gebhart/patrepeval huggingface dataset:
Interference of BAD (Bcl-xL/Bcl-2-Associated Death Promoter)-Induced Apoptosis in Mammalian Cells by 14–3-3 Isoforms and P11 (1997)

Apoptosis and survival of diverse cell types are under hormonal control, but intracellular mechanisms regulating cell death are unclear. The Bcl-2/Ced-9 family of proteins contains conserved Bcl-2 homology regions that mediate the formation of homo- or heterodimers important for enhancing or suppressing apoptosis. Unlike most other members of the Bcl-2 family, BAD (Bcl-xL/Bcl-2 associated death promoter), a death enhancer, has no C-terminal transmembrane domain for targeting to the outer mitochondrial membrane and nuclear envelope. We hypothesized that BAD, in addition to binding Bcl-xL and Bcl-2, may interact with proteins outside the Bcl-2 family. Using the yeast two-hybrid system to search for BAD-binding proteins in an ovarian fusion cDNA library, we identified multiple cDNA clones encoding different isoforms of 14-3-3, a group of evolutionally conserved proteins essential for signal transduction and cell cycle progression. Point mutation of BAD in one (S137A), but not the other (S113A), putative binding site found in diverse 14-3-3 interacting proteins abolished the interaction between BAD and 14-3-3 without affecting interactions between BAD and Bcl-2. Because the S137A BAD mutant presumably resembles an underphosphorylated form of BAD, we used this mutant to screen for additional BAD-interacting proteins in the yeast two-hybrid system. P11, a nerve growth factor-induced neurite extension factor and member of the calcium-binding S-100 protein family, interacted strongly with the mutant BAD but less effectively with the wild type protein. In Chinese hamster ovary (CHO) cells, transient expression of wild type BAD or its mutants increased apoptotic cell death, which was blocked by cotransfection with the baculovirus-derived cysteine protease inhibitor, P35. Cotransfection with 14-3-3 suppressed apoptosis induced by wild type or the S113A mutant BAD but not by the S137A mutant incapable of binding 14-3-3. Furthermore, cotransfection with P11 attenuated the proapoptotic effect of both wild type BAD and the S137A mutant. For both 14-3-3 and P11, direct binding to BAD was also demonstrated in vitro. These results suggest that both 14-3-3 and P11 may function as BAD-binding proteins to dampen its apoptotic activity. Because the 14-3-3 family of proteins could interact with key signaling proteins including Raf-1 kinase, protein kinase C, and phosphatidyl inositol 3 kinase, whereas P11 is an early response gene induced by the neuronal survival factor, nerve growth factor, the present findings suggest that BAD plays an important role in mediating communication between different signal transduction pathways regulated by hormonal signals and the apoptotic mechanism controlled by Bcl-2 family members.
Halogen‐Bridged Methylnaphthyl Palladium Dimers as Versatile Catalyst Precursors in Coupling Reactions (2021)

Halogen-bridged methylnaphthyl (MeNAP) palladium dimers are presented as multipurpose Pd-precursors, ideally suited for catalytic method development and preparative organic synthesis. By simply mixing with phosphine or carbene ligands, they are in situ converted into well-defined monoligated complexes. Their catalytic performance was benchmarked against state-of-the-art systems in challenging Buchwald-Hartwig, Heck, Suzuki and Negishi couplings, and ketone arylations. Their use enabled record-setting activities, beyond those achievable by optimization of the ligand alone. The MeNAP catalysts permit syntheses of tetra-ortho-substituted arenes and bulky anilines in near-quantitative yields at room temperature, allow mono-arylations of small ketones, and enable so far elusive cross-couplings of secondary alkyl boronic acids with aryl chlorides.
Iterative tuning of engine speed controller for launch control applications in sport motorcycles (2018)

In this work, engine rotational speed controller tuning issue is analyzed. To cope with actuation limitations, controller tuning is addressed in an iterative framework by means of the Iterative Feedback Tuning method. Subsequent iterations are needed to gain information on the controlled system and to meet closed-loop performance defined by means of a reference model. Finally, tuning results are discussed and closed-loop performance are analyzed.
Effects of Streptozotocin-induced Diabetes on Insulin Binding, Glucose Transport, and Intracellular Glucose Metabolism in Isolated Rat Adipocytes (1979)

Insulin receptors and various aspects of glucose metabolism were studied in isolated adipocytes from insulin-deficient streptozotocin (STZ)-treated diabetic rats. Severe diabetes was induced by high dose (55 mg/kg) STZ administration and mild diabetes was induced by low dose (40 mg/kg) STZ treatment. The high dose STZ group (morning plasma glucose level of 511 ± 32 mg/dl) became markedly catabolic and gained weight at a rate of only 0.6 ± 0.9 g/day as compared with 6.7 ± 0.8 g/day for controls. The low dose STZ group gained weight at a near normal rate (5.8 ± 0.7 g/day) despite modest hyperglycemia (morning plasma glucose 214 ± 36 ng/100 ml) and hypoinsulinemia. Insulin binding to receptors was increased 25% in the low dose group due to greater receptor capacity with no change in affinity and was increased 105% in the high dose group due to enhanced receptor affinity and capacity. Glucose transport activity was decreased in adipocytes from the diabetic animals, and, in addition, all aspects of intracellular glucose metabolism studied were depressed. These effects were greatest in the high dose group. In summary, (a) in severely diabetic, catabolic animals, insulin binding to receptors is increased due to enhanced receptor capacity and affinity; in mildly diabetic rats only receptor capacity is increased; (b) glucose transport activity and intracellular pathways of glucose metabolism are impaired in insulin-deficient diabetic animals, most likely due to hypoinsulinemia; and (c) the cellular insulin resistance of insulin-deficient diabetes is due to multiple defects in effector systems distal to the insulin receptor.
Supplementary Video 1a from Targeted Anti–Vascular Endothelial Growth Factor Receptor-2 Therapy Leads to Short-term and Long-term Impairment of Vascular Function and Increase in Tumor Hypoxia (2023)

&lt;p&gt;Representative cine-loop obtained using ultrasound biomicroscopic (UBM) imaging (as explained in Materials and Methods) corresponding to MDA-MB-231 tumor xenograft treated with DC101 for a 3-week period.&lt;/p&gt;
Challenges of a Fast Diagnostic to Inform Screening of Retired Batteries (2022)

With the increased pervasiveness of Lithium-ion batteries, there is growing concern for the amount of retired batteries that will be entering the waste or recycling stream before they are fully utilized. Although aged batteries no longer meet the demands of their first application, many still have a significant portion of their initial capacity remaining for use in secondary applications, but evaluating this capacity is difficult and time intensive. In this paper, we investigate the use of cell (or parallel sets of cells) internal resistance as a surrogate of the capacity of parallel cells. We also highlight the challenges of testing batteries as a full pack despite the cell-to-cell variability from lack of balancing and differences in resistance and capacity. First, we verify that the charge-interrupt resistance from parallel cell pairs from twelve retired battery packs can eliminate the need for the hybrid pulse power characterization (HPPC) test as long as the charge-interrupt tests were not applied at low cell pair terminal voltages. Then, the relation between cell internal resistance and capacity across the various packs is investigated. Initial experimental results from this study show a correlation between internal resistance and remaining capacity which can be approximated with a linear ft, suggesting internal resistance measurements taken above a threshold cell pair terminal voltage may be a suitable initial screening metric for aged batteries.
Nearest-neighbor caching for content-match applications (2009)

Motivated by contextual advertising systems and other web applications involving efficiency-accuracy tradeoffs, we study similarity caching. Here, a cache hit is said to occur if the requested item is similar but not necessarily equal to some cached item. We study two objectives that dictate the efficiency-accuracy tradeoff and provide our caching policies for these objectives. By conducting extensive experiments on real data we show similarity caching can significantly improve the efficiency of contextual advertising systems, with minimal impact on accuracy. Inspired by the above, we propose a simple generative model that embodies two fundamental characteristics of page requests arriving to advertising systems, namely, long-range dependences and similarities. We provide theoretical bounds on the gains of similarity caching in this model and demonstrate these gains empirically by fitting the actual data to the model. Copyright is held by the International World Wide Web Conference Committee (IW3C2).
The smallest carbon nanotube (2001)

Abstract We report here the discovery of the smallest possible carbon nanotube. This has a diameter of 4 Å, which is the narrowest attainable that can still remain energetically stable, as predicted by theory. These nanotubes are confined inside multiwalled carbon nanotubes and their diameter corresponds to that of a C20 dodecahedron with a single carbon atom at each of its twenty apices. Unlike larger carbon nanotubes, which, depending on their diameter and helicity, can be either metallic or semiconducting, these smallest nanotubes are always metallic.
Video retrieval using an MPEG-7 based inference network (2002)

This work proposes a model for video retrieval based upon the inference network model. The document network is constructed using video metadata encoded using MPEG-7 and captures information pertaining to the structural aspects (video breakdown into shots and scenes), conceptual aspects (video, scene and shot content) and contextual aspects (context information about the position of conceptual content within the document). The retrieval process a) exploits the distribution of evidence among the shots to perform ranking of different levels of granularity, b) addresses the idea that evidence may be inherited during evaluation, and c) exploits the contextual information to perform constrained queries.
Coded modulation using differential encoding over Rayleigh fading channels (2003)

Multilevel coding and bit-interleaved coded modulation using differential encoding and non-coherent reception over flat fading channels are assessed. In order to achieve high bandwidth efficiencies differential encoding is done with respect to phase, as well as with respect to amplitude of APSK constellations. Assuming the channel to be slowly time-varying, encoding and detection are based on blocks of N consecutive symbols (multiple symbol detection). In this paper, we provide the code design and present simulation results. It is shown that only for multilevel coding multiple symbol detection provides significant gains.
Study to Lower Cu Pillar Flip-Chip Failure Rate (2019)

Abstract Cu pillar flip-chip die technology has proved reliable and is widely used in chip-to-package mobile module products. There was a time when customers considered 500ppm (Parts per million) an acceptable defect rate. Now, tier 1 customers expect a defect rate of less than 50ppm. This high customer expectation drove this in-depth research and problem solve. Our main work includes: 1) Mapping and analyzing initial defects. 2) Developing an effective way to detect a low defect rate. 3) 3D mechanical modeling that focuses on multiple failure interfaces and modes. 4) Simulating stress factors and their impacts. 5) Verifying hypothesis with assembly design of experiment (DOE) and ultimately improved yield.
Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane (2021)

Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs-withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.
Distribution of proneuropeptide Y‐derived peptides in the brain of Rana esculenta and Xenopus laevis (1993)

The distribution of proneuropeptide Y-containing perikarya and nerve fibers in the brain of Rana esculenta and Xenopus laevis was determined with antisera directed toward neuropeptide Y and the carboxyl terminal flanking peptide. The distribution of proneuropeptide Y-like immunoreactivity was similar in both anurans. In the telencephalon, immunoreactive perikarya were found in the olfactory bulb, all subdivisions of the pallium, the septum, pars lateralis of the amygdala, the nucleus accumbens, and the anterior preoptic area. In the diencephalon, labelled perikarya were detected in the ventromedial, ventrolateral and central thalamic nuclei, the magnocellular preoptic nucleus, the suprachiasmatic nucleus, the posterior tuberculum, and the infundibulum. Amacrine-like cells were stained in the retina. In the pretectal area, posterior thalamic neurons showed intense, Golgi-like immunostaining. In the mesencephalon, immunoreactive cells were found in the reticular nucleus, the anteroventral tegmental nucleus, the optic tectum, the interpeduncular nucleus, and the torus semicircularis. In the rhombencephalon, labelled perikarya were detected in the secondary visceral nucleus, the central gray, the nucleus of the solitary tract, the dorsal column nuclei, and the spinal nucleus of the trigeminal nerve. Immunoreactive nerve fibers were observed in all areas of the brain that contained labelled perikarya. The densest accumulations were found in the accessory olfactory bulb, pars lateralis of the amygdala, the ventral habenula, the posterior pituitary, the optic tectum, the interpeduncular nucleus, and the saccular nucleus. The distribution of proneuropeptide Y-like immunoreactivity in the anuran brain showed many similarities to the distribution described for the amniote brain.
Evaluation of left ventricular volume and mass with breath-hold cine MR imaging. (1993)

Left ventricular (LV) volumes and mass were evaluated in 10 healthy volunteers with breath-hold cine magnetic resonance (MR) imaging. The results were compared with those obtained with conventional cine MR imaging. The breath-hold studies showed no ghosting artifact, and cardiac edges were clearly identified because of the reduced blurring. Measurements of LV end-diastolic volume (LVEDV), LV end-systolic volume (LVESV), and LV mass obtained with breath-hold cine MR imaging showed close correlation with those obtained with conventional cine MR imaging (r = .98, .97, and .99, respectively). The interobserver variabilities for LVEDV, LVESV, and LV mass determined with breath-hold cine MR imaging (4.0%, 8.0%, and 3.7%, respectively) were equal to or less than those determined with conventional cine MR imaging (4.0%, 8.6%, and 5.0%, respectively). The authors conclude that breath-hold cine MR imaging is highly useful because an accurate assessment of cardiac function is obtained in less than 5 minutes.
Receiver performance-complexity tradeoff in LTE MU-MIMO transmission (2011)

Multi-user multiple-input and multiple-output (MU-MIMO) transmission scheme provides potential gain in terms of system capacity in spatial correlated scenarios and is considered as one of the key technologies in Long Term Evolution (LTE) systems. The goal of this paper is to gain insight into MU-MIMO detection concepts and their implementation aspects. Various receiver architectures are investigated and their performance are assessed through an advanced link-level simulator. The motivation to study the MU-MIMO detectors rises from the weakness of the co-channel interference-unaware single user detector, the conventional detector for single user MIMO transmission. The most essential problem of these conventional single user detectors in MU-MIMO is the failing to detect signals under the residual interference caused by co-scheduled user, which reduces the performance of the detector. Different practical scenarios have been considered in the evaluation process, namely low and high spatial correlation channels with real channel estimation and feedback delay. Our investigation has shown that single user receivers, such as maximum ratio combiner, show generally poor performance in MU-MIMO scenario and as such they should be neglected for practical implementation. Furthermore, we have shown that the interference rejection combiner achieves the best performance-complexity tradeoff and outperforms conventional single user detectors only with a small increase of computation efforts in signal processing.
Extracting Message Sequence Charts from Hindi Narrative Text (2020)

Swapnil Hingmire, Nitin Ramrakhiyani, Avinash Kumar Singh, Sangameshwar Patil, Girish Palshikar, Pushpak Bhattacharyya, Vasudeva Varma. Proceedings of the First Joint Workshop on Narrative Understanding, Storylines, and Events. 2020.
The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube (2015)

As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon-based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress-strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress-strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed.
Power Harvesting System in Mobile Phones and Laptops using Piezoelectric Charge Generation (2010)

Abstract—This paper targets the transformation of mechanical energy to electrical energy using piezoelectric materials. With piezoelectric materials, it is possible to harvest power from vibrating structures. It has been proven that, micro to milliwatts of power can be generated from vibrating materials. In gadgets like mobile phones, television remotes, laptops and other devices which employ key depressions for operation, mechanical vibrations are produced while pressing the keys. If these vibrations are successfully harvested, the resulting energy could serve as an ancillary source of energy for charging the batteries. This paper presents a model of piezoelectric transducer for a gadget like, mobile phone, prototype of the power scavenging circuit, and the overall circuit for charging the mobile battery using the generated energy. Index Terms—Charge development, Diaphragm type piezoelectric crystal, Key depressions, Piezoelectric effect.
3D–2D registration in mobile radiographs: algorithm development and preliminary clinical evaluation (2015)

An image-based 3D-2D registration method is presented using radiographs acquired in the uncalibrated, unconstrained geometry of mobile radiography. The approach extends a previous method for six degree-of-freedom (DOF) registration in C-arm fluoroscopy (namely 'LevelCheck') to solve the 9-DOF estimate of geometry in which the position of the source and detector are unconstrained. The method was implemented using a gradient correlation similarity metric and stochastic derivative-free optimization on a GPU. Development and evaluation were conducted in three steps. First, simulation studies were performed that involved a CT scan of an anthropomorphic body phantom and 1000 randomly generated digitally reconstructed radiographs in posterior-anterior and lateral views. A median projection distance error (PDE) of 0.007 mm was achieved with 9-DOF registration compared to 0.767 mm for 6-DOF. Second, cadaver studies were conducted using mobile radiographs acquired in three anatomical regions (thorax, abdomen and pelvis) and three levels of source-detector distance (~800, ~1000 and ~1200 mm). The 9-DOF method achieved a median PDE of 0.49 mm (compared to 2.53 mm for the 6-DOF method) and demonstrated robustness in the unconstrained imaging geometry. Finally, a retrospective clinical study was conducted with intraoperative radiographs of the spine exhibiting real anatomical deformation and image content mismatch (e.g. interventional devices in the radiograph that were not in the CT), demonstrating a PDE = 1.1 mm for the 9-DOF approach. Average computation time was 48.5 s, involving 687 701 function evaluations on average, compared to 18.2 s for the 6-DOF method. Despite the greater computational load, the 9-DOF method may offer a valuable tool for target localization (e.g. decision support in level counting) as well as safety and quality assurance checks at the conclusion of a procedure (e.g. overlay of planning data on the radiograph for verification of the surgical product) in a manner consistent with natural surgical workflow.