than 1.29%. Increasing the distance between the surface and the sensor also increased the sensitivity which increases linearly, R(2) = 0.99. Finally, this measurement setup was proposed to measure very low frequency mechanical oscillations applied to the laser device, up to 0.01 Hz in this work. The results have shown that increasing the distance between the surface and the optical flow sensor also increases the sensitivity and the measurement range.
Poly(methyl methacrylate) CE microchips replicated from poly(dimethylsiloxane) templates for the determination of cations (2006)

A novel method for the rapid fabrication of poly(methyl methacrylate) (PMMA) microfluidic chips using poly(dimethylsiloxane) (PDMS) templates has been demonstrated. The PDMS molds were fabricated by soft lithography. The dense prepolymerized solution of methyl methacrylate containing thermal and UV initiators was allowed to polymerized between a PDMS template and a piece of a 1 mm thick commercial PMMA plate under a UV lamp. The images of microchannels on the PDMS template were precisely replicated into the synthesized PMMA substrates during the UV-initiated polymerization of the prepolymerized solution on the surface of the PMMA plate at room temperature. The polymerization could be completed within 10 min under ambient temperature. The chips were subsequently assembled by thermal bonding of the channel plate and the cover sheet. The new fabrication method obviates the need for specialized replication equipment and reduces the complexity of prototyping and manufacturing. Nearly 20 PMMA chips were replicated using a single PDMS mold. The attractive performance of the new microfluidic chips has been demonstrated by separating and detecting cations in connection with contactless conductivity detection. The fabricated PMMA microchip has also been successfully employed for the determination of potassium and sodium in environmental and biological samples.
State of the Art in Example‐Based Motion Synthesis for Virtual Characters in Interactive Applications (2010)

Abstract Animated virtual human characters are a common feature in interactive graphical applications, such as computer and video games, online virtual worlds and simulations. Due to dynamic nature of such applications, character animation must be responsive and controllable in addition to looking as realistic and natural as possible. Though procedural and physics‐based animation provide a great amount of control over motion, they still look too unnatural to be of use in all but a few specific scenarios, which is why interactive applications nowadays still rely mainly on recorded and hand‐crafted motion clips. The challenge faced by animation system designers is to dynamically synthesize new, controllable motion by concatenating short motion segments into sequences of different actions or by parametrically blending clips that correspond to different variants of the same logical action. In this article, we provide an overview of research in the field of example‐based motion synthesis for interactive applications. We present methods for automated creation of supporting data structures for motion synthesis and describe how they can be employed at run‐time to generate motion that accurately accomplishes tasks specified by the AI or human user.
Production and characterization of monoclonal antibodies specific for the transmembrane protein of simian immunodeficiency virus from the African green monkey (1988)

Mouse monoclonal antibodies were produced against simian immunodeficiency virus (SIV) from the African green monkey (SIVAGM). The antibodies reacted with the transmembrane protein of all five SIVAGM isolates but not with those of SIVs from the rhesus macaque and mandrill or of human immunodeficiency virus type 1 or type 2, indicating that they recognize a species-specific epitope strongly conserved in SIVAGM. The transmembrane proteins of several SIVAGM isolates were found to vary in molecular size, even in the deglycosylated form after N-glycanase treatment, indicating heterogeneity of the SIVAGM isolates.
Structural changes of synthetic paulingite (Na,H-ECR-18) upon dehydration and CO<sub>2</sub> adsorption (2015)

Abstract The structure of dehydrated calcined ECR-18, synthetic paulingite, topology type PAU, unit cell composition Na 132 H 28 Si 512 Al 160 O 1344 , has been determined by Rietveld refinement against synchrotron X-ray powder diffraction data. Upon dehydration the symmetry of Na,H-ECR-18 changes from <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>I</m:mi> <m:mi>m</m:mi> <m:mover> <m:mn>3</m:mn> <m:mo>¯</m:mo> </m:mover> <m:mi>m</m:mi> </m:mrow> </m:math> $Im\bar 3m$ to <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>I</m:mi> <m:mover> <m:mn>4</m:mn> <m:mo>¯</m:mo> </m:mover> <m:mn>3</m:mn> <m:mi>m</m:mi> <m:mo>,</m:mo> </m:mrow> </m:math> $I\bar 43m,$ with a corresponding decrease of cubic unit cell a parameter from 34.89412(1) Å to 33.3488(3) Å. This occurs as the framework distorts to afford closer coordination of Na + cations by framework O atoms in 8-ring window sites of the seven cage types present. Na + cations in 8R sites block the access of N 2 molecules to the internal pore space at 77 K but CO 2 adsorption at 308 K is observed, and is postulated to occur via a ‘trapdoor’ mechanism. In situ PXRD during CO 2 adsorption at pressures up to 10 bar show reversible broadening of diffraction peaks that is attributed to local crystallographic strain.
Extract from the Leaves of<i>Toona sinensis Roemor</i>Exerts Potent Antiproliferative Effect on Human Lung Cancer Cells (2002)

Recent study indicated that the components of Toona sinensis Roemor have potent anti-inflammatory and analgesic effects. These components have also been reported to inhibit the growth of boils in vivo. In this study, we investigated the effect of crude extract from the leaves of Toona sinensis Roemor on the proliferation of A549 lung cancer cells. We found that the extract effectively blocked cell cycle progression by inhibiting the expression of cyclin D1 and E in A549 cells. Additionally, incubation of the extract led to activation of caspase-3-like proteases and apoptotic cell death. Conversely, the extract did not show any significant cytotoxic effect on primarily cultured human foreskin fibroblasts or MRC-5 human lung fibroblasts. Therefore, antiproliferative action of the extract is specific for tumor cells. Our results suggest that the components of Toona sinensis Roemor have potent anticancer effects in vitro and identification of the useful components in the extract may lead to the development of a novel class of anticancer drugs.
The Distributed Firing Squad Problem (1989)

The distributed firing squad problem is defined in the context of a synchronous distributed system where the correct processors operate in lock-step synchrony but do not share a global clock. If one or more correct processors receive a command to start a firing squad synchronization, then at some future time all correct processors must “fire” (formally, enter a special state) at exactly the same step. For various fault models, upper and lower bounds are proved on the number of faulty processors that can be tolerated and on the number of rounds of communication required between the reception of the start command and firing. For example, if a firing squad protocol is resilient to t fail-stop faults, then at least $t + 1$ rounds are necessary and sufficient. For the case of Byzantine faults with authentication where the faulty processors can take steps in between the synchronous steps of the correct processors, the firing squad problem can be solved in $t + 5$ rounds, provided that $n > 3t$, where n is the number of processors and t is the number of faults, and the problem cannot be solved at all if $n \leqq 3t$. Moreover, in the case that $n \leqq 3t$, the impossibility of a firing squad protocol holds even for a weaker “timing fault model” where all processors generate messages correctly according to the protocol, but the faulty processors can affect the system by slightly slowing down or speeding up messages.
Non‐peptide antagonists, CP‐96,345 and RP 67580, distinguish species variants in tachykinin NK<sub>1</sub> receptors (1993)

1. The potency of the non-peptide antagonists CP-96,345 and RP 67580 on NK1 receptor-stimulated [3H]-inositol phosphate accumulation in cell lines or tissue from three different species has been examined. 2. We have used: UC11 cells, derived from a human astrocytoma, and rat LRM55 glial cells, both of which express large numbers of functional NK1 receptors, and the well characterized guinea-pig ileum which expresses both NK1 and NK3 receptors. 3. RP 67580 has an approximately 25 fold lower affinity for NK1 receptors in human UC11 cells (Kd = 194 nM) than in rat LRM55 cells (Kd = 7.9 nM), in contrast CP-96,345 has an approximately 200 fold lower affinity in rat LRM55 cells (Kd = 210 nM) relative to human UC11 cells (Kd = 0.99 nM). The pharmacological profile of CP-96,345 and RP 67580 in guinea-pig ileum was similar to that observed in human UC11 cells. 4. In conclusion, we have demonstrated that previously reported species differences in binding affinities for the non-peptide NK1 antagonists, CP-96,345 and RP 67580, are also observed in inhibition of NK1 receptor stimulated hydrolysis of inositol phospholipids.
Preferential loss of IL‐2–secreting CD4+ T helper cells in chronic HCV infection† (2005)

Hepatitis C virus (HCV) becomes persistent in the majority of infected individuals. In doing so, the virus evades host adaptive immune responses, although the mechanisms responsible in this evasion are not clear. Several groups have demonstrated weak or absent HCV-specific CD4+ T cell responses during chronic HCV infection using proliferation assays and, more recently, class II tetramers. However, the functional status of HCV-specific CD4+ T cells in resolved and persistent infection is poorly understood. Using interferon gamma (IFN-gamma) and interleukin 2 (IL-2) enzyme-linked immunospot assays, we analyzed cytokine secretion patterns in chronically infected patients and compared them with those with resolved infection. In the spontaneous resolver group, strong IL-2 secretion in relation to IFN-gamma secretion was observed. However, in the persistently infected group, a consistent and significant loss of IL-2-secreting cells, compared with IFN-gamma-secreting cells, was identified. In vitro addition of IL-2 had a substantial effect in restoring CD4+ T cell activity. In conclusion, failure of IL-2 secretion, as opposed to physical deletion or complete functional unresponsiveness, appears to be an important determinant of the status of CD4+ T cell populations in chronic HCV infection. Loss of IL-2 secretory capacity may lead to disruption of IFN-gamma and proliferative function in vivo-a status that characterizes the cellular immune response in both CD4+ and CD8+ compartments in chronic disease.