gebhart/patrepeval huggingface dataset:
Integrated Status and Effectiveness Monitoring Program - Entiat River Rotary Screw Traps,Snorkel Surveys, and Steelhead Redd Surveys, 2008. (2009)

The USFWS Mid-Columbia River Fishery Resource Office (MCRFRO) operated two rotary screw traps on the Entiat River as part of the Integrated Status and Effectiveness Monitoring Program from March through November of 2008. Along with the smolt traps, juvenile emigrants were also captured at remote locations throughout the Entiat watershed and its major tributary, the Mad River. A total of 16,782 wild salmonids were PIT tagged during the study period. Of this, 3,961(23.6%) were wild Oncorhynchus mykiss, 6,987 (41.6%) were wild spring run O. tshawytscha, and 5,591 (33.3%) were identified as wild O. tshawytscha of unknown run. Rotary screw trap efficiencies averaged 40.3% at the upper (Rkm 11.0) trap and 7.8% for the lower (Rkm 2.0) trap. These efficiencies were pooled for emigrant O. tshawytscha and O. mykiss. The MCRFRO conducted effectiveness monitoring snorkel surveys at 24 sites during the winter period and 30 sites during the summer and fall periods of 2008 as part of the Integrated Status and Effectiveness Monitoring Program in the Entiat River. The 2008 steelhead spawning grounds surveys were conducted weekly in the main Entiat River from rkm 1.1 to 44.2. A total of 222 steelhead redds were identified over the period from February 28 to June 16 2008 with April being the peak spawning month. Approximately 80% of the steelhead redds were located downstream of the rkm 26.
Adipose Depots Possess Unique Developmental Gene Signatures (2010)

We have previously demonstrated that subcutaneous and intra-abdominal adipose tissue show different patterns of expression for developmental genes (Shox2, En1, Tbx15 Hoxa5, Hoxc8, and Hoxc9), and that the expression level of Tbx15 and Hoxa5 in humans correlated with the level of obesity and fat distribution. To further explore the role of these developmental genes in adipose tissue, we have characterized their expression in different adipose depots in mice, and studied their regulation in obesity and by fasting. Developmental and adipogenic gene expression was compared in two subcutaneous and three intra-abdominal white adipose tissue (WAT) depots as well as brown adipose tissue (BAT) from lean or obese mice in a fed or fasting state. Each of these six adipose depots display a unique pattern of developmental gene expression, whereas expression of adipogenic transcription factors PPARgamma2 C/EBPalpha, beta, and Delta showed constant expression levels in all depots. Expression levels of developmental genes were similar in obese (ob/ob and high-fat diet (HFD)) and lean mice in most depots. Fasting systematically decreased expression of Hoxc8, PPARgamma2, and increased C/EBPDelta in both lean and ob/ob mice, but produced only variable changes in the expression of other developmental and adipogenic genes. These data indicate that each fat depot has a unique developmental gene expression signature, which is largely independent of nutritional state. This finding further supports a fundamental role of developmental genes in fat distribution and the development and/or function of specific adipose tissue depots.
ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis (2020)

Meiotic recombination is initiated by SPO11-induced double-strand breaks (DSBs). In most mammals, the methyltransferase PRDM9 guides SPO11 targeting, and the ATM kinase controls meiotic DSB numbers. Following MRE11 nuclease removal of SPO11, the DSB is resected and loaded with DMC1 filaments for homolog invasion. Here, we demonstrate the direct detection of meiotic DSBs and resection using END-seq on mouse spermatocytes with low sample input. We find that DMC1 limits both minimum and maximum resection lengths, whereas 53BP1, BRCA1 and EXO1 play surprisingly minimal roles. Through enzymatic modifications to END-seq, we identify a SPO11-bound meiotic recombination intermediate (SPO11-RI) present at all hotspots. We propose that SPO11-RI forms because chromatin-bound PRDM9 asymmetrically blocks MRE11 from releasing SPO11. In Atm<sup>-/-</sup> spermatocytes, trapped SPO11 cleavage complexes accumulate due to defective MRE11 initiation of resection. Thus, in addition to governing SPO11 breakage, ATM and PRDM9 are critical local regulators of mammalian SPO11 processing.
Modeling Language Transformations (2003)

The advent of model driven software engineering necessitates that there are frameworks and techniques that enable the translation of software expressed in one language to another language. Although the ability to do this is not new, compilers have long been addressing this need for programming languages; existing techniques are bespoke for the source and target language. The diverse nature of software applications demands that software engineers use (and adapt) a wide range of different languages to express software. In this paper we present a framework and approach for rapidly describing transformations between languages using transformation patterns.
Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web (2014)

Pharmacological research is hampered by scattered data which have to be retrieved by varying methods and in different data formats. This heterogeneity increases research costs and limits throughput. Over the last two years, the Open PHACTS Discovery Platform [1] has been developed as a centralized repository, integrating pharmacological data from a variety of information resources and providing tools and services to query these integrated data in pharmacological research.

Following an application-oriented approach, the Open PHACTS project started with the definition of potential use cases in the form of prioritized research questions [2], most of which can only be answered by accessing multiple data sources in the web. The development of the platform as well as the services has been guided by these questions.

Here, we present the ChemBioNavigator (CBN) [3], a web application allowing to navigate the Open PHACTS chem-bio space with a focus on small molecules and their targets. CBN comprises of a large visualization area with different view modes and two information panels, allowing a deeper insight in information for compounds and targets. It allows interactive exploration of compound sets through sorting and subset selection as well as extending sets by substructure or similarity search. The relation between compounds and targets is defined by assay data from the Discovery Platform. Each compound and each target is annotated with information from multiple data sources which is provided together with the provenance for each data point.

In this contribution we roughly outline the OpenPHACTS/CBN technology and present a number of high-priority research questions, highlight the advantages of exploiting the integrated data through the CBN's smart and intuitive interface.
meta-Iodobenzylguanidine uptake in the hypertensive–diabetic rat heart: a marker for myocardial dysfunction? (1994)

The purpose of this study was to investigate the cardiac adrenergic neuronal changes induced by diabetes and hypertension by using an analogue of norepinephrine, meta-iodobenzylguanidine (MIBG), and to compare these changes with the contractile state of ventricular papillary muscle. The tissue concentration of norepinephrine in the cardiac apex was also measured for direct comparison with [ 123 I]MIBG uptake. One week following the induction of diabetes by streptozotocin injection (55 mg/kg, i.v.), male Sprague – Dawley rats were given subcutaneous injections of a hypertension-inducing agent, deoxycorticosterone acetate (DOC A, 25 mg/kg), or DOCA vehicle twice weekly for 3, 6, 9, or 12 weeks. At the end of each time point, the animals were injected intravenously (15 mCi/mg; 1 Ci = 37 GBq) with [ 123 I]MIBG. The results showed a progressive decrease in MIBG uptake into the hearts of diabetic, hypertensive, and diabetic–hypertensive rats during the 12-week observation period, compared with the control group. However, length–tension papillary muscle studies at 12 weeks indicated that only the diabetic group had a diminished performance compared with control. Furthermore, an inverse relationship was observed between MIBG uptake and norepinephrine levels in the cardiac apex of the diabetic and diabetic–hypertensive groups. Therefore, we concluded that either MIBG does not provide an accurate indication of adrenergic integrity or that there is no relationship between sympathetic activity and myocardial function at the time points measured. MIBG did not prove to be a useful marker for myocardial dysfunction in diabetic rats.Key words: diabetes, deoxycorticosterone acetate hypertension, meta-iodobenzylguanidine, adrenergic function, heart.
CFD Investigation of Gear Pump Mixing Using Deforming/Agglomerating Mesh (2006)

A moving-deforming grid study was carried out using a commercial computational fluid dynamics (CFD) solver, FLUENT® 6.2.16. The goal was to quantify the level of mixing of a lower-viscosity additive (at a mass concentration below 10%) into a higher-viscosity process fluid for a large-scale metering gear pump configuration typical in plastics manufacturing. Second-order upwinding and bounded central differencing schemes were used to reduce numerical diffusion. A maximum solver progression rate of 0.0003 revolutions per time step was required for an accurate solution. Fluid properties, additive feed arrangement, pump scale, and pump speed were systematically studied for their effects on mixing. For each additive feed arrangement studied, the additive was fed in individual stream(s) into the pump-intake. Pump intake additive variability, in terms of coefficient of spatial variation (COV), was &gt;300% for all cases. The model indicated that the pump discharge additive COV ranged from 45% for a single centerline additive feed stream to 5.5% for multiple additive feed streams. It was found that viscous heating and thermal/shear-thinning characteristics in the process fluid slightly improved mixing, reducing the outlet COV to 3.2% for the multiple feed-stream case. The outlet COV fell to 2.0% for a half-scale arrangement with similar physics. Lastly, it was found that if the smaller unit’s speed were halved, the outlet COV was reduced to 1.5%.
Simulation of Polyethylene (1983)

Both Brownian and molecular dynamics simulations have been performed for polyethylene fluids. The polymer is represented as a backbone skeleton of carbon atoms with flexible bonds and angles in addition to a torsional rotational potential. Conformational transitions g ⇄ t are observed to occur with an activation energy of one barrier height, although some second-neighbor cooperativity is observed. Reaction rates have been measured from first passage times using hazard analysis and also from orientational and conformational autocorrelation functions. The dynamics of vectors along and perpendicular to the polymer chain have been studied. The time dependence of the correlation functions can be reasonably fitted on the basis of a model with three types of processes. The two fastest correspond to independent conformational transitions and to two-bond correlated transitions. A much slower process, probably related to concerted motion of large segments of the chain, is also observed.
Combined Application of Methyl-Beta-Cyclodextrin and Reduced Glutathione to the In Vitro Fertilization of Cryopreserved C57BL/6 Mouse Sperm. (2011)

Sperm cryopreservation is useful for the effective storage of genomic resources derived from genetically engineered mice. The benefits of sperm cryopreservation include the saving of space and costs relating to the upkeep of each mouse lineage, the potential avoidance of a genetic drift during the storage term, and the ease of transporting the mice between research facilities. However, embryos need to be obtained using in vitro fertilization (IVF) in order to reproduce live animals from frozen/thawed sperm. In general, the fertility of frozen/thawed sperm taken from C57BL/6 mice, which is mainly used as a base for genetically engineered mice, is severely lower than that of fresh sperm. Previously, we reported that methyl-β-cyclodextrin (MBCD) dramatically improved the fertility of frozen/thawed C57BL/6 mouse sperm. MBCD effectively induces sperm capacitation by facilitating a cholesterol efflux from the cells. Recently, an interesting report was published on the topic of the supportive effects of reduced glutathione (GSH) on improving the fertility of mouse sperm. However, the action mechanism of GSH during the fertilization process is not fully understood. In this study, we examined the most efficient timing of GSH treatment and the combined effects of MBCD and GSH on the rate of fertilization for IVF using frozen/thawed C57BL/6 mouse sperm. As a result, we found that the presence of GSH in the fertilization medium increased the fertilization rate whereas GSH had no effects in the medium of sperm preincubation, and that the elevation of fertilization rates started at 0.5 mM GSH and reached a peak at 1.0 mM GSH (0 mM: 66%, 0.5 mM: 79% and 1.0 mM: 92%). We also discovered that the MBCD and GSH independently increased the rate of fertilization, while a combination of MBCD and GSH exhibited the highest fertilization rate in each group (control: 14%, MBCD: 65%, GSH: 36% and MBCD + GSH: 87%). In summary, we have demonstrated a novel IVF method using the combined application of MBCD for sperm preincubation and GSH for IVF, in order to achieve a high and stable fertilization rate in frozen/thawed C57BL/6 mouse sperm. (poster)
A 4-Kb 1-to-8-bit Configurable 6T SRAM-Based Computation-in-Memory Unit-Macro for CNN-Based AI Edge Processors (2020)

Previous SRAM-based computing-in-memory (SRAM-CIM) macros suffer small read margins for high-precision operations, large cell array area overhead, and limited compatibility with many input and weight configurations. This work presents a 1-to-8-bit configurable SRAM CIM unit-macro using: 1) a hybrid structure combining 6T-SRAM based in-memory binary product-sum (PS) operations with digital near-memory-computing multibit PS accumulation to increase read accuracy and reduce area overhead; 2) column-based place-value-grouped weight mapping and a serial-bit input (SBIN) mapping scheme to facilitate reconfiguration and increase array efficiency under various input and weight configurations; 3) a self-reference multilevel reader (SRMLR) to reduce read-out energy and achieve a sensing margin 2x that of the mid-point reference scheme; and 4) an input-aware bitline voltage compensation scheme to ensure successful read operations across various input-weight patterns. A 4-Kb configurable 6T-SRAM CIM unit-macro was fabricated using a 55-nm CMOS process with foundry 6T-SRAM cells. The resulting macro achieved access times of 3.5 ns per cycle (pipeline) and energy efficiency of 0.6-40.2 TOPS/W under binary to 8-b input/8-b weight precision.
Studying trophic interactions between a plant pathogen and two different antagonistic microorganisms using a 13 C‐labeled compound and isotope ratio mass spectrometry (2012)

This work demonstrates that IRMS can be used for the in-depth study of direct parasitism and interaction process between biocontrol agents and labeled pathogens, allowing the screening of potential new BCAs.
Pro-inflammatory responses and oxidative stress induced by ZnO nanoparticles in vivo following intravenous injection. (2015)

This study shows the ZnO induced pro-inflammatory response in vivo, that this response may be related to oxidative stress, and to show hepatic damage at an early stage.
Investigation of proNT/NMN secretion from small cell lung carcinoma cells using a mouse xenograft model (2012)

Proneurotensin/neuromedin N (proNT/NMN), the precursor of neurotensin (NT) and neuromedin N (NMN), is produced by cancer tissues derived from the pancreas and colon. NT stimulates tumor growth and proliferation through its receptors; however, little is known about the precursor molecule in cancer tissues. We previously demonstrated that proNT/NMN is secreted from small cell lung carcinoma (SCLC) cell lines in serum-free conditioned medium, but not from non-small cell lung carcinoma (NSCLC) cell lines. It was suggested that this precursor may serve as a tumor marker for SCLC. In this study, we established in vivo xenograft models to evaluate the possibility of proNT/NMN as a specific tumor marker. SBC3 cells, derived from human SCLC, were inoculated into mice, and the proNT/NMN levels in plasma and tumor tissues were detected using specific antibodies. In contrast to control mouse plasma, the proNT/NMN levels in tumor-bearing mice increased as the tumors grew, and the elevated plasma proNT/NMN levels were decreased by tumor resection. Moreover, proNT/NMN was expressed in SBC3 tumors, suggesting that proNT/NMN was secreted into blood from the tumor, and this secretion may be specific to SCLC.
Photo-EPR Studies on Low-Energy Electron-Irradiated 4H-SiC (2009)

Photoexcitation electron paramagnetic resonance (photo-EPR) was used to determine deep levels related to the carbon vacancy (VC) in 4H-SiC. High-purity free-standing n-type 4H-SiC epilayers with concentration of intrinsic defects (except the photo-insensitive SI1 center) below the detection limit of EPR were irradiated with low-energy (200 keV) electrons to create mainly VC and defects related to the C sublattice. The simultaneous observation of and signals, their relative intensity changes and the absence of other defects in the sample provide a more straight and reliable interpretation of the photo-EPR results. The study suggests that the (+|0) level of VC is located at ~EC–1.77 eV in agreement with previously reported results and its single and double acceptor levels may be at ~ EC–0.8 eV and ~ EC–1.0 eV, respectively.
Derived Properties of Rectangular Wing Based on Eigenstructure of Lifting Line Theory (2020)

At the heart of many numerical implementations of lifting line theory (LLT) is the matrix relating vortex strength to downwash. This type of matrix is a symmetric Toeplitz matrix which has well-studied properties, including recent research that has developed methods to identify the asymptotics of individual eigenvalues and eigenvectors of infinite Toeplitz matrices. This paper explores applying the method to the lifting line matrix to identify its eigenstructure, and demonstrates using them to develop an accurate estimate of the coefficients of lift and induced drag of a rectangular wing.
AMPERSAND: Argument Mining for PERSuAsive oNline Discussions (2020)

Argumentation is a type of discourse where speakers try to persuade their audience about the reasonableness of a claim by presenting supportive arguments. Most work in argument mining has focused on modeling arguments in monologues. We propose a computational model for argument mining in online persuasive discussion forums that brings together the micro-level (argument as product) and macro-level (argument as process) models of argumentation. Fundamentally, this approach relies on identifying relations between components of arguments in a discussion thread. Our approach for relation prediction uses contextual information in terms of fine-tuning a pre-trained language model and leveraging discourse relations based on Rhetorical Structure Theory. We additionally propose a candidate selection method to automatically predict what parts of one's argument will be targeted by other participants in the discussion. Our models obtain significant improvements compared to recent state-of-the-art approaches using pointer networks and a pre-trained language model.
Recovery of Heavy And Conventional Oils From Pressure-depleted Reservoirs Using Horizontal Wells (1994)

Abstract Production of oil from reservoirs overlain by a gas cap causes the gas-oil interface to advance towards the producer and curve downwards. With conventional wells, the rate of production that is required for the operation to be economic is usually too high to avoid production of free gas. However, with horizontal wells, the critical production rate is higher and may allow economic operation without gas production. A stable interface can be maintained closer to the well giving much higher recoveries for comparable rates. Gravity stabilized, vertical gas displacement can also be utilized in reservoirs underlain by an active aquifer. In such operations, if the producer is kept at a potential equivalent to that of the aquifer, then free water production can also be avoided. The pressure is maintained by-the injection of the gas so that the oil is pushed out rather than sucked out. Equations relating the critical flow rate to maintain stability of the interface and the recovery are' developed in the paper and compared to experimental data from vertical Hele-Shaw models. The study examines the effect of production rate, well spacing, initial height of the reservoir and the type of fluid on the recovery for downward displacement of oil by gas to horizontal wells located at the base of the reservoir. Experiments have been carried out at conditions both above and below the critical rate. It is found that at very high rates the interface becomes unstable almost instantaneously and oil is displaced by a dominant finger of gas. At lower rates the interface is stable for most of the displacement and larger recoveries are obtained. More closely spaced wells and higher initial height of the reservoir give much better rates and recoveries. The agreement between the predictions and experimental data is good. Introduction There are many oil reservoirs in the world which have either an active water layer below the oil zone or a gas cap above it or both. Production of oil from such reservoirs causes the oil-water interface, or the gas-oil interface, to move towards the production well. The interface becomes curved and, with conventional wells, assumes a shape resembling that of a cone; this phenomenon is known as coning, either water coning or gas coning (Figure 1) or both. Coning, because it allows bypass of free gas or water, creates serious inefficiencies: loss of production, lower oil cut, poor sweep of the reservoir and lesser recovery of the oil in place. Mathematically, gas coning and water coning are analogous. Although this paper addresses gas coning, the ideas presented here are applicable to either case. FIGURE 1: Concept of coning. (Available in full paper) There exists a maximum rate, called the critical rate, for production of oil without bypass of free gas. This critical rate is usually too low to be economic. Horizontal wells offer an attractive alternative in some cases where conventional wells have poor performance due to coning problems. A horizontal well usually has a more extended contact with the reservoir than a vertical well.
THE EFFECT OF PUBLICIZED EXECUTIONS ON HOMICIDE IN CALIFORNIA (1998)

ABSTRACT A requisite of theories of the impact of capital punishment is citizen awareness of executions. However, this criterion is often left unmeasured. Further, the current literature utilizes nationwide data, which introduces aggregation bias. The present paper addresses these issues, testing a death dip hypothesis with data on publicized executions in California. Monthly data are employed to capture any short term effect. A multivariate regression analysis finds that a publicized execution is associated with a decrease of 2.6 homicides, or a 12.7percent decrease in the month of the publicized execution. Publicized executions were associated with a total decrease of 99 homicides during the time period analyzed. The model explains 41 percent of the variance in homicide. The death dip after an execution is interpreted from a blend of the normative validation, victim mobilization, and deterrence perspectives.