gebhart/patrepeval huggingface dataset:
Anatomic communications between the three retroperitoneal spaces: determination by CT-guided injections of contrast material in cadavers. (1995)

Our findings show pathways and extensions of the perirenal, anterior pararenal, and posterior pararenal spaces that should be considered when assessing a variety of retroperitoneal diseases. Perinephric collections, such as hematomas and urinomas, have at least a potential conduit across the midline or into the pelvis. Our study explains how blood from a ruptured abdominal aortic aneurysm may enter either perinephric space. Anterior pararenal processes, such as pancreatitis or appendicitis, can extend into the pelvis or cross the midline, and posterior pararenal blood from trauma can also flow into the pelvis.
Test-driven synthesis (2014)

Programming-by-example technologies empower end-users to create simple programs merely by providing input/output examples. Existing systems are designed around solvers specialized for a specific set of data types or domain-specific language (DSL). We present a program synthesizer which can be parameterized by an arbitrary DSL that may contain conditionals and loops and therefore is able to synthesize programs in any domain. In order to use our synthesizer, the user provides a sequence of increasingly sophisticated input/output examples along with an expert-written DSL definition. These two inputs correspond to the two key ideas that allow our synthesizer to work in arbitrary domains. First, we developed a novel iterative synthesis technique inspired by test-driven development---which also gives our technique the name of test-driven synthesis---where the input/output examples are consumed one at a time as the program is refined. Second, the DSL allows our system to take an efficient component-based approach to enumerating possible programs. We present applications of our synthesis methodology to end-user programming for transformations over strings, XML, and table layouts. We compare our synthesizer on these applications to state-of-the-art DSL-specific synthesizers as well to the general purpose synthesizer Sketch.
Development of an On-Board Fuel Reforming Catalyst for a Gasoline Engine (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;On-board hydrogen generation technology using a fuel reforming catalyst is an effective way to improve the fuel efficiency of automotive internal combustion engines. The main issue to be addressed in developing such a catalyst is to suppress catalyst deterioration caused by carbon deposition on the catalyst surface due to sulfur adsorption. Enhancing the hydrocarbon and water activation capabilities of the catalyst is important in improving catalyst durability. It was found that the use of a rare earth element is effective in improving the water activation capability of the catalyst. Controlling the hydrocarbon activation capability of the catalyst for a good balance with water activation was also found to be effective in improving catalyst durability.&lt;/div&gt;&lt;/div&gt;
(100) Preferred Orientation of Spinel-Type Iron Oxide Films Prepared by Plasma-Enhanced Metalorganic Chemical Vapor Deposition (1995)

Spinel-type iron oxide films were prepared on glass substrates at 400° C by plasma-enhanced metalorganic chemical vapor deposition using iron (III) acetylacetonate and oxygen as source gas and oxidizing gas, respectively. The effects of angle (θ) of the source and oxygen gas nozzle to the substrate surface, applied negative dc bias voltage and addition of reducing gas, H 2 , on the orientation of the films have been investigated. Highly crystalline and (100)-oriented spinel-type iron oxide films were obtained under conventional conditions only when θ was lower than 20°. However, even for θ higher than 20°, highly crystalline and (100)-oriented films could be obtained by applying negative dc bias voltage or adding H 2 during the deposition. Magnetic properties and microstructures of the films were also examined.
5-Endo Trig Oxidative Radical Cyclizations of Ugi-3CR Products toward 1,4-Imidazolidinones (2020)

A 5-<i>endo</i> trig oxidative radical cyclization of benzylamine-derived Ugi three-component reaction products rapidly affords imidazolidinones with three diversity elements. This adaptation of our previously described multicomponent reaction-oxidation methodology further showcases manipulation of the diversity elements in multicomponent reaction products via oxidative radical cyclizations, which generates highly decorated privileged heterocycles.
Theory of Stark Shifts in Quantum Wells Consisting of Highly Anisotropic Molecular Crystalline Thin Films (1993)

Heterostructures consisting of crystalline organic semiconductors can be layered in nearly defect-free structures due to the weak van der Waals bonding between molecules. [1] As a result of their crystalline order, these films have exhibited enormous anisotropies in both their conductive and dielectric properties. [2,3] Moreover, the relatively large exciton binding energy results in an exciton absorption peak deep in the band gap, which leads to large Stark shifts useful for optical modulation. Due to the unique electrical and optical properties of this class of materials, it is useful to understand how crystalline organic multiple quantum wells (MQWs) behave in an electric field.
Linear Programming in the Allocation of Milk Resources for Cheese Making (1986)

To use linear programming, the cheese making process can be modeled as a resource conversion process. The relationship between input milk resources and output products can be analyzed using mass balance assumptions. The variables used in the linear programming model will represent the pounds of each milk resource chosen to formulate a vat of cheese milk. Additional variables will be used to represent the pounds of cream to be removed from a milk resource that has the potential to have cream removed. Three objectives that could be considered are 1) maximize net returns, 2)maximize cheese yield, or 3) minimize cost. A hypothetical example is used to illustrate how the cheese making process can be modeled. This linear programming model depends on formulas that relate ratio of casein to fat of milk to the fat on the dry basis of the cheese. Sensitivity analysis is performed to determine at what cost a milk resource not in the optimal formulation will replace a milk resource currently in the optimal formulation. The linear programming model can be an effective management tool in the allocation of milk resources for cheese making.
ChemInform Abstract: Design and Synthesis of Conformationally Constrained Arginal Thrombin Inhibitors. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Compact TE/TM-pass polarizer based on lithium niobate on insulator ridge waveguides (2012)

We propose TE/TM-pass polarizer based on loss mechanism in leaky lithium niobate on insulator ridge waveguides. We show compact polarizers can be designed for both TE and TM polarizations by changing the height of waveguide.
ChemInform Abstract: Total Synthesis of Mycalolides A and B Through Olefin Metathesis. (2016)

Abstract The key steps of the asymmetric total synthesis of the trisoxazole marine macrolides, mycalolides A and B, are the convergent construction of highly functionalized C‐1—C‐19 trisoxazole and C‐20—C‐35 side chain segments using the olefin metathesis and esterification as well as the Julia—Kocienski olefination and enamide formation.
Assessment of on-line burnup monitoring of pebble bed reactor fuel using passive gamma-ray spectrometry (2005)

An investigation was performed to assess the feasibility of passive gamma-ray spectrometry assay as an approach for on-line burnup determination for the Modular Pebble Bed Reactor (MPBR). In addition to its inherently safe design, a unique feature of this reactor is its multi-pass fuel cycle in which graphite fuel pebbles are randomly loaded and continuously cycled through the core until they reach their prescribed End-of-Life burnup limit (/spl sim/80,000 MWD/MTU). Therefore, unlike the situation with conventional light water reactors, depending solely on computational methods to perform in-core fuel management will be highly inaccurate. As a result, an on-line measurement approach becomes the only accurate method to assess whether a particular pebble has reached its End-of-Life burnup limit. The results of this investigation indicate that the fission products Cs-137 and Eu-154 provide accurate, and power-history-independent signatures that can be directly correlated with burnup. Furthermore, depending on the fuel manufacturing process, artificially introduced dopants (e.g., Co) can provide gamma-ray lines that are usable for burnup monitoring. In fact, it was found that the relative activity of Co-60 to Cs-134 could form an accurate burnup indicator that is independent of power history. In this case, the use of a relative indicator has several advantages, among which is the elimination of the need for absolute knowledge of the detector full energy peak efficiency curve, and the establishment of a system quality assurance figure of merit based on the peak area ratio of the Co lines.
All the Feels: A dexterous hand with large-area tactile sensing (2022)

High cost and lack of reliability has precluded the widespread adoption of dexterous hands in robotics. Furthermore, the lack of a viable tactile sensor capable of sensing over the entire area of the hand impedes the rich, low-level feedback that would improve learning of dexterous manipulation skills. This paper introduces an inexpensive, modular, robust, and scalable platform -- the DManus -- aimed at resolving these challenges while satisfying the large-scale data collection capabilities demanded by deep robot learning paradigms. Studies on human manipulation point to the criticality of low-level tactile feedback in performing everyday dexterous tasks. The DManus comes with ReSkin sensing on the entire surface of the palm as well as the fingertips. We demonstrate effectiveness of the fully integrated system in a tactile aware task -- bin picking and sorting. Code, documentation, design files, detailed assembly instructions, trained models, task videos, and all supplementary materials required to recreate the setup can be found on https://sites.google.com/view/roboticsbenchmarks/platforms/dmanus.
115 CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT (CRISPR)/Cas9-DIRECTED INACTIVATION OF PORCINE INTERLEUKIN-1B AS A MODEL TO STUDY ENDOMETRIAL RECEPTIVITY AND CONCEPTUS ATTACHMENT (2014)

Embryonic losses in livestock range from 20 to 40%, with two-thirds of these losses occurring in the peri-implantation period. An understanding of successful pregnancy establishment in pigs is important for translational research and commercial pig production. Failure of conceptus-maternal communication is a major contributor to this loss, yet the molecular control of this process remains unclear. Engineered nucleases such as the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system enable precise modification of the genome compared with traditional gene targeting. In the present study, we hypothesised that the CRISPR/Cas9 system can be used to efficiently produce genetically modified embryo models in the pig that will answer key questions about the complex molecular dialogue between conceptus and maternal uterus. We focused on interleukin-1ß (IL1B), a cytokine believed to contribute to rapid trophoblast elongation and pregnancy establishment in pigs. The pig is unique in having 2 forms of the IL1B gene: the systemic form (IL1B) and the conceptus form (IL1BL) that is expressed only at peri-implantation. The coding sequence of the 2 forms of IL1B share 92% similarity. Our objective was to develop 2 types of cloned swine embryos, each with a CRISPR/Cas9-mediated gene inactivation of either IL1B or ILB1L. To target unique regions of IL1B and IL1BL in our fetal fibroblast somatic cell nuclear transfer (SCNT) donor cells, existing Sus scrofa genome data (10.2 annotation) was combined with donor cell Illumina high-throughput sequencing and Sanger sequencing of PCR products to produce consensus IL1B and IL1BL sequences used for targeted disruption. We developed a CRISPR/Cas9 pipeline to identify potential targets 20 nucleotides in length to disrupt the IL1BL and IL1B start codon, while at the same time screening for any potential off-target matches. The pipeline was able to select a group of 11 CRISPR single-chain guide RNAs (sgRNAs; 6 for IL1B and 5 for IL1BL) from an initial library of 413 sgRNAs. Porcine fibroblasts cultured in DMEM, 15% fetal bovine serum, and 10 mg mL–1 gentamicin were trypsinized and transferred to electroporation medium (75% cytosalts, 25% Opti-MEM), diluted to 1 million cells in 200 µL, and added to 2 mm gap electroporation cuvettes. Cells received 2 µg of pairs of sgRNAs bracketing the start codon and were electroporated with three 1-ms square wave pulses at 250 V. Transfected cells were resuspended in DMEM and plated at low density (~50 cells/plate). The Surveyor Nuclease assay was used to determine a minimum of 5 unique cleavage products in the target DNA in each gene form for heterogeneous cell populations. Clonal populations of targeted cells are currently being characterised for use in SCNT and embryo transfer to identify the effects of IL1B/IL1BL disruption on key molecular pathways during early development (Days 8, 12, and 18 of gestation).
Neural Networks, Hypersurfaces, and Radon Transforms (2019)

Connections between integration along hypersufaces, Radon transforms, and neural networks are exploited to highlight an integral geometric mathematical interpretation of neural networks. By analyzing the properties of neural networks as operators on probability distributions for observed data, we show that the distribution of outputs for any node in a neural network can be interpreted as a nonlinear projection along hypersurfaces defined by level surfaces over the input data space. We utilize these descriptions to provide new interpretation for phenomena such as nonlinearity, pooling, activation functions, and adversarial examples in neural network-based learning problems.
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’ (2020)

While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.
Chronic effects of pulmonary artery stenosis on hemodynamic and structural development of the lungs (2012)

Pulmonary artery (PA) stenosis is a difficult obstructive defect to manage since clinicians cannot know a priori which obstructions to treat and when. Prognosis of PA stenosis and its chronic effects on lung development are poorly understood. This study aimed to characterize the hemodynamic and structural effects of PA stenosis during development. Fourteen male Sprague-Dawley rats underwent left PA (LPA) banding at age 21 days, and 13 underwent sham operation. Hemodynamic and structural impacts were studied longitudinally at 20, 36, 52, 100, and 160 days. Chronic LPA banding resulted in a significant reduction in LPA flow (P < 0.0001) and size of both proximal LPA (P < 0.0001) and distal LPA (P < 0.01), as well as a significant increase in flow and size of the right PA (P < 0.05) throughout development. Flows and sizes adapted such that normal levels of wall shear were restored after banding. At 160 days, LPA banding resulted in a significant decrease in left lung volume and an increase in right lung volume but no significant differences in total lung volume. There was an elevation of proximal LPA pressure as well as right ventricular hypertrophy in the banded animals. The banded lung exhibited arterial disorganization, loss of vessels, and enlargement of its bronchial arteries, whereas the contralateral lung showed signs of vascular pathology. There are consequences on development of both lungs in the presence of an LPA stenosis at young age. These results suggest that early intervention may be necessary to optimize left lung growth and minimize right lung vascular pathology.
Protect or potentiate: The Role of Common Medications in Response to Radiotherapy (2019)

Stereotactic radiosurgery is a viable treatment option for lung cancer. Lung cancer often metastasizes to the brain. Metastases are often difficult to access and treat without adverse complications that may significantly depreciate the quality of life. Tumor response to radiotherapy varies between patients, and treatment-resistant cells are most likely to metastasize. Sufficient response requires tumor cell death and may be inhibited in cases where cells feature heightened radiation resistance. However, radiation can alter cellular signaling within the tumor and with nearby cells (bystander effect). The purpose of this investigation is to determine whether common medications modulate lung tumor cell susceptibility to radiation. Lung adenocarcinoma non-small cell lung cancer (NSCLC) cells were preconditioned with medication, irradiated with varying doses of radiation, and evaluated for cell viability and the presence of cleaved poly ADP ribose polymerase (PARP), an indicator of apoptosis. We evaluated medications used for the treatment of pain/inflammation, cardiovascular ailments, high cholesterol, diabetes, and epilepsy. We identified aspirin, propranolol, and an ACE inhibitor + metformin regimen as agents that provide temporary resistance against low-dose (2.5 Gy) radiation. Conferred resistance is overcome by high-dose (20 Gy) radiation exposure. Additionally, PARP was positive in Metformin+ACE treated cells 20 days post-irradiation, suggesting a shift in radiation-induced toxicity that is not mitigated by common medication.
Short-Term Oxandrolone Administration Stimulates Net Muscle Protein Synthesis in Young Men1 (1999)

Short term administration of testosterone stimulates net protein synthesis in healthy men. We investigated whether oxandrolone [Oxandrin (OX)], a synthetic analog of testosterone, would improve net muscle protein synthesis and transport of amino acids across the leg. Six healthy men [22+/-1 (+/-SE) yr] were studied in the postabsorptive state before and after 5 days of oral OX (15 mg/day). Muscle protein synthesis and breakdown were determined by a three-compartment model using stable isotopic data obtained from femoral arterio-venous sampling and muscle biopsy. The precursor-product method was used to determine muscle protein fractional synthetic rates. Fractional breakdown rates were also directly calculated. Total messenger ribonucleic acid (mRNA) concentrations of skeletal muscle insulin-like growth factor I and androgen receptor (AR) were determined using RT-PCR. Model-derived muscle protein synthesis increased from 53.5+/-3 to 68.3+/-5 (mean+/-SE) nmol/min.100 mL/leg (P < 0.05), whereas protein breakdown was unchanged. Inward transport of amino acids remained unchanged with OX, whereas outward transport decreased (P < 0.05). The fractional synthetic rate increased 44% (P < 0.05) after OX administration, with no change in fractional breakdown rate. Therefore, the net balance between synthesis and breakdown became more positive with both methodologies (P < 0.05) and was not different from zero. Further, RT-PCR showed that OX administration significantly increased mRNA concentrations of skeletal muscle AR without changing insulin-like growth factor I mRNA concentrations. We conclude that short term OX administration stimulated an increase in skeletal muscle protein synthesis and improved intracellular reutilization of amino acids. The mechanism for this stimulation may be related to an OX-induced increase in AR expression in skeletal muscle.
ChemInform Abstract: Perovskite as Light Harvester: A Game Changer in Photovoltaics (2014)

Abstract Review: 95 refs.
Quantum Dot Superluminescent Diodes for Optical Coherence Tomography: Device Engineering (2010)

We present a 18 mW fiber-coupled single-mode superluminescent diode with 85 nm bandwidth for application in optical coherence tomography (OCT). First, we describe the effect of quantum dot (QD) growth temperature on optical spectrum and gain, highlighting the need for the optimization of epitaxy for broadband applications. Then, by incorporating this improved material into a multicontact device, we show how bandwidth and power can be controlled. We then go on to show how the spectral shape influences the autocorrelation function, which exhibits a coherence length of <;11 μm, and relative noise is found to be 10 dB lower than that of a thermal source. Finally, we apply the optimum device to OCT of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> skin and show the improvement that can be made with higher power, wider bandwidth, and lower noise, respectively.
Influence of stimulated Brillouin scattering on phase modulated signals in optical fibres (1990)

The formation of sharp amplitude modulations of a phase-modulated coherent optical (PSK) signal in the presence of stimulated Brillouin scattering (SBS) has been studied numerically. The results are in agreement with recent experiments and establish SBS as the origin of the amplitude modulations.
EXPERIMENTAL EVALUATION OF HEAT TRANSFER, PRESSURE DROP, AND FOULING MITIGATION POTENTIAL IN FINNED, DIMPLED, AND BARE TUBE BUNDLES (2008)

This paper presents a comparative evaluation of three heat transfer surfaces, namely, bare, finned, and dimpled tubes. Bare and finned tubes are widely employed by heat transfer equipment across multiple industries, while dimpled tubes are on their way to the market of convective passages of typical industrial process heating equipment. The dimpled tube bundles were evaluated against the bare and finned tube bundles in a laboratory as well as in a field environment. The obtained results clearly demonstrate the superior performance of the dimpled tubes over the traditional finned tubes in the evaluated range of geometry and regime parameters.