gebhart/patrepeval huggingface dataset:
In Situ Hydraulic Conductivity Tests for Compacted Clay (1989)

This paper summarizes the state of the art for in situ conductivity testing of compacted clay soils. Nine methods of testing are reviewed: (1) The Boutwell permeameter; (2) constant‐head borehole permeameters, e.g., the Guelph permeameter; (3) porous probes, e.g., the BAT device; (4) open, single‐ring infiltrometers; (5) open, double‐ring infiltrometers; (6) closed, single‐ring infiltrometers, (7) sealed, double‐ring infiltrometers; (8) the air‐entry permeameter; and (9) lysimeter pans. Installation procedures are given, equations for calculating hydraulic conductivity are presented, simplifying assumptions are listed, and case histories are reviewed. Each type of permeameter has advantages. The Boutwell permeameter is especially convenient for measurement of the vertical and horizontal hydraulic conductivity. Borehole permeameters and porous probes provide data relatively quickly but permeate a relatively small volume of soil. Of the permeameters that can permeate large volume of soil, the sealed double‐ring infiltrometer and pan lysimeter are the most versatile.
Comparative Modeling and Molecular Dynamics Simulation of Substrate Binding in Human Fatty Acid Synthase: Enoyl Reductase and β-Ketoacyl Reductase Catalytic Domains (2015)

Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and β-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and β-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.
Richard J. Evans, The Feminist Movement in Germany, 1890'1933 (London and Beverly Hills: Sage, 1976. (1977)

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CLOPS: A DSL for Command Line Options (2009)

Programmers often write custom parsers for the command line input of their programs. They do so, in part, because they believe that both their program’s parameterization and their option formats are simple. But as the program evolves, so does the parameterization and the available options. Gradually, option parsing, data structure complexity, and maintenance of related program documentation becomes unwieldy. This article introduces a novel DSL called CLOPS that lets a programmer specify command line options and their complex inter-dependencies in a declarative fashion. The DSL is supported by a tool that generates the following features to support command line option processing: (1) data structures to represent option values, (2) a command line parser that performs validity checks, and (3) command line documentation. We have exercised CLOPS by specifying the options of a small set of programs like ls, gzip, and svn which have complex command line interfaces. These examples are provided with the Open Source release of the CLOPS system.
Attenuating gene expression (AGE) for vaccine development (2013)

Live attenuated vaccines are adept in stimulating protective immunity. Methods for generating such vaccines have largely adopted strategies used with Salmonella enterica. Yet, when similar strategies were tested in other gram-negative bacteria, the virulence factors or genes responsible to incapacitate Salmonella often failed in providing the desired outcome. Consequently, conventional live vaccines rely on prior knowledge of the pathogen's virulence factors to successfully attenuate them. This can be problematic since such bacterial pathogens normally harbor thousands of genes. To circumvent this problem, we found that overexpression of bacterial appendages, e.g., fimbriae, capsule, and flagella, could successfully attenuate wild-type (wt) Salmonella enterica serovar Typhimurium. Further analysis revealed these attenuated Salmonella strains conferred protection against wt S. Typhimurium challenge as effectively as genetically defined Salmonella vaccines. We refer to this strategy as attenuating gene expression (AGE), a simple efficient approach in attenuating bacterial pathogens, greatly facilitating the construction of live vaccines.
THE DIABETIC FOOT (2000)

Foot complications in diabetics often lead to amputation. Ulceration is the most common complication in the diabetic forefoot and underlies more than 90% of cases of pedal osteomyelitis. The diagnosis of osteomyelitis is, nevertheless, difficult, and imaging is an important part of the work‐up. Plain radiographs, although useful for anatomical information, are neither sensitive nor specific. Three‐phase bone scintigraphy is sensitive but not specific. Labeled leucocyte scintigraphy and MRI are both useful and are complementary to one another. Labeled leucocyte scintigraphy is valuable for diagnosis as well as follow‐up of pedal osteomyelitis. MRI offers exquisite anatomical detail, which is invaluable for guiding surgical management. The principal complication in the mid and hind foot is the neuropathic or Charcot joint. Although infection of the neuropathic joint is infrequent, its diagnosis is difficult. The extensive bony changes that accompany this disorder severely diminish the value of radiography and bone scintigraphy. It is not always possible to distinguish the marrow oedema of neuropathy from that of osteomyelitis and the role of MRI in the evaluation of this entity is still uncertain. Uptake of labeled leucocytes in the absence of infection may occur and is owing, at least in part, to haematopoietically active marrow. Combined leucocyte/marrow scintigraphy holds considerable promise for identifying the infected Charcot joint.
Block copolymers derived from azobiscyanopentanoic acid. XI. Properties of silicone–PMMA block copolymers prepared via polysiloxane(azobiscyanopentanamide)s (1988)

Abstract Mechanical, thermal, and surface properties of poly(dimethylsiloxane)–poly(methyl methacrylate) block copolymers (PDMS‐ b ‐PMMA) prepared by the use of polysiloxane(azobiscyanopentanamide)s were intensively investigated. The mechanical strength of block copolymers was found to decrease with an increase of siloxane contents. Dynamic mechanical analysis (DMA) of block copolymers having long siloxane chain length (SCL) and high siloxane content revealed the existence of two glass transitions attributable to microphase separation of two segments. Differential scanning calorimetry (DSC) also gave some evidence of microphase separation supporting the DMA results. It was observed that the incorporation of PDMS segments in block copolymers improved thermal stability of PMMA, as confirmed by thermogravimetric analysis. Surface analysis of the block copolymers films cast from several solutions indicated surface accumulation of PDMS segments, as revealed by water contact angle and ESCA measurements.
Comparisons of Different Assays for the Thyroid-Stimulating Antibody of Graves’ Disease* (1983)

Various current methods for the assay of the thyroid-stimulating antibody of Graves' disease (TSAb) were assessed for comparative sensitivity and specificity. Five procedures were examined in detail: I) increase in cAMP in human thyroid slices; II) inhibition of [125I]TSH binding to human thyroid membranes, particulate or III) solubilized; IV) inhibition of [125I]TSH binding to guinea pig fat cell membranes, particulate or V) solubilized. The minimum effective concentration of TSH (microunits per ml) in these assays was: I) 5; IV) 12.5; V) 25 and II and III) 100. The guinea pig fat systems (IV and V) were more sensitive than the human thyroid assays (II and III) in terms of the concentration of TSH required for 50% inhibition of binding. Five preparations of TSAb-immunoglobulin G were found in general to have constant relative potency in the five assay systems, but individual immunoglobulins G were variable in their effects when data in the five procedures were compared directly. It is probable that, in addition to TSAb, other antibodies, more or less specific for the human thyroid, influenced the TSH binding inhibition assays to a variable extent. The above TSH binding inhibition assays were carried out with solutions or suspensions of receptor preparations. Solid phase systems, using microtiter plates for TBI assays, were assessed in less detail. Human thyroid, particulate or solubilized, was ineffective (little specific binding of [125I]TSH), but a particulate preparation of guinea pig fat cell membranes was an efficient basis for a solid phase TBI system. Solid phase assessment with [125I]staphylococcal protein A of binding of thyroid autoantibodies to human thyroid membranes was not specific for TSAb.
A Study on Women's Health Status for Setting up Women's Health Nursing Center and Developing Health Program (1999)

The purpose of this paper was to identify the performance of health promoting lifestyles and health perception over 18 years old women living Wonju city so that the results will be based for setting up women's health nursing center. The subjects were 1080 women selected by stratified and purposive sampling. The data were collected by self reporting questionnaire and interview from May to June, 1998. Data were analyzed by SPSS win program. The results were as follows : 1. The range of age was 18-84 years, The proportion according to women's lifecycle was premarital group 20.0%, delivery and rearing group 49.9%, over middle aged-elderly group 29.8%. 2. The mean menarchial age was 15.2 and menopausal age was 48. Mean frequenices of pregnancy is 2.4 and artificical abortion rate is 36.4%. Primary cause of abortion was unwanted babies 42.8%. The practice rate of family planning was 79.4% and permanent sterilization rate was 37.6%. 3. Fatigue was predominated problem in target population. Depression and headache was predominated in premarital group, headache and nervous felling in delivery and rearing group, arthritis and loss of memory in over middle aged-elderly group. 4. Only 13.7% of the target population make some efforts for their health in compare to 85.9% have attention for their health. Perception of unhealthy rate was 9.1% in premarital group, 24.8% in delivery and rearing group, 30.1% in middle aged-elderly group. 5. The average score of the HPLP(Health Promoting Lifestyle Profile) was 2.41. The variable with the highest degree of performance was interpersonal relationship, whereas the one with the lowest degree was the professional health maintenance. The significant difference was found in HPLP according to age, residential area, marital status, educational level, income level. 6. Majority(95.1%) of the target population agreed on necessity for women's health nursing center. Proper location area was presented to women's center and public health center. The priority for health education program was proper diet, family health, stress management, and exercise. In conclusion, we should prepare the education program for women's health according to women's lifecycle, because health perception, HPLP, and education program needed was differentiated in women's lifecycle. Also we suggest that women's health nursing center based community was needed for proper management of women's health.
Design and Implementation of a Generic Energy-Harvesting Framework Applied to the Evaluation of a Large-Scale Electronic Shelf-Labeling Wireless Sensor Network (2010)

Most wireless sensor networks (WSNs) consist of battery-powered nodes and are limited to hundreds of nodes. Battery replacement is a very costly operation and a key factor in limiting successful large-scale deployments. The recent advances in both energy harvesters and low-power communication systems hold promise for deploying large-scale wireless green-powered sensor networks (WGSNs). This will enable new applications and will eliminate environmentally unfriendly battery disposal. This paper explores the use of energy harvesters to scavenge power for nodes in a WSN. The design and implementation of a generic energy-harvesting framework, suited for a WSN simulator as well as a real-life testbed, are proposed. These frameworks are used to evaluate whether a carrier sense multiple access with collision avoidance scheme is sufficiently reliable for use in emerging large-scale energy harvesting electronic shelf label (EHESL) systems (i.e., 12000 labels in a star topology). Both the simulator and testbed experiments yielded an average success rate up to 92%, with an arrival rate of 40 transceive cycles per second. We have demonstrated that our generic energy-harvesting framework is useful for WGSN research because the simulator allowed us to verify the achieved results on the real-life testbed and vice versa.
Field evaluation of 2 collar-mounted activity meters for detecting cows in estrus on a large pasture-grazed dairy farm (2012)

This study tested the hypothesis that a commercially available system for detecting estrus based on cow activity would perform similarly to that of typical, visual assessment of mounting indicators placed on the tail head of the cow. The hypothesis was applied to a large, pasture-grazed, seasonal-calving dairy herd, and the technology was tested as a stand-alone system. One of 2 types of commercially available collar-mounted activity meters was fitted to 635 cows, and the activity data collected during the 37-d artificial breeding period were analyzed. The first collar-mounted activity meter monitored activity only (AO collars), whereas the second meter measured activity and rumination characteristics (AR collars). Only activity data were used in the current study. Activity-based estrus alerts were initially identified using the default activity threshold value recommended by the manufacturer, but a range of activity threshold values was then analyzed to determine their effect on estrus detection performance. Milk progesterone data and insemination records were used to identify gold standard positive (n = 835) and negative (n = 22,660) estrus dates, to which activity alerts were compared. Visual assessment of mounting indicators resulted in a manual detection performance of 91.3% sensitivity (SN), 99.8% specificity (SP), and 94.5% positive predictive value (PPV). The AR collars achieved 76.9, 99.4, and 82.4% for SN, SP, and PPV, whereas the AO collars achieved 62.4, 99.3, and 76.6% for SN, SP, and PPV, respectively. The observed performance of the activity systems may be underestimated due to test design and applied assumptions, including determining the date of estrus. Lowering the activity threshold from the default value improved sensitivity but the number of false positive alerts was considered to become unmanageable from a practical perspective as sensitivity reached peak values. Time window analysis, receiver operating characteristic curves, and curves of SN and PPV were found to be useful in the analysis and interpretation of results. They generate relevant performance data that allow for meaningful comparisons between similar studies. Although the 2 activity systems tested did not perform to the high level of manual estrus detection found in this study, the potential exists for these systems to be a valuable tool on farms with lower estrus detection performance or for farmers managing larger herds.
Development of an Internet Home Automation System using Java and Dynamic DNS Service (2005)

This paper presents the design and implementation of an Internet home automation system. The design is based on an embedded controller which is connected to a PC-based home Web server via RS232 serial port. The home appliances are connected to the input/output ports and the sensors are connected to the analog/digital converter channels of the embedded controller. The software of the system is based on the combination of Keil C, Java Server Pages, and JavaBeans, and dynamic DNS service (DDNS) client. Password protection is used to block the unauthorized from accessing to the server. The system is scalable and allows additional appliances to be added to it with no major changes to its core, the home appliances can be monitored and controlled locally, or remotely through a web browser from anywhere in the world provided that an Internet access is available.
Microfluidic systems in PCB technology (2005)

In this paper a technology for the production of microfluidic systems is presented. In an overview the design and properties of produced fluidic elements are described. The basic element is a thermal driven micro pump using FR4 as basic material. A design of a pressure sensor in PCB using polyimide membranes demonstrates how to overcome problems with bad material properties like thermal expansion coefficient and the dependence of elastic constant on humidity of polyimide. The compensation of the pressure force with electrostatic force is one possibility for the elimination of material properties of membrane. The ability of the technology to integrate microfluidic elements, optical sensors and electronics in a monolithic PCB-stack is demonstrated by a development of a flow-injection-analysis (FIA). This analysis system contains two micro pumps, one fluid mixer, one optical detector, and one reservoir for the fluidic reagent and, of course, the electronics for the amplification of sensor-signals and the control unit for pumps. The correct functionality of the PCB-FIA is demonstrated by the detection of iron (III) ions using the reagent Thiocyanat.
A murine model of ulcerative colitis: induced with sinusitis-derived superantigen and food allergen (2005)

Introducing Sinusitis-derived SEB-containing SWF to the gastrointestinal tract compromised colonic mucosal barrier function increasing epithelial permeability to luminal macromolecular protein in mice. The SWF facilitated colonic mucosal sensitization to luminal antigen. Multiple challenging the sensitized colonic mucosa with specific antigen OVA induced inflammation, induced a condition similar to human ulcerative colitis.
Phenotypic analysis of mice expressing exclusively apolipoprotein B48 or apolipoprotein B100. (1996)

Apolipoprotein (apo)-B is found in two forms in mammals: apo-B100, which is made in the liver and the yolk sac, and apo-B48, a truncated protein made in the intestine. To provide models for understanding the physiologic purpose for the two forms of apo-B, we used targeted mutagenesis of the apo-B gene to generate mice that synthesize exclusively apo-B48 (apo-B48-only mice) and mice that synthesize exclusively apo-B100 (apo-B100-only mice). Both the apo-B48-only mice and apo-B100-only mice developed normally, were healthy, and were fertile. Thus, apo-B48 synthesis was sufficient for normal embryonic development, and the synthesis of apo-B100 in the intestines of adult mice caused no readily apparent adverse effects on intestinal function or nutrition. Compared with wild-type mice fed a chow diet, the levels of low density lipoprotein (LDL)-cholesterol and very low density lipoprotein- and LDL-triacylglycerols were lower in apo-B48-only mice and higher in the apo-B100-only mice. In the setting of apo-E-deficiency, the apo-B100-only mutation lowered cholesterol levels, consistent with the fact that apo-B100-lipoproteins can be cleared from the plasma via the LDL receptor, whereas apo-B48-lipoproteins lacking apo-E cannot. The apo-B48-only and apo-B100-only mice should prove to be valuable models for experiments designed to understand the purpose for the two forms of apo-B in mammalian metabolism.
AnScalable Matrix Computing Unit Architecture for FPGA, and SCUMO User Design Interface (2019)

High dimensional matrix algebra is essential in numerous signal processing and machine learning algorithms. This work describes a scalable square matrix-computing unit designed on the basis of circulant matrices. It optimizes data flow for the computation of any sequence of matrix operations removing the need for data movement for intermediate results, together with the individual matrix operations’ performance in direct or transposed form (the transpose matrix operation only requires a data addressing modification). The allowed matrix operations are: matrix-by-matrix addition, subtraction, dot product and multiplication, matrix-by-vector multiplication, and matrix by scalar multiplication. The proposed architecture is fully scalable with the maximum matrix dimension limited by the available resources. In addition, a design environment is also developed, permitting assistance, through a friendly interface, from the customization of the hardware computing unit to the generation of the final synthesizable IP core. For N × N matrices, the architecture requires N ALU-RAM blocks and performs O ( N 2 ) , requiring N 2 + 7 and N + 7 clock cycles for matrix-matrix and matrix-vector operations, respectively. For the tested Virtex7 FPGA device, the computation for 500 × 500 matrices allows a maximum clock frequency of 346 MHz, achieving an overall performance of 173 GOPS. This architecture shows higher performance than other state-of-the-art matrix computing units.
A modified Trastuzumab antibody for the immunohistochemical detection of HER-2 overexpression in breast cancer (2005)

The immunohistochemical determination of HER-2 to identify patients with advanced breast cancer candidates for Trastuzumab treatment proved neither accurate nor fully reliable, possibly because none of the current reagents detects the specific antigenic site target of Trastuzumab. To circumvent this problem, we conjugated the NH2 groups of Trastuzumab with biotin, and the compound obtained, designated BiotHER, was added directly to tissue sections. Biotin-labelling was revealed with horseradish peroxidase-conjugated streptavidin. Specificity and sensitivity of BiotHER immunostaining with respect to HER-2 amplification were tested on 164 breast carcinoma samples. BiotHER staining was detected on the tumour cell membrane of 12% of all specimens and in 49% specimens with gene amplification, while absent in nonamplified tumours. Predictivity of BiotHER status with respect to the clinical outcome was analysed in 54 patients with HER-2 amplified advanced breast cancer treated with Trastuzumab plus chemotherapy. BiotHER staining, detected in 50% of tumours with HER-2 amplification, was an independent predictor of clinical outcome. In fact, BiotHER positivity was independently associated with increased likelihood of tumour response and reduced risk of tumour progression and death. Biotinylated Trastuzumab can thus be used for immunohistochemical detection of HER-2 overexpression in breast cancer, and has the potential to identify patients likely to benefit from Trastuzumab treatment.