gebhart/patrepeval huggingface dataset:
Direct determination of diploid genome sequences (2016)

ABSTRACT Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses and, in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed, free of reference bias, but nearly all were constructed by merging homologous loci into single ‘consensus’ sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing and one using thousands of clone pools. Here we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ~1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new ‘pushbutton’ algorithm, Supernova. Each computation took two days on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.
Comparative Testing of Pulse Oximeter Probes (2004)

We studied the performance of pulse oximeter probes in a simulated environment. Our results show significant differences between some probes that affect the accuracy of measurement.
Performance Improvements from a Concave/Convex Planning Surface - Wiggle Hull (2014)

Concave camber can increase lift and Lift to Drag of a planing hull. The impact of camber and its limitations for a planing hull are reviewed, including model tests. The adverse impacts of low trims and excessive camber are discussed. A practical planing hull with significant concave camber must have convexity, at least forward to accommodate the bow. This hull type is generically referred to as a Wiggle Hull and recent investigations to develop such a hull are presented. The prediction method developed for this investigation is described.
Dynamic Stability Performance of Autonomous Microgrid Involving High Penetration Level of Constant Power Loads (2021)

Nowadays, behaving as constant power loads (CPLs), rectifiers and voltage regulators are extensively used in microgrids (MGs). The MG dynamic behavior challenges both stability and control effectiveness in the presence of CPLs. CPLs characteristics such as negative incremental resistance, synchronization, and control loop dynamic with similar frequency range of the inverter disturb severely the MG stability. Additionally, the MG stability problem will be more sophisticated with a high penetration level of CPLs in MGs. The stability analysis becomes more essential especially with high-penetrated CPLs. In this paper, the dynamic stability performance of an MG involving a high penetration level of CPLs is analyzed and investigated. An autonomous MG engaging a number of CPLs and inverter distributed generations (DGs) is modeled and designed using MATLAB. Voltage, current, and power controllers are optimally designed, controlling the inverter DGs output. A power droop controller is implemented to share the output DGs powers. Meanwhile, the current and voltage controllers are employed to control the output voltage and current of all DGs. A phase-locked loop (PLL) is essentially utilized to synchronize the CPLs with the MG. The controller gains of the inverters, CPLs, power sharing control, and PLL are optimally devised using particle swarm optimization (PSO). As a weighted objective function, the error in the DC voltage of the CPL and active power of the DG is minimized in the optimal problem based on the time-domain simulation. Under the presence of high penetrated CPLs, all controllers are coordinately tuned to ensure an enhanced dynamic stability of the MG. The impact of the highly penetrated CPLs on the MG dynamic stability is investigated. To confirm the effectiveness of the proposed technique, different disturbances are applied. The analysis shows that the MG system experiences the instability challenges due to the high penetrated CPLs. The simulation results confirm the effectiveness of the proposed method to improve the MG dynamic stability performance.
Catalytic hydrothermal gasification of biomass for the production of hydrogen-containing feedstock (methane) (2008)

Hydrothermal processing can be used to treat wet biomass by converting the organic contaminants to gases. When the system is operated as a metal catalyzed process at nominally 350°C and 21 MPa (so-called low-temperature gasification), it can produce a methane/carbon dioxide product gas from water slurries of biomass. This process can be utilized for both waste disposal and energy recovery. Catalyst stability in an aqueous processing environment is a major hurdle for use of such a system. Development of useful catalyst formulations has been achieved through bench-scale process development work. Catalyst lifetimes in excess of 5000h have been shown. Protection of the catalyst from feedstock impurities is a second major issue, which is more prominent in the biomass applications. Systems are under development to address mineral matter and sulfur contaminants.
Laser‐Printed Organic Thin‐Film Transistors (2019)

Figure The error was due to an incorrect conversion while calculating the electric field magnitude, F. The findings and conclusions presented in the original article are not affected. An updated version of Figure The pre-factor
Synthesis of a Specified, Silica Molecular Sieve by Using Computationally Predicted Organic Structure‐Directing Agents (2014)

Crystalline molecular sieves are used in numerous applications, where the properties exploited for each technology are the direct consequence of structural features. New materials are typically discovered by trial and error, and in many cases, organic structure-directing agents (OSDAs) are used to direct their formation. Here, we report the first successful synthesis of a specified molecular sieve through the use of an OSDA that was predicted from a recently developed computational method that constructs chemically synthesizable OSDAs. Pentamethylimidazolium is computationally predicted to have the largest stabilization energy in the STW framework, and is experimentally shown to strongly direct the synthesis of pure-silica STW. Other OSDAs with lower stabilization energies did not form STW. The general method demonstrated here to create STW may lead to new, simpler OSDAs for existing frameworks and provide a way to predict OSDAs for desired, theoretical frameworks.
Solar Glaze Hazard Analysis Tool v. 3.0 (2015)

SGHAT predicts the occurrence and intensity of glare caused by a user-specified solar panel array when viewed from one or more observation points. An interactive mapping interface is used to determine the latitude, longitude and elevation of the array and observation points. The presence and intensity of glare is then calculated along a given time interval throughout the year, based on the position of the sun. The potential ocular hazard is also reported. The maximum energy production of the solar array is also estimated so that alternative designs can be compared to determine the design that yields the most energy production while mitigating glare.
Layer-By-Layer Fabrication of Large and Thick Human Cardiac Muscle Patch Constructs With Superior Electrophysiological Properties (2021)

Engineered cardiac tissues fabricated from human induced pluripotent stem cells (hiPSCs) show promise for ameliorating damage from myocardial infarction, while also restoring function to the damaged left ventricular (LV) myocardium. For these constructs to reach their clinical potential, they need to be of a clinically relevant volume and thickness, and capable of generating synchronous and forceful contraction to assist the pumping action of the recipient heart. Design prerequisites include a structure thickness sufficient to produce a beneficial contractile force, prevascularization to overcome diffusion limitations and sufficient structural development to allow for maximal cell communication. Previous attempts to meet these prerequisites have been hindered by lack of oxygen and nutrient transport due to diffusion limits (100-200 μm) resulting in necrosis. This study employs a layer-by-layer (LbL) fabrication method to produce cardiac tissue constructs that meet these design prerequisites and mimic normal myocardium in form and function. Thick (>2 mm) cardiac tissues created from hiPSC-derived cardiomyocytes, -endothelial cells (ECs) and -fibroblasts (FBs) were assessed, <i>in vitro</i>, over a 4-week period for viability (<6% necrotic cells), cell morphology and functionality. Functional performance assessment showed enhanced <i>t</i>-tubule network development, gap junction communication as well as previously unseen, physiologically relevant conduction velocities (CVs) (>30 cm/s). These results demonstrate that LbL fabrication can be utilized successfully to create prevascularized, functional cardiac tissue constructs from hiPSCs for potential therapeutic applications.
Effects of porcine somatotropin dosage and lysine level on growth performance of growing pigs (1991)

Eighty crossbred barrows initially weighing 70.5 lb were used in a 5 wk trial to determine the optimum dosage of porcine somatotropin (PST) required to promote maximum growth response in growing pigs fed diets containing either 1.0 or 2.0% lysine. Pigs received a daily injection of placebo or 2, 4, or 8 mg pST in combination with one of two experimental diets containing either 1.0 or 2.0% dietary lysine. Increasing the dosage of pST of pigs fed both diets resulted in an increase in average daily gain (ADG), a reduction in average daily feed intake (ADFI), and an improvement in feed conversion (F/G). Average backfat, calculated from ultrasonic measurements at the first rib, last rib, and last lumbar vertebra, was reduced in pigs fed both diets as pST dosage increased. Serum pST increased and urea nitrogen decreased for pigs fed both diets as pST dosage increased. The improvement in ADG and F/G of pigs fed both diets was quadratic, indicating that a plateau was achieved between 4 and 8 mg/d pST administration. The serum urea nitrogen response appeared to plateau near 8 mg/d. The combination of these response criteria indicates that the dosage required for maximum response is about 7 mg/d pST, whereas the more optimum level of pST administration may be about 5 mg/d for growing pigs fed diets containing 1.0 or 2.0% lysine.; Swine Day, Manhattan, KS, November 21, 1991
Abstract AS05: Metabolomic signatures in sera from early stage ovarian cancer patients (2015)

Abstract PURPOSE: Lack of symptoms as well as the deficiency of highly specific biomarkers has resulted in only a quarter of ovarian cancer cases being diagnosed in stage I. Early detection combined with conventional therapies has resulted in 5-year survival rates up to 90%, while 5-year overall survival is less than 30% for women with advanced stage ovarian cancer. An effective screening strategy for early diagnosis would be particularly advantageous for ovarian cancer patients. Investigation into characteristic metabolomic patterns for disease has the potential to detect changes in cells, tissues, and biofluids that can aid in diagnosis at an early stage. METHODS: Serum samples were collected from early-stage serous papillary or endometrioid ovarian cancer (n=26) and normal patients (n=40) and analyzed using ultra high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-MS) and tandem mass spectrometry (MS/MS). Metabolites were extracted from blood serum by precipitating proteins with methanol, lyophilization, and solvent reconstitution prior to MS analysis in both positive and negative electrospray ionization modes. Metabolic features were extracted with MZmine software. Untargeted multivariate statistical analysis employing support vector machine (SVM) learning methods, genetic algorithms and recursive feature elimination (RFE) selected a panel of metabolites that differentiates between the age-matched samples with better than 92% sensitivity and 91% specificity in all cases tested. RESULTS: Comparison of metabolic phenotypes of ovarian cancer with normal metabolic signatures revealed unique metabolite patterns for ovarian cancer. From multivariate statistical analysis, panels consisting of 17-35 metabolic features from serum samples were found to differentiate between early stage cancer and normal with very high accuracy, sensitivity, and specificity. CONCLUSIONS: Poor early diagnosis complicates collection of large patient cohorts for more detailed studies. Our preliminary work demonstrated that metabolites in serum samples may be useful for detecting early-stage ovarian cancer and support conducting larger, more focused studies. (Grant support: Marsha Rivkin Ovarian Cancer Challenge Grant; Ovarian Cancer Research Fund (OCRF)) Citation Format: David A. Gaul, Christina M. Jones, Maria Eugenia Monge, Long Q. Tran, Martin M. Matzuk, John F. McDonald*, Facundo M. Fernandez*. Metabolomic signatures in sera from early stage ovarian cancer patients [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS05.
STACL: Simultaneous Translation with Implicit Anticipation and Controllable Latency using Prefix-to-Prefix Framework (2018)

Simultaneous translation, which translates sentences before they are finished, is useful in many scenarios but is notoriously difficult due to word-order differences. While the conventional seq-to-seq framework is only suitable for full-sentence translation, we propose a novel prefix-to-prefix framework for simultaneous translation that implicitly learns to anticipate in a single translation model. Within this framework, we present a very simple yet surprisingly effective wait-k policy trained to generate the target sentence concurrently with the source sentence, but always k words behind. Experiments show our strategy achieves low latency and reasonable quality (compared to full-sentence translation) on 4 directions: zhen and deen.
Trajectory based Arabic Sign Language Recognition (2018)

Deaf and hearing impaired people use their hand as a tongue to convey their thoughts by performing descriptive gestures that form the sign language. A sign language recognition system is a system that translates these gestures into a form of spoken language. Such systems are faced by several challenges, like the high similarities of the different signs, difficulty in determining the start and end of signs, lack of comprehensive and bench marking databases. This paper proposes a system for recognition of Arabic sign language using the 3D trajectory of hands. The proposed system models the trajectory as a polygon and finds features that describes this polygon and feed them to a classifier to recognize the signed word. The system is tested on a database of 100 words collected using Kinect. The work is compared with other published works using publicly available dataset which reflects the superiority of the proposed technique. The system is tested for both signer-dependent and signer-independent recognition.
High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes (2011)

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of both C. thermocellum and T. saccharolyticum. Fermentation of 92 g/liter Avicel by this coculture resulted in 38 g/liter ethanol, with acetic and lactic acids below detection limits, in 146 h. These results demonstrate that ethanol production by thermophilic, cellulolytic microbes is amenable to substantial improvement by metabolic engineering.
ChemInform Abstract: SPECTINOMYCIN CHEMISTRY. II. THE SYNTHESIS OF 6′‐SUBSTITUTED SPECTINOMYCIN ANALOGS (1981)

Abstract Aufgrund der breiten antibiotischen Wirkung von Spectinomycin (I) werden modifizierte Derivate (V), z.B. ausgehend von (II) und (III), über z.B. Zwischenstufen der Art (IV) hergestellt.
Characterization of the Thyrotropin Binding Pocket (2002)

A panel of monoclonal antibodies (mAbs) to the thyrotropin receptor (TSHR) was prepared using three different immunization strategies. The mAbs obtained (n = 138) reacted with linear epitopes covering most of the TSHR extracellular domain and with conformational epitopes. mAbs that bound to five different regions of the TSHR (amino acids [aa] 32-41, aa 36-42, aa 246-260, aa 277-296, and aa 381-385) were able to inhibit (125)I-labeled thyrotropin (TSH) binding to solubilized TSHR preparations. Fab and immunoglobulin G (IgG) preparations were similarly effective inhibitors for mAbs reactive with aa 246-260, aa 277-291 and aa 381-385 suggesting that these three regions of the TSHR are involved in TSH binding. In contrast mAbs reactive with aa 32-41 and aa 36-42 were not effective at inhibiting TSH binding when Fab preparations were used, suggesting that these N terminal regions of the TSHR were less critical for TSH binding. Our studies suggest that three distinct and discontinuous regions of the TSHR (aa 246-260 and 277-296 on the TSHR A subunit) and aa 381-385 (on the TSHR B subunit) fold together to form a complex TSH binding pocket. Alignment of the aa sequences of these three regions in TSHRs from different species indicates that they are highly conserved.
Increased Mass Transport at Lithographically Defined 3-D Porous Carbon Electrodes (2010)

Increased mass transport due to hemispherical diffusion is observed to occur in 3D porous carbon electrodes defined by interferometric lithography. Enhanced catalytic methanol oxidation, after modifying the porous carbon with palladium nanoparticles, and uncharacteristically uniform conducting polymer deposition into the structures are demonstrated. Both examples result in two regions of hierarchical porosity that can be created to maximize surface area, via nanostructuring, within the extended porous network, while taking advantage of hemispherical diffusion through the open pores.
Abstract 3897: A novel function for threonyl-tRNA synthetase as a stimulator of angiogenesis and endothelial cell migration. (2013)

Abstract In mammalian systems, several aminoacyl-tRNA synthetases are known to have distinct non-canonical functionality. For the first time, we demonstrate that human threonyl-tRNA synthetase (TARS) induces angiogenesis through endothelial cell signaling, and this induction can be blocked by the borrelidin derivative compound BC194. Upon stimulation with vascular endothelial growth factor (VEGF) or tumor necrosis factor-alpha (TNF-α), human endothelial cells secrete TARS into the extracellular space. Extracellular TARS induces and BC194 inhibits angiogenesis in both in vitro tube formation assays and in vivo chick chorioallantoic membrane assays. Furthermore, the anti-angiogenic effects of BC194 are specific to its inhibition of TARS angiogenic activity rather than an indirect stress response. Additional evidence supports a stimulatory role for TARS in endothelial cell migration as a mechanism for its angiogenic activity. Taken together, these findings reveal a previously undefined function for TARS as an angiogenesis inducer stimulated by hypoxic and inflammatory signals. Detecting or intervening in the non-canonical extracellular TARS signaling pathway may thus provide a novel means of diagnosing or treating angiogenesis and inflammatory responses involved in cancer. Citation Format: Tamara Williams, Adam Mirando, Christopher Francklyn, Karen M. Lounsbury. A novel function for threonyl-tRNA synthetase as a stimulator of angiogenesis and endothelial cell migration. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3897. doi:10.1158/1538-7445.AM2013-3897
Automatic Measurement of Ultrasound-Estimated Bladder Weight (UEBW) from Three-Dimensional Ultrasound. (2005)

Ultrasound-estimated bladder weight (UEBW) has the promise to become an important indicator for the diagnosis of bladder outlet obstruction. Our goal was to develop and evaluate an approach to accurately, consistently, conveniently, and noninvasively measure UEBW using three-dimensional (3D) ultrasound imaging. A 3D image of the bladder is acquired using a handheld ultrasound machine. The infravesical region of the bladder is delineated on this 3D data set to enable the calculation of bladder volume and the bladder surface area. The outer anterior wall of the bladder is delineated to enable the calculation of the bladder wall thickness. The UEBW is measured as a product of the bladder surface area, bladder wall thickness, and bladder muscle specific gravity. The UEBW was measured on 20 healthy male subjects and each subject was imaged several times at different bladder volumes to evaluate the consistency of the UEBW measurement. Our approach measured the average UEBW among healthy subjects to be 42 g (SD = 6 g). The UEBW was found to be fairly consistent with an average standard deviation of 4 g across a single subject at different bladder volumes between 200 mL and 400 mL. Our surface area measurements show that the bladder shape is significantly nonspherical.
Phase alignment of multiple surface coil data for reduced bandwidth and reconstruction requirements (1997)

Multiple element surface coils are often used in clinical MRI to increase the image signal-to-noise ratio (S/N). Use of multicoils typically requires increased net sampling bandwidth and data processing for each coil element. A phase-alignment technique is described which combines the signals from all coil elements before image reconstruction, greatly relaxing the technical requirements of the standard multicoil methods. Hardware and software implementations allow reduction of the reconstruction requirement to that of a single coil. The hardware implementation additionally allows a significant reduction in the net sampling bandwidth. The method is applicable to high speed MRI techniques, as demonstrated in phantoms and volunteers.