gebhart/patrepeval huggingface dataset:
Bortezomib antagonizes microtubule-interfering drug-induced apoptosis by inhibiting G2/M transition and MCL-1 degradation (2013)

Inhibition of the proteasome is considered as a promising strategy to sensitize cancer cells to apoptosis. Recently, we demonstrated that the proteasome inhibitor Bortezomib primes neuroblastoma cells to TRAIL-induced apoptosis. In the present study, we investigated whether Bortezomib increases chemosensitivity of neuroblastoma cells. Unexpectedly, we discover an antagonistic interaction of Bortezomib and microtubule-interfering drugs. Bortezomib significantly attenuates the loss of cell viability and induction of apoptosis on treatment with Taxol and different vinca alkaloids but not with other chemotherapeutics, that is, Doxorubicin and Cisplatinum. Importantly, Bortezomib inhibits G2/M transition by inhibiting proteasomal degradation of cell cycle regulatory proteins such as p21, thereby preventing cells to enter mitosis, the cell cycle phase in which they are most vulnerable to antitubulin chemotherapeutics. Consequently, Bortezomib counteracts Taxol-induced mitotic arrest and polyploidy, as shown by reduced expression of PLK1 and phosphorylated histone H3. In addition, Bortezomib antagonizes Taxol-mediated degradation of MCL-1 during mitotic arrest by preventing cells to enter mitosis and by inhibiting the proteasome. Downregulation of MCL-1 is critically required for Taxol-induced apoptosis, as overexpression of a phosphomutant MCL-1 variant, which is resistant to degradation, significantly diminishes Taxol-triggered apoptosis. Vice versa, attenuation of Bortezomib-mediated accumulation of MCL-1 by knockdown of MCL-1 significantly enhances Taxol/Bortezomib-induced apoptosis. Thus, Bortezomib rescues Taxol-induced apoptosis by inhibiting G2/M transition and mitigating MCL-1 degradation. The identification of this antagonistic interaction of Bortezomib and microtubule-targeted drugs has important implications for the design of Bortezomib-based combination therapies.
Supplementary Table 2 from Somatic Hypermethylation of <i>MSH2</i> Is a Frequent Event in Lynch Syndrome Colorectal Cancers (2023)

Supplementary Table 2 from Somatic Hypermethylation of &lt;i&gt;MSH2&lt;/i&gt; Is a Frequent Event in Lynch Syndrome Colorectal Cancers
A paradigm for distributed detection under communication constraints (2002)

We present a new paradigm for the decentralized detection problem under communication constraints. In this problem, local sensors send a hard decision or the likelihood ratio itself to the fusion center based on the specified communication constraint. An optimal system is designed by minimizing the risk function. Also, a simpler system design procedure based on Ali-Silvey distances is presented.
Physical and chemical properties of the regional mixed layer of Mexico's Megapolis (2009)

Abstract. The concentration of gases and aerosol particles have been measured at the mountain site of Altzomoni, 4010 m in altitude, located 60 km southeast of Mexico City, 50 km east of Puebla and 70 km northeast of Cuernavaca. The objective of this study was to evaluate the properties of gases and particles in the Regional Mixed Layer (RML) of Mexico's Megapolis. Altzomoni is generally above the RML from late evening until late morning at which time the arrival of the RML is marked by increasing concentrations of CO and aerosol particles that reach their maxima in mid-afternoon. The average diurnal cycles for fourteen days in March, 2006 were evaluated during which time the synoptic scale circulation had three principal patterns: from the east (E), southwest (SW) and west northwest (WNW). The original hypothesis was that air arriving from the direction of Mexico City would have much higher concentrations of anthropogenic gases and particles than air from Puebla or Cuernavaca, due to the relatively large differences in populations. In fact, not only were the average, maximum concentrations of CO and O3 (0.3 and 0.1 ppmv) approximately the same for air originating from the WNW and E, but the average maximum concentrations of Peroxyacyl nitrates (PAN,PPN) and particle organic matter (POM) in air from the E exceeded those in air from the WNW. Comparisons of measurements from the mountain site with those made by aircraft during the same period, using the same type of aerosol mass spectrometer, show that the total masses of POM, NO3−, SO42− and NH4+ were approximately the same from aircraft measurements made over Mexico City and when winds were from the east at the mountain site. In contrast 75% of the total aerosol mass at the mountain site was POM whereas over Mexico City the fraction of POM was less than 60%. The measurements suggest the occasional influence of emissions from the nearby volcano, Popocatepetl, as well as possible incursions of biomass combustion; however, the large concentrations of O3, PAN and POM suggest that secondary processes are the major source for these gases and particles. The similar concentrations in gases and particles when air is coming from the E and NWN raises the possibility of recirculation of air from Mexico City and the importance of this mechanism for impacting the regional air quality.
Digital filtering using logarithmic arithmetic (1971)

A method of computation is described in which all signals are encoded logarithmically, giving a great improvement in dynamic range compared with fixed-point linearly encoded arithmetic. Two ways of adding or subtracting logarithmically encoded numbers are suggested, together with a logarithmic digital-analogue convertor.
Interactive pediatric emergency checklists to the palm of your hand ‐ How the Pedi Crisis App traveled around the world (2017)

Google Analytics correlates session activity with geographic location based on local Internet service provider logs. Pedi Crisis had 1 252 active users (both new and returning) and 4 140 sessions across 108 countries during the 3-month study period. Returning users used the app longer and viewed significantly more screens that new users (mean screen views: new users 1.3 [standard deviation +/-1.09, 95% confidence interval 1.22-1.55]; returning users 7.6 [standard deviation +/-4.19, 95% confidence interval 6.73-8.39]P<.01) CONCLUSIONS: Pedi Crisis was used worldwide within days of its release and sustained utilization beyond initial publication. The proliferation of handheld electronic devices provides a unique opportunity for professional societies to improve the worldwide dissemination of guidelines and evidence-based cognitive aids.
Interferon-induced revertants of ras-transformed cells: resistance to transformation by specific oncogenes and retransformation by 5-azacytidine. (1987)

Prolonged alpha/beta interferon (IFN-alpha/beta) treatment of NIH 3T3 cells transformed by a long terminal repeat-activated Ha-ras proto-oncogene resulted in revertants that maintained a nontransformed phenotype long after IFN treatment had been discontinued. Cloned persistent revertants (PRs) produced large amounts of the ras-encoded p21 and were refractile to transformation by EJras DNA and by transforming retroviruses which carried the v-Ha-ras, v-Ki-ras, v-abl, or v-fes oncogene. Transient treatment either in vitro or in vivo with cytidine analogs that alter gene expression by inhibiting DNA methylation resulted in transformation of PR, but not of NIH 3T3, cells. The PR retransformants reverted again with IFN, suggesting that DNA methylation is involved in IFN-induced persistent reversion.
Data from MCPIP1 Selectively Destabilizes Transcripts Associated with an Antiapoptotic Gene Expression Program in Breast Cancer Cells That Can Elicit Complete Tumor Regression (2023)

&lt;div&gt;Abstract&lt;p&gt;The ability of cancer cells to evade apoptosis is dictated by a shift in the balance between proapoptotic and antiapoptotic gene expression programs. Monocyte chemotactic protein-induced protein 1 (MCPIP1) is a zinc-finger RNA binding protein with important roles in mediating inflammatory responses. Overexpression of MCPIP1 in different cancer cell types has been implicated in eliciting an antitumor response, but a direct role of MCPIP1 in apoptosis has not been established. In this study, we demonstrate that MCPIP1 functions as a potent tumor suppressor that induces apoptosis of breast tumor cells by selectively enhancing mRNA decay of antiapoptotic gene transcripts, including &lt;i&gt;Bcl2L1, Bcl2A1, RelB, Birc3&lt;/i&gt;, and &lt;i&gt;Bcl3&lt;/i&gt;. Mechanistically, MCPIP1 physically interacted with a stem–loop structure in the 3′ untranslated region of these transcripts through its PIN domain, causing mRNA destabilization. Furthermore, we found that MCPIP1 expression was repressed in breast tumor cells, and overexpression of MCPIP1 induced apoptosis, whereas its depletion enhanced cancer cell proliferation. Moreover, MCPIP1 induction &lt;i&gt;in vivo&lt;/i&gt; resulted in complete regression of established tumors and a significant reduction in metastatic disease. Notably, low MCPIP1 expression in tumor samples from breast cancer patients was strongly associated with poor survival over 13 years of follow-up. Collectively, our results highlight that MCPIP1 is a new tumor suppressor in breast cancer that induces cell death by tipping the balance in favor of proapoptotic gene expression. &lt;i&gt;Cancer Res; 76(6); 1429–40. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Wnt5a promotes differentiation of human dental papilla cells (2010)

Wnt5a promoted differentiation of HDPCs.
Simultaneous pharmacokinetic assessment of phytopharmaceuticals in fenugreek extract using LC–MS/MS in Sprague–Dawley rats (2023)

Fenugreek seeds are used in numerous marketed herbal formulations with therapeutic benefits. Some of its bioactive components such as 4-hydroxyisoleucine, trigonelline, raffinose, and pinitol are reported to possess potential therapeutic activities, such as antibacterial, antidiabetic, stomach stimulant, and anti-invasive, against hyperandrogenism and other allied diseases, including polycystic ovary syndrome. A fully validated, selective, and sensitive bioanalytical method for the simultaneous rapid quantification of the aforementioned bioactive components has been developed using hyphenated liquid chromatography electrospray tandem mass spectrometry. The analytes were separated within 5 min using gradient elution in a C18 column at a flow rate of 0.5 ml/min. Plasma protein precipitation technique was employed to isolate the analytes from the samples. Oral pharmacokinetic profile of the four bioactive components in Sprague-Dawley rats was further evaluated using noncompartmental analysis using Phoenix WinNonlin software.
Solid Phase Derivatizations in HPLC: Polymeric Permanganate Oxidations of Alcohols and Aldehydes in HPLC-SPR (1983)

Abstract On-line or off-line oxidations of various alcohols, aldehydes, and ketones can now be performed in conjunction with high performance liquid chromatography (HPLC), utilizing a newly developed polymeric permanganate solid phase reactor (SPR). These derivatization reactions are compatible with most reversed phase and normal phase solvents for HPLC separations, and many of these oxidations can be accomplished in real-time, on-line, at or above room temperature. Such HPLC-SPR approaches for chemical modifications and derivatizations of various oxidizable analytes provide a useful and quite practical newer approach for the HPLC-ultraviolet (UV) detection of appropriate analyte species. Difference chromatography, often with improved UV detection, can be used to confirm the suspected presence of a particular oxidizable analyte in a complex sample matrix. All of these solid phase derivatizations utilize conventional, commercially available HPLC instruments and accessories. These HPLC-SPR oxidation methods for chemical derivatization have also been applied to certain real world samples, in order to demonstrate the overall value and applicability of such analytical approaches.
Sensibility following Innervated Free TRAM Flap for Breast Reconstruction: Part II. Innervation Improves Patient-Rated Quality of Life (2009)

This study demonstrates that innervation of free TRAM flaps used for breast reconstruction not only improves sensibility but also has a positive effect on patient-rated quality of life.
Spatiotemporal soliton laser (2014)

Spatiotemporal solitons (STSs) are waves that are localized in all three dimensions of space as well as in time. They are of interest intrinsically as well as for ultrafast optical information processing, but their experimental observation remains a major challenge in nonlinear science. Two decades of investigation of STSs in optics has yielded only a few experimental demonstrations in conservative media. We present the realistic design and modeling of a solid-state laser that depends on the formation of dissipative STSs, which balance nonlinear gain and loss as well as linear and nonlinear phases. Numerical calculations show that stable, three-dimensional solitons can form in lasers containing self-focusing nonlinear materials with large normal dispersion. Experimental realization will be challenging but appears to be technologically achievable.
PSO in Two-Wheeled Self-Balancing Robot Control Research (2014)

Two self-balancing robot is a nonlinear, multivariable, intrinsically unstable motion control system, For traditional LQR controller feedback matrix optimization problem is difficult to determine, Particle swarm optimization algorithm to optimize the LQR controller feedback matrix, The simulation results show, Utilizing particle swarm optimized LQR controller improves the stability of the system, reducing the system overshoot and oscillation frequency.
Process for in-plane and out-of-plane single-crystal-silicon thermal microactuators (1996)

A process to manufacture single-crystal thermal actuators using silicon fusion bonding and electrochemical etch stop is presented. The process permits the simultaneous creation of in-plane and out-of-plane thermal actuators together with levers suitable for both directions of actuation. A final dry-release step is used, permitting the manufacture of MOS or bipolar devices in conjunction with actuators. Out-of-plane actuation of vertically levered devices has been demonstrated. The −3 dB response frequency of out-of-plane actuators is approximately 1000 Hz in air. Novel levered in-plane devices which achieve deflections of up to 200 μm have been fabricated. An estimate of the upper bound of thermal actuator efficiency is presented.
Extract and leaf powder effect of Artemisia annua on performance, cellular and humoral immunity in broilers (2013)

Summary The effects of methanolic extract and leaf powder of Artemisia annua were studied on performance, cellular and humoral immunity in 240 Cobb broiler chicks in a completely randomized design. Control group did not receive any treatment. The chicks in the second and third groups were fed with feed which contained 2000 and 4000 ppm plant extract in diet and in the groups 4, 5 and 6 chicks received 0.5, 1 and 1.5% of dietary Artemisia annua leaf powder, respectively. Daily feed intake, daily weight gain and feed conversion ratio (performance) were measured. Skin response to phytohemagglutinin-P (PHA-P) injected intradermally on day 16 was measured 24 and 48 h after injection. The birds were immunized with sheep red blood cells (SRBC) on days 8 and 22 of age and serum antibody levels produced in response to SRBC were measured on days 21, 28, 35 and 42. The weights of thymus and bursa of fabricius were also measured after slaughter. The results indicated that plant extract and leaf powder increased daily weight gain and reduced daily feed intake and feed conversion ratio (P<0.05). Plant extract and leaf powder increased cellular immunity on PHA-P injection after 24 and 48 h (P<0.05). Artemisia annua extract and leaf powder increased total anti-SRBC and IgG titer in experimental groups compared to control group (P<0.05). Thymus and bursa of fabricius weights were increased in treatment groups (P<0.05). It is concluded that Artemisia annua extract and leaf powder increases performance, cellular and humoral immunity of broilers.
Whole Genome Amplification of Sodium Bisulfite-Treated DNA Allows the Accurate Estimate of Methylated Cytosine Density in Limited DNA Resources (2006)

Sodium bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to sodium bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)--and compared with those obtained from bisulfite-treated DNA not subjected to WGA. Our data indicates that the DNA methylation profiles obtained from WGA of sodium bisulfite-treated DNA are consistent with those obtained from non-WGA DNA. The average difference in methylation percentage calculated from the two sets of template using MS-SNuPE was 4%. If our results are replicated on other genomic loci, WGA may become a useful technique in DNA methylation studies.
Device-to-Device Millimeter Wave Communications: Interference, Coverage, Rate, and Finite Topologies (2016)

Emerging applications involving device-to-device communication among wearable electronics require gigabits per second throughput, which can be achieved by utilizing millimeter-wave (mmWave) frequency bands. When many such communicating devices are indoors in close proximity, such as in a train, car, or airplane cabin, interference can be a serious impairment. This paper uses stochastic geometry to analyze the performance of mmWave networks with a finite number of interferers in a finite network region. Prior work considered either lower carrier frequencies with different antenna and channel assumptions, or a network with an infinite spatial extent. In this paper, human users not only carry potentially interfering devices, but also act to block interfering signals. Using a sequence of simplifying assumptions, accurate expressions for coverage and rate are developed that capture the effects of key antenna characteristics, such as directivity and gain, and are a function of the finite area and number of users. The assumptions are validated through a combination of analysis and simulation. The main conclusions are that mmWave frequencies can provide gigabits per second throughput even with omni-directional transceiver antennas, and larger, more directive antenna arrays give better system performance.
Faithful and Plausible Explanations of Medical Code Predictions (2021)

Machine learning models that offer excellent predictive performance often lack the interpretability necessary to support integrated human machine decision-making. In clinical medicine and other high-risk settings, domain experts may be unwilling to trust model predictions without explanations. Work in explainable AI must balance competing objectives along two different axes: 1) Explanations must balance faithfulness to the model's decision-making with their plausibility to a domain expert. 2) Domain experts desire local explanations of individual predictions and global explanations of behavior in aggregate. We propose to train a proxy model that mimics the behavior of the trained model and provides fine-grained control over these trade-offs. We evaluate our approach on the task of assigning ICD codes to clinical notes to demonstrate that explanations from the proxy model are faithful and replicate the trained model behavior.
An Approach to Pose-Based Action Recognition (2013)

We address action recognition in videos by modeling the spatial-temporal structures of human poses. We start by improving a state of the art method for estimating human joint locations from videos. More precisely, we obtain the K-best estimations output by the existing method and incorporate additional segmentation cues and temporal constraints to select the ``best'' one. Then we group the estimated joints into five body parts (e.g. the left arm) and apply data mining techniques to obtain a representation for the spatial-temporal structures of human actions. This representation captures the spatial configurations of body parts in one frame (by spatial-part-sets) as well as the body part movements(by temporal-part-sets) which are characteristic of human actions. It is interpretable, compact, and also robust to errors on joint estimations. Experimental results first show that our approach is able to localize body joints more accurately than existing methods. Next we show that it outperforms state of the art action recognizers on the UCF sport, the Keck Gesture and the MSR-Action3D datasets.
Dimerization of lipocalin allergens (2015)

Lipocalins are one of the most important groups of inhalant animal allergens. The analysis of structural features of these proteins is important to get insights into their allergenicity. We have determined two different dimeric crystal structures for bovine dander lipocalin Bos d 2, which was earlier described as a monomeric allergen. The crystal structure analysis of all other determined lipocalin allergens also revealed oligomeric structures which broadly utilize inherent structural features of the β-sheet in dimer formation. According to the moderate size of monomer-monomer interfaces, most of these dimers would be transient in solution. Native mass spectrometry was employed to characterize quantitatively transient dimerization of two lipocalin allergens, Bos d 2 and Bos d 5, in solution.
Oncogenic GNAQ and GNA11 Drive Tumorigenesis and Hyper‐Pigmentation in a Zebrafish Model of Human Uveal Melanoma (2015)

Uveal melanoma is the most common intraocular cancer, with an estimated 2000 cases diagnosed yearly in the U.S. Tumors arise from melanocytes in the choroid, iris, and ciliary body. Treatment typically includes proton beam therapy, and as such, the availability of tissue samples for research is limited. Approximately 50% of patients diagnosed with the disease develop untreatable liver metastases within 15 years. There is an urgent need to develop an animal model for uveal melanoma, in order to discover new therapeutics and understand disease initiation and progression. Approximately 83% of human uveal melanoma tumors have activating mutations in GNAQ or GNA11. Signaling pathways known to cause cell proliferation and survival are active downstream of mutated GNAQ or GNA11, but the exact signals responsible for metastasis remain to be discovered. We have developed a zebrafish model for human uveal melanoma by expressing mutated human GNA11 Q209L or GNAQ Q209L under control of the zebrafish melanocyte‐restricted mitfa promoter. Several lines have been identified that stably express either of the transgenes, Tg(mitfa:GNAQ Q209L ) or Tg(mitfa:GNA11 Q209L ) . These fish have been crossed to p53 M214K fish to facilitate tumor onset through a multi‐hit tumorigenic process. Tg(mitfa:GNAQ Q209L );p53 M214K and Tg(mitfa:GNA11 Q209L );p53 M214K zebrafish show hyper‐pigmentation in their skin and eyes. Fish develop tumors as early as 6 months of age. Our current efforts focus on the characterization of the tumors and the pigmentation defects. This model has revealed new mechanisms in pigmentation development and has provided insight into disease pathogenesis and metastasis.