gebhart/patrepeval huggingface dataset:
Supplementary Figures 1 through 6 from Integrin αvβ6 Promotes an Osteolytic Program in Cancer Cells by Upregulating MMP2 (2023)

&lt;p&gt;PDF - 529K, Expression of alphavbeta6 does not affect PC3-2 integrin profile (S1); alphavbeta6 promotes osteolysis in vivo (S2); alphavbeta6 increases osteolytic lesions and osteoclast recruitment in vivo (S3); Downregulation of alphavbeta6 reduces MMP2 levels in RWPE cells (S4); Exogenous expression of alphavbeta6 and alphavbeta3 in C4-2B transfectants (S5); MMP2 is co-expressed with alphavbeta6 in human prostate cancer osteolytic metastases (S6).&lt;/p&gt;
Outage probability of wireless networks with directional antennas (2005)

In this paper, we consider wireless networks with directional antennas using slotted ALOHA medium access control. The channel model incorporates the effects of propagation loss and shadowing with Rayleigh fading. By deriving the cumulative distribution function of the signal-to-interference-and-noise ratio of a certain link in the network, the outage probability of the link is analyzed. In particular, the analysis works for arbitrary beam patterns of the directional antennas used in the networks. Moreover, we propose a new parameter, the array interference factor (AIF), which fully characterizes the performance of any beam pattern in a wireless network over fading channels. Using a beam pattern with smaller AIF will give a better performance than other beam patterns with larger AIF values. The analysis of this paper enables us to find the optimal mobile density and the most efficient transmission power setting for such wireless networks.
A PROBE IMPACT SENSOR FOR FRUIT FIRMNESS MEASUREMENT (1991)

A probe sensor was developed for measuring the impact characteristics of various fruits and predicting firmness. The sensor was operated by an air cylinder which released and returned an impact mass in the probe body. The acceleration of the mass was recorded. Algorithms were developed to analyze shape characteristics of the impact force (Vp=peak accelerometer output, tp=time to peak acceleration, and c2=Vp/tp2). Correlation coefficients between penetrometer firmness and Vp were 0.92, 0.80, and 0.55 for peaches, pears, and apples, respectively. Results for peaches and pears were slightly better than the previous system of a fruit striking a flat rigid surface. Local variations in firmness around the apple surface increased the variability in sensor response, resulting in low correlations with firmness measurements.
Design for testability—A survey (1983)

This paper discusses the basics of design for testability. A short review of testing is given along with some reasons why one should test. The different techniques of design for testability are discussed in detail. These include techniques which can be applied to today's technologies and techniques which have been recently introduced and will soon appear in new designs.
A Revisit of Action Detection Using Improved Trajectories (2018)

In this paper, we revisit trajectory-based action detection in a potent and non-uniform way. Improved trajectories have been proven to be an effective model for motion description in action recognition. In temporal action localization, however, this approach is not efficiently exploited. Trajectory features extracted from uniform video segments result in significant performance degradation due to two reasons: (a) during uniform segmentation, a significant amount of noise is often added to the main action and (b) partial actions can have negative impact in classifier's performance. Since uniform video segmentation seems to be insufficient for this task, we propose a two-step supervised non-uniform segmentation, performed in an online manner. Action proposals are generated using either 2D or 3D data, therefore action classification can be directly performed on them using the standard improved trajectories approach. We experimentally compare our method with other approaches and we show improved performance on a challenging online action detection dataset.
Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions (2021)

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant-bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two <i>Paenibacillus</i> sp. strains and one <i>Erwinia gerundensis</i> strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant-bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.
LMP1 Protein from the Epstein-Barr Virus Is a Structural CD40 Decoy in B Lymphocytes for Binding to TRAF3 (2005)

Epstein-Barr virus is a human herpesvirus that causes infectious mononucleosis and lymphoproliferative malignancies. LMP1 (latent membrane protein-1), which is encoded by this virus and which is essential for transformation of B lymphocytes, acts as a constitutively active mimic of the tumor necrosis factor receptor (TNFR) CD40. LMP1 is an integral membrane protein containing six transmembrane segments and a cytoplasmic domain at the C terminus that binds to intracellular TNFR-associated factors (TRAFs). TRAFs are intracellular co-inducers of downstream signaling from CD40 and other TNFRs, and TRAF3 is required for activation of B lymphocytes by LMP1. Cytoplasmic C-terminal activation region 1 of LMP1 bears a motif (PQQAT) that conforms to the TRAF recognition motif PVQET in CD40. In this study, we report the crystal structure of this portion of LMP1 C-terminal activation region-1 (204PQQATDD210) bound in complex with TRAF3. The PQQAT motif is bound in the same binding crevice on TRAF3 where CD40 is bound, providing a molecular mechanism for LMP1 to act as a CD40 decoy for TRAF3. The LMP1 motif is presented in the TRAF3 crevice as a close structural mimic of the PVQET motif in CD40, and the intermolecular contacts are similar. However, the viral protein makes a unique contact: a hydrogen bond network formed between Asp210 in LMP1 and Tyr395 and Arg393 in TRAF3. This intermolecular contact is not made in the CD40-TRAF3 complex. The additional hydrogen bonds may stabilize the complex and strengthen the binding to permit LMP1 to compete with CD40 for binding to the TRAF3 crevice, influencing downstream signaling to B lymphocytes and contributing to dysregulated signaling by LMP1.
Physics and Simulation of Smallest Plasmonic Semiconductor Nano-Disk Laser at Near Surface Plasmon Resonance (2013)

Semiconductor plamsonic nanodisk lasers (SPNDL) are investigated at near silver-semiconductor plasmon resonance region. We show via simulation the size of SPNDL at 600nm has effective mode volume 1.31×10−4 λ03, smallest of any lasers to date.
Dissecting the Human Response to Staphylococcus aureus Systemic Infections (2021)

<i>Staphylococcus aureus</i> is a common human commensal and the leading cause of diverse infections. To identify distinctive parameters associated with infection and colonization, we compared the immune and inflammatory responses of patients with a diagnosis of invasive <i>S. aureus</i> disease to healthy donors. We analyzed the inflammatory responses founding a pattern of distinctive cytokines significantly higher in the patients with invasive disease. The measure of antibody levels revealed a wide antibody responsiveness from all subjects to most of the antigens, with significantly higher response for some antigens in the invasive patients compared to control. Moreover, functional antibodies against toxins distinctively associated with the invasive disease. Finally, we examined the genomic variability of isolates, showing no major differences in genetic distribution compared to a panel of representative strains. Overall, our study shows specific signatures of cytokines and functional antibodies in patients with different primary invasive diseases caused by <i>S. aureus</i>. These data provide insight into human responses towards invasive staphylococcal infections and are important for guiding the identification of novel preventive and therapeutic interventions against <i>S. aureus</i>.
In vivo micro-imaging of apoptosis in a murine xenograft model of human lung adenocarcinoma (2014)

Background: Resistance to apoptosis is a hallmark of cancer that can be reversed by chemotherapy drugs and targeted therapies, including cisplatin and erlotinib. In vivo in situ imaging of apoptosis may be useful for the early assessment of drug activity. The aim of this study is to investigate whether in vivo micro-imaging of apoptosis is correlated with treatment response in a murine xenograft model of human lung cancer. Methods: A549 (EGFR wild type), H1650 (carrying EGFR exon 19 deletion, sensitive to Erlotinib) and H1975 (carrying EGFR mutations L858R and T790M, resistant to Erlotinib) cell lines were used to induce subcutaneous tumors in Nude mice. In vivo micro-imaging of apoptosis in experimental tumors was performed using fibered confocal fluorescence microscopy (FCFM) after intra-venous injection of a fluorogenic caspase 3 substrate. Tumors were treated by cisplatin (10mg/kg) (5 mice, A549 xenografts), erlotinib (25mg/kg) (6 mice, 2 A549, 2 H1650, 2 H1975), or vehicle (6 mice, 2 A549, 2 H1650, 2 H1975). Results: In A549 xenografts treated by cisplatin, apoptosis was detected in vivo at 24h post-treatment. Fluorescence intensity ratio (FIR) was significantly higher compared to untreated tumors (16.9+/-3.1 vs 4.8+/-2.1 respectively, p&lt;0.001). 24h after treatment by erlotinib, FIR in H1650 erlotinib sensitive tumors was significantly higher than in A549 tumors, and than in H1975 erlotinib resistant tumors (12.2+/-2.4 vs 6.1+/-1.2 vs 1.9+/-0.7 respectively, p&lt;0.01). Conclusion : In vivo micro-imaging of apoptosis is possible and appears able to predict tumor response in a xenograft model of EGFR mutated human lung adenocarcinoma.
Paraneoplastic Syndrome (2014)

Rare and diagnostically challenging, paraneoplastic syndromes can appear months to years before detection of their underlying neoplasms and are associated with rapidly progressive neurologic deficits, including cochleovestibulopathy and death. Less than 20 cases of paraneoplastic cochleovestibulopathy have been reported in the online database PubMed. We present three recent cases: one patient with a history of B-cell follicular lymphoma who developed dermatomyositis and hearing loss before detection of lymphoma recurrence in his anterior chest wall, a second patient with sudden asymmetric hearing loss, found to have a 12-cm renal mass before death, and a third with fluctuating bilateral hearing loss who was ultimately found to have a thymoma. Although characterized as type VI (non-immune rapidly progressive sensorineural hearing loss) within the Harris autoimmune inner ear disease classification system, the mechanism of paraneoplastic cochleovestibulopathy is not well understood. Although specific anti-neuronal antibodies such as anti-Hu may be associated with other paraneoplastic neurologic disorders, these antibodies have limited diagnostic utility with paraneoplastic cochleovestibulopathy. Steroids have limited efficacy with regard to hearing recovery, whereas intravenous immunoglobulin has been shown to be of benefit. These recent cases demonstrate how auditory and vestibular deficits may be indicative of a rare but potentially life-threatening occult neoplasm where timely diagnosis is critical. We believe that understanding paraneoplastic cochleovestibulopathy is of interest across a broad range of clinical practices.
Orbital mapping of energy bands and the truncated spin polarization in three-dimensional Rashba semiconductors (2016)

Associated with spin-orbit coupling (SOC) and inversion symmetry breaking, Rashba spin polarization opens an avenue for spintronic applications that was previously limited to ordinary magnets. However, spin-polarization effects in actual Rashba systems are far more complicated than what conventional single-orbital models would suggest. By studying via density functional theory and a multiorbital $k\ifmmode\cdot\else\textperiodcentered\fi{}p$ model a three-dimensional bulk Rashba system (free of complications by surface effects), BiTeI, we find that the physical origin of the leading spin-polarization effects is SOC-induced hybridization between spin and multiple orbitals, especially those with nonzero orbital angular momenta. In this framework we establish a general understanding of the orbital mapping, common to the surface of topological insulators and the Rashba system. Consequently, the intrinsic mechanism of various spin-polarization effects---which pertain to all Rashba systems, even those with global inversion symmetry---is understood as a manifestation of the orbital textures. This finding suggests a route for designing high-spin-polarization materials by considering the atomic-orbital content.
Efficient Heat Transfer in a Laminar Flow System by Hydrodynamic Manipulation (2009)

The effects of flow manipulation on the heat transfer performance of a laminar flow system were investigated. The combination of series of fins and oscillating flow was used due to its inherent advantage of triggering very complex transient interaction of eddies and flow deflection within the system. The investigations were performed with fluids providing Prandtl numbers Pr &amp;gt; 10. Steady Reynolds number in the range of 50 &amp;lt; Re &amp;lt; 1200 were studied. The duct with a hydraulic diameter Dh = 15 mm contains series of non-conducting fins. All geometrical parameters remain constant. Low frequency oscillation f &amp;lt; 100 Hz was used in order to obtain oscillation effects mainly dominated by oscillation velocity, and to avoid attenuation of the oscillation amplitude A in the device. Based on the experimental data, a correlation equation was developed. The energy dissipation as a result of applied oscillation was also determined by phase resolved measurements of the pressure difference and liquid displacement. The heat transfer coefficients were found to be dynamically controlled by the oscillations. The results show efficient heat transfer within the system due to the applied oscillation especially at low flow rates. At higher flow rates, the effect of the flow oscillation on the heat transfer performance of the system diminishes. With oscillating finned flow, the influence of the geometrical parameter Dh/L is not significant due to enhanced fluid mixing and repeated thermal boundary layer rearrangement as a result of the flow oscillation. The predictions of the correlation are reasonable. The results of the CFD show that for the fin spacing to be significant on the effectiveness of the finned system, the oscillating flow velocity must be higher than the mean flow velocity. Enhanced heat transfer performance is possible with increasing fin height but theoretically, this yields high pressure drop and increased pumping power. The calculated power input due to oscillation is comparatively low and decreases towards increasing net flow rates where the pulsating flow has a diminishing effect and the system approaches non-pulsating flow behaviour.
Preparation of Monodispersed Nanoparticles by Electrostatic Assembly of Keggin‐Type Polyoxometalates and 1,4,7‐Triazacyclononane‐Based Transition‐Metal Complexes. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The Effect of a Lower-Limb Sensory Prosthesis on Balance and Gait in People With Peripheral Neuropathy (2017)

Peripheral neuropathy (PN), commonly caused by diabetes mellitus, is a debilitating condition that currently affects approximately 20 million Americans. Chronic symptoms of PN often involve pain and weakness of the lower limbs, with eventual sensation loss on the plantar surfaces of the feet. According to epidemiological studies, reduced foot sole sensation has been linked to decreased standing stability [1] and an increased risk of falling [2]. Consequently, cost-effective interventions are needed to improve balance and mobility in this population. A growing body of research suggests that vibrotactile cues delivered to sensate areas of the lower limb may be an effective way to provide information about foot sole pressure to PN patients who experience poor balance control. Indeed, sensory substitution devices that provide vibrotactile feedback have been shown to aid in balance and improve postural control in various patient populations [3–7]. However, none of these technologies have been based on measurements of foot pressure nor have they been used as a balance prosthesis. The goal of this study was to investigate the effect of a new external lower-limb sensory prosthesis, the Walkasins™, on the balance and gait of individuals with PN who experience balance problems [8]. Walkasins™ consist of two parts: a leg unit and a foot pad (Figure 1). The leg unit wraps around the lower leg of the user and contains electronics for reading foot pad pressure signals, a microprocessor, and four vibrating motors that provide gentle tactile sensory cues to the front, back, medial, and lateral surfaces of the user’s leg. These cues reflect real-time foot pressure information at a location above the ankle where skin sensation is still present. The leg unit has a power button, two status LEDs, and a reset button (not shown in Figure 1). Power is supplied by a rechargeable internal battery. The foot pad is a thin consumable sole insert that can be cut to size and fit into a regular shoe. The foot pad connects to the leg unit through a physical cable. In this study, subjects performed gait and balance assessments with and without the Walkasins™ turned on in order to determine its short-term effects.
CDMA multi-user interference cancellation with reference symbol aided estimation of channel parameters (2002)

A novel multi-stage successive interference cancellation scheme is proposed which operates on the reverse CDMA link using BPSK modulation, coherent detection and reference symbols to obtain channel estimates. Single user analysis shows that the performance of the coherent detector with reference symbols is approximately 1.5 dB worse than that of an ideal coherent receiver on Rayleigh flat fading and frequency selective fading channel. Optimization of the parameters arising in the context of system implementation was also investigated. The results of a single cell multi-user investigation show that substantial capacity improvements can be obtained with successive interference cancellation using reference symbol channel estimates.
Biological activity of A-289099: an orally active tubulin-binding indolyloxazoline derivative. (2003)

In this report, we describe the antitumor activity of A-289099, an indolyloxazoline derivative with antimitotic activity. A-289099 decreased the proliferation of a variety of cells with EC(50) values ranging from 5.1 to 12.8 nM in a P-glycoprotein-independent manner. In cultured cells, microtubules depolymerized in a time- and dose-dependent manner when treated with A-289099. In competition-binding assays, A-298099 competed with [(3)H]colchicine for binding to tubulin (K(i) = 0.65 micro M); however, it did not compete with [(3)H]paclitaxel or [(3)H]vincristine. There was an accumulation of cells in G(2)-M after treatment with A-289099 for 8 h and a subsequent increase in a subdiploid population and an increase in caspase-3 activity, indicative of apoptosis after treatment for 24 and 48 h. The antitumor activities of A-289099 were evaluated using the syngeneic M5076 murine reticulum sarcoma flank tumor model. Animals size-matched for established tumors ( approximately 350 mm(3)) were dosed p.o. (50 mg/kg every day) for 11 days starting on day 10 postinoculation. Tumors from A-289099-treated animals regressed throughout the 11-day dosing period with a percentage of the average treated-tumor-volume divided by the average vehicle-control-tumor-volume (% T/C) value of 11% after treatment for 7 days. Examination of tumor sections revealed an increase in internucleosomal DNA fragmentation or cell death within the central core after drug-treatment. A decrease in the perfusion of tumors was observed after drug-treatment that was localized primarily to the central core and closely associated with the regions of cell death. In summary, our findings indicate A-289099 is a promising, orally active tubulin-binding compound with antitumor activity in vivo.
Temperature Directs the Majority‐Rules Principle in Supramolecular Copolymers Driven by Triazine–Benzene Interactions (2023)

Supramolecular copolymers have typically been studied in the extreme cases, such as self-sorting or highly mixed copolymer systems, while the intermediate systems have been less understood. We have reported the temperature-dependent microstructure in copolymers of triazine- and benzene-derivatives based on charge-transfer interactions with a highly alternating microstructure at low temperatures. Here, we investigate the temperature-dependent copolymerization further and increase the complexity by combining triazine- and benzene-derivatives with opposite preferred helicities. In this case, intercalation of the benzene-derivative into the triazine-derivative assemblies causes a helical inversion. The inversion of the net helicity was rationalized by comparing the mismatch penalties of the individual monomers, which indicated that the benzene-derivative dictates the helical screw-sense of the supramolecular copolymers. Surprisingly, this was not reflected in further investigations of slightly modified triazine- and benzene-derivatives, thus highlighting that the outcome is a subtle balance between structural features, where small differences can be amplified due to the competitive nature of the interactions. Overall, these findings suggest that the temperature-dependent microstructure of triazine- and benzene-based supramolecular copolymers determines the copolymer helicity of the presented system in a similar way as the mixed majority-rules phenomenon.