gebhart/patrepeval huggingface dataset:
A top-down, step up approach to pharmacogenetic discovery using CEPH family cell lines (2005)

Background/Aims Previously Watters et al. (PNAS, 2004) found strong cell viability dose-response for 5-FU (0.21–0.70), and identified QTLs (chromosome 9: LOD=3.4) using public microsatellite data. We try to localize these toxicity genes using the HapMap published SNPs. Methods 30 CEPH HapMap trio cell lines, treated with 9 different doses of 5-FU, were analyzed at 4928 SNPs in the chromosome 9 QTL region. We used various statistical methods (179 SNPs were significant at p<0.05, uncorrected), including the False Discovery Rate, Storey's Q, and Sequential Multiple Decision Procedures (SMDP). Results Five SNPs were chosen as significant signals by SMDP at a power of 95% (but requiring only 78% of the sample), with sequential R2 of 0.16, 0.16, 0.17, 0.17, 0.11 respectively. Subselecting LD tag SNPs (Lazarus et al., 2004) reduces the number by nearly half, thus improving power. We employ a step up strategy from single SNPs to LD blocks to haplotypes, and finally to gene-based associations. Conclusions CEPH family cell lines are a powerful, unique resource for in vitro phamacogenetic toxicity gene discovery. Clinical Pharmacology & Therapeutics (2005) 77, P8–P8; doi: 10.1016/j.clpt.2004.11.031
An Efficient Scheme for Nonlinear Modeling and Predistortion in Mixed-Signal Systems (2006)

A novel identification and predistortion scheme of weakly nonlinear systems for mixed-signal devices, which takes into account practical implementation aspects, is presented. It is well known that for the identification of weakly nonlinear systems, despite the spectral regrowth, it suffices to sample the input-output (I/O) data of the system at the Nyquist rate of the input signal. Many applications such as linearization and mixed-signal simulations require system models at a higher sampling rate than Nyquist. Up to now, the construction of such high-rate models has been done by oversampling the corresponding I/O data. This leads to high computational complexity, ill posedness of the estimation, and high demand on the analog-to-digital-converter sampling rate for the implementation. This brief discusses an efficient way to obtain high-rate models and predistorters from low-rate models and shows the validity of the proposed scheme for a very-high-speed-digital-subscriber-line power amplifier, where an adjacent channel power supression of 20 dB is achieved
Conceptual studies on the integration of a nuclear reactor system to a manned rover for Mars missions (1991)

Multiyear civilian manned missions to explore the surface of Mars are thought by NASA to be possible early in the next century. Expeditions to Mars, as well as permanent bases, are envisioned to require enhanced piloted vehicles to conduct science and exploration activities. Piloted rovers, with 30 kWe user net power (for drilling, sampling and sample analysis, onboard computer and computer instrumentation, vehicle thermal management, and astronaut life support systems) in addition to mobility are being considered. The rover design, for this study, included a four car train type vehicle complete with a hybrid solar photovoltaic/regenerative fuel cell auxiliary power system (APS). This system was designed to power the primary control vehicle. The APS supplies life support power for four astronauts and a limited degree of mobility allowing the primary control vehicle to limp back to either a permanent base or an accent vehicle. The results showed that the APS described above, with a mass of 667 kg, was sufficient to provide live support power and a top speed of five km/h for 6 hours per day. It was also seen that the factors that had the largest effect on the APS mass were the life support power, the number of astronauts, and the PV cell efficiency. The topics covered include: (1) power system options; (2) rover layout and design; (3) parametric analysis of total mass and power requirements for a manned Mars rover; (4) radiation shield design; and (5) energy conversion systems.
In-situ monitoring of powder bed fusion of metals using eddy current testing (2022)

Powder bed fusion of metals (PBF-LB/M) is the most commonly used additive manufacturing process for the layerwise production of metal parts. Although the technology has developed rapidly in recent years, manufactured parts still lack consistent quality primarily owing to process-inherent variability, and the lack of effective sensing technologies enabling the ability to control the process during part production. Thus, there are high costs caused by rigorous post-process part inspection steps required to provide compliant part certificates. In contrast to typically deployed in-situ sensing technologies, eddy current testing (ECT) is a standardized nondestructive testing (NDT) technique able to provide compliant part certificates during post-process inspection according to existing standards. This study investigates the potential of ECT as an in-situ process monitoring technology for PBF-LB/M. Parts made from AlSi10Mg were manufactured on a PBF-LB/M machine using different process parameters yielding different relative densities ranging from 99%– 99.7%. During the build cycle, the parts were measured layer-by-layer with an ECT system mounted on the machine recoater. Signal analysis methods were developed which effectively separate and calibrate the electrical conductivity component (relative electrical conductivity) and the distance component (lift-off) of the ECT signals. The relative electrical conductivity was then compared to X-ray micro-computed tomography (μCT) measurement data demonstrating that layer-to-layer differences in relative density of about 0.1% can be successfully detected via ECT. In addition, the lift-off was used to monitor the thickness of the consolidated layers and the layer-to-layer part height. The results show that ECT is an effective technology for in-situ monitoring of the relative part density paving the way for deploying ECT for in-situ NDT of PBF-LB/M-manufactured parts.
Observer-Based Consensus of Nonlinear Positive Multi-Agent Systems with Saturated Control Input (2022)

This paper presents the distributed pinning consensus solution for nonlinear positive multi-agent systems with nonlinear control input by applying observer-based control protocols. The network topology is considered as a directed and fully connected structure. By considering sector input nonlinearities and various forms of topologies, two kinds of state observers involving standard observer and distributed pinning observer are presented for each regarded nonlinear agent by applying a novel analysis directly dealing with the nonlinear input and nonlinear system dynamics. The measured local output detail outlines the first observer, and the other observer is achieved via the corresponding output detail of its adjacent agents. Based on further observed state details, a distributed pinning observer-based strategy is derived for the leader-follower non-negative global consensus of the nonlinear positive multi-agent system. Additionally, two multi-step algorithms are proposed to set up the observer gains and each protocol criterion. Performance evaluations are provided to confirm the proposed control method and illustrate the effectiveness of the derived non-negative consensus observer-based protocols.
Liquid crystal effects on bacterial viability (2005)

The primary objective of this research was to test the hypothesis that lyotropic chromonic liquid crystals (neutral grey, red 14, blue 27, cromolyn) are not toxic to bacteria as compared with surfactant‐based lyotropic (CPCl and CsPFO) or thermotropic (5CB and E7) liquid crystals. Biocompatibility of most liquid crystals is currently unknown and is required for the development of systems interfacing liquid crystals and biological systems. Potential liquid crystal toxicity was evaluated by two methods. The first examined bacterial survival measured by bacterial growth over 24 hours, after exposure to various liquid crystals. The second toxicity method evaluated liquid crystal effects on bacterial membrane permeability using two fluorescent dyes. Three different types of bacteria were evaluated to assess bacterial structure differences with respect to liquid crystal toxicity. The results of this study indicate that lyotropic chromonic liquid crystals are not toxic to bacteria, whereas thermotropic and surfactant‐based lyotropic liquid crystals are toxic to one or more forms of bacteria. We conclude that lyotropic chromonic liquid crystals may be the preferred material in designing liquid crystal‐based systems that interact with biological systems, especially in the use of liquid crystal‐based biosensors.
Micelle-Encapsulated Quantum Dot-Porphyrin Assemblies as in Vivo Two-Photon Oxygen Sensors (2015)

Micelles have been employed to encapsulate the supramolecular assembly of quantum dots with palladium(II) porphyrins for the quantification of O2 levels in aqueous media and in vivo. Förster resonance energy transfer from the quantum dot (QD) to the palladium porphyrin provides a means for signal transduction under both one- and two-photon excitation. The palladium porphyrins are sensitive to O2 concentrations in the range of 0-160 Torr. The micelle-encapsulated QD-porphyrin assemblies have been employed for in vivo multiphoton imaging and lifetime-based oxygen measurements in mice with chronic dorsal skinfold chambers or cranial windows. Our results establish the utility of the QD-micelle approach for in vivo biological sensing applications.
Electrospun polyacrylonitrile nanofibrous biomaterials (2008)

An N-halamine precursor, 3-(5'-methyl-5'-hydantoinyl)acetanilide (I), was synthesized in our laboratory and loaded onto electrospun polyacrylonitrile fiber to prepare nanosized biocidal materials, which could be rendered antimicrobial by exposure to household bleach. Differential scanning calorimetry was used to study the thermal properties of the nanofibers with and without the N-halamine precursor and its chlorinated derivative loaded. Scanning electron microscopy demonstrated that the ultrafine fibers formed with diameters from 250 to 600 nm. Chlorinated nanofibrous mats composed of the fibers were challenged with Staphylococcus aureus (ATCC 6538) and Escherichia coli O157:H7 (ATCC 43895); they showed promising inactivation efficacies against the two bacterial species within 5 minutes of contact. Potential uses of the antimicrobial fibers include filters for industrial water and air disinfection and protective clothing.
Physical Data Warehousing Design (2009)

Recently, organizations have increasingly emphasized applications in which current and historical data are analyzed and explored comprehensively, identifying useful trends and creating summaries of the data in order to support high-level decision making. Every organization keeps accumulating data from different functional units, so that they can be analyzed (after integration), and important decisions can be made from the analytical results. Conceptually, a data warehouse is extremely simple. As popularized by Inmon (1992), it is a “subject-oriented, integrated, time-invariant, nonupdatable collection of data used to support management decision-making processes and business intelligence”. A data warehouse is a repository into which are placed all data relevant to the management of an organization and from which emerge the information and knowledge needed to effectively manage the organization. This management can be done using data-mining techniques, comparisons of historical data, and trend analysis. For such analysis, it is vital that (1) data should be accurate, complete, consistent, well defined, and time-stamped for informational purposes; and (2) data should follow business rules and satisfy integrity constraints. Designing a data warehouse is a lengthy, time-consuming, and iterative process. Due to the interactive nature of a data warehouse application, having fast query response time is a critical performance goal. Therefore, the physical design of a warehouse gets the lion’s part of research done in the data warehousing area. Several techniques have been developed to meet the performance requirement of such an application, including materialized views, indexing techniques, partitioning and parallel processing, and so forth. Next, we briefly outline the architecture of a data warehousing system.
Isolation of Recombinant Phage-Displayed Antibodies Recognizing Skin Keratinocytes (2004)

Advances in our understanding of biology at the molecular level are very much driven by improvements in the scientist's tool box. Such improvements may not only be an introduction of new techniques like polymerase chain reaction, but as much an increment of for example the sensitivity of existing methods. The in vitro generation of antibodies using phage display is one such technique, which continuously has been developed since its introduction more than 10 yr ago. As a result, selection of phage-displayed antibodies is emerging as a proteomic tool for the identification of differentially expressed cell surface antigens. Here, a method is described that enables the rapid isolation of a panel of recombinant antibodies recognizing epidermal skin keratinocytes. The method exploits the properties of a protease sensitive helper phage and facilitates the isolation of affinity-binders after a single round of selection. This assures a high diversity of binders owing to the reduction of experimental noise.
PPARδ preserves a high resistance to fatigue in the mouse medial gastrocnemius after spinal cord transection (2015)

The results indicate a conversion toward slower, more oxidative, and less fatigable muscle properties with overexpression of PPARδ. Importantly, the elevated fatigue resistance was maintained after ST, suggesting that enhanced PPARδ expression, and possibly small molecule agonists, could ameliorate the increased fatigability routinely observed in chronically paralyzed muscles.
Invited paper: Resilient and energy-secure power management (2017)

We present an industrial design perspective on power management. We focus primarily on server and mainframe class processors. However, recent advances in very low voltage (VLV) research in support of cognitive platforms of the future are also considered. A particular focus is on the special attention that needs to be placed on resilience and energy-secure design principles. The paper discusses how reliability gaps in power management hardware and/or algorithms can expose gaps in security in terms of so-called power attacks. We discuss current industrial practice and describe key challenges that need to be addressed by the research community in this regard. This is designed to be a tutorial-style survey and analysis paper.
Comparison of Patient-Specific Instruments with Standard Surgical Instruments in Determining Glenoid Component Position (2012)

Novel three-dimensional preoperative planning, coupled with patient and implant-specific instrumentation, allows the surgeon to better define the preoperative pathology, select the optimal implant design and location, and then accurately execute the plan at the time of surgery.
Calcium flux and endogenous calcium content in isolated mammalian growth-plate chondrocytes, hyaline-cartilage chondrocytes, and hepatocytes. (1985)

The role of chondrocyte mitochondria in endochondral ossification has been the subject of intensive investigation and controversy. The purpose of this study was to quantitate the endogenous calcium content and the maximum capacity for calcium accumulation and release in isolated mammalian growth-plate chondrocytes and hyaline-cartilage chondrocytes. The results indicated that the mitochondria of the isolated growth-plate and hyaline-cartilage chondrocytes possess a greater endogenous calcium content, a greater capacity for calcium accumulation, and a larger labile Ca+2 pool than do the mitochondria of hepatocytes. Growth-plate and hyaline-cartilage mitochondria had an endogenous calcium content of 908 and 142 nanomoles of Ca+2 per milligram of mitochondrial protein. The growth-plate mitochondria had a maximum calcium capacity of 5249 nanomoles of Ca+2 per milligram of mitochondrial protein. In comparison, the mitochondria of hepatocytes had a much smaller endogenous-calcium content and a smaller maximum Ca+2 capacity: twenty-one and 3262 nanomoles of Ca+2 per milligram of mitochondrial protein, respectively. The mitochondrial labile-calcium pool in both growth-plate and hyaline-cartilage chondrocytes was twofold greater than that in the mitochondria of hepatocytes. Chondrocyte mitochondria released approximately 2400 nanomoles of Ca+2 per milligram of mitochondrial protein, whereas hepatocyte mitochondria released 1200 nanomoles of Ca+2 per milligram. These results suggest that the chondrocyte mitochondria are specialized for calcium transport and are important in the calcification of the extracellular matrix of the growth plate.
Experience of a decade with endoscopic embryo transfer/implantation (HEED and SEED), improving results while reducing risks and side effects from IVF (2014)

Changes over the past two decades have offered many advantages in gynecologic patient care, surgery and medicine. These changes have continued the past five years, more importantly, with advances in science and technology. While most changes have been of great benefit for patients and physicians, some may have negative effects in areas related to cost, reimbursement and patient-physician relationship without overall improvement in patient morbidity. The gynecologic physician may have their greatest challenge in dealing with these changes while not forgetting basic surgical and patient care methods. Our task is to provide current gynecologic medicine that is cost-effective, quality andevidence-based care while achieving both patient and personal satisfaction.
Definitive Characterization of CA 19-9 in Resectable Pancreatic Cancer Using a Reference Set of Serum and Plasma Specimens (2015)

The validation of candidate biomarkers often is hampered by the lack of a reliable means of assessing and comparing performance. We present here a reference set of serum and plasma samples to facilitate the validation of biomarkers for resectable pancreatic cancer. The reference set includes a large cohort of stage I-II pancreatic cancer patients, recruited from 5 different institutions, and relevant control groups. We characterized the performance of the current best serological biomarker for pancreatic cancer, CA 19-9, using plasma samples from the reference set to provide a benchmark for future biomarker studies and to further our knowledge of CA 19-9 in early-stage pancreatic cancer and the control groups. CA 19-9 distinguished pancreatic cancers from the healthy and chronic pancreatitis groups with an average sensitivity and specificity of 70-74%, similar to previous studies using all stages of pancreatic cancer. Chronic pancreatitis patients did not show CA 19-9 elevations, but patients with benign biliary obstruction had elevations nearly as high as the cancer patients. We gained additional information about the biomarker by comparing two distinct assays. The two CA 9-9 assays agreed well in overall performance but diverged in measurements of individual samples, potentially due to subtle differences in antibody specificity as revealed by glycan array analysis. Thus, the reference set promises be a valuable resource for biomarker validation and comparison, and the CA 19-9 data presented here will be useful for benchmarking and for exploring relationships to CA 19-9.
Effect of NKISK on tendon lengthening: An in vivo model for various clinically applicable dosing regimens (2008)

One proposed mechanism of tendon lengthening is the "sliding fibril" hypothesis, in which tendons lengthen through the sliding of discontinuous fibrils after release of decorin-fibronectin interfibrillar bonds. The pentapeptide NKISK has been reported to inhibit the binding of decorin, a proteoglycan on the surface of collagen fibrils, to fibronectin, a tissue adhesion molecule, which are thought to play a role in interfibrillar binding. Prior investigations have demonstrated that NKISK produces in vivo tendon lengthening. This study investigates the effect of potential clinically applicable NKISK injection regimens in an in vivo model. One hundred and thirteen male Sprague-Dawley rats were divided into 15 different treatment groups, each receiving percutaneous patellar tendon injections of NKISK, QKTSK (a "nonsense" pentapeptide), or PBS of varying volumes, concentrations, and injection schedules. Following sacrifice, the patellar tendon lengths were measured in all groups, and biomechanical testing was performed with comparisons made to the contralateral, untreated control limbs. Tendon lengthening was significantly greater (p < or = 0.05) in nearly all NKISK-treated tendons as compared to PBS- and QKTSK-treated tendons and was dose-dependent. Measured lengthening was less in rats whose sacrifice was delayed following the final injection of NKISK, which likely indicates recontraction of lengthened tendons, but they remained significantly longer than the controls. Biomechanical testing did not reveal significant differences in ultimate load, modulus, stiffness, or displacement. This study demonstrates that NKISK given in clinically plausible dosing regimens produces dose-dependent tendon lengthening in an in vivo setting with minimal effects on the mechanical properties of the treated tendons.
BORIS, a novel cancer-testis antigen, is a potential target for immunotherapy in epithelial ovarian cancer (2005)

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Development and characterization of next generation eWLB (embedded Wafer Level BGA) packaging (2012)

The shrinkage of the pitches and pads at the chip to package interface is happening much faster than the shrinkage at the package to board interface. This interconnection gap requires fan-out packaging, where the package size is larger than the chip size in order to provide a sufficient area to accommodate the 2nd level interconnects. eWLB is a type of fan-out WLP that has the potential to realize any number of interconnects with standard pitches at any shrink stage of the wafer node technology. eWLB is one of key advanced packages because of advantages of higher number of I/Os, process easiness and integration flexibilities. Furthermore, it enables to integrate multiple dies vertically and horizontally in one package without using substrates. Thus, recently eWLB technology is moving forward to next generation packages, such as multi-die, low profile package and 3D SiP. This paper reports developments of next generation eWLB for advanced packaging solutions. A new portfolio of next generation package configurations: small outline eWLB, double-side 3D eWLB and eWLL (embedded Wafer Level Land Grid Array) are developed and characterized. And the reliability study was carried out in depth by experimental approaches. Successful reliability characterization results on different package configurations are reported that demonstrate next generation eWLB as an enabling technology for miniaturized, fine pitch, high density 3D and advanced silicon packaging solutions.