gebhart/patrepeval huggingface dataset:
Complex regulation of the global regulatory gene csrA: CsrA‐mediated translational repression, transcription from five promoters by Eσ70 and EσS, and indirect transcriptional activation by CsrA (2011)

CsrA of Escherichia coli is an RNA-binding protein that globally regulates gene expression by repressing translation and/or altering the stability of target transcripts. Here we explored mechanisms that control csrA expression. Four CsrA binding sites were predicted upstream of the csrA initiation codon, one of which overlapped its Shine-Dalgarno sequence. Results from gel shift, footprint, toeprint and in vitro translation experiments indicate that CsrA binds to these four sites and represses its own translation by directly competing with 30S ribosomal subunit binding. Experiments were also performed to examine transcription of csrA. Primer extension, in vitro transcription and in vivo expression studies identified two σ⁷⁰-dependent (P2 and P5) and two σ(S) -dependent (P1 and P3) promoters that drive transcription of csrA. Additional primer extension studies identified a fifth csrA promoter (P4). Transcription from P3, which is indirectly activated by CsrA, is primarily responsible for increased csrA expression as cells transition from exponential to stationary-phase growth. Taken together, our results indicate that regulation of csrA expression occurs by a variety of mechanisms, including transcription from multiple promoters by two sigma factors, indirect activation of its own transcription, as well as direct repression of its own translation.
Open-end winding induction motor driven with indirect matrix converter for common-mode elimination (2007)

In this article a novel scheme using matrix converter is proposed for control of three phase machines. The analysis shows that the scheme has several benefits. By eliminating the common mode voltage from the three phases of the machine the motor bearing current is entirely removed. The maximum insulation stress in the motor winding is limited to the peak value of input phase voltage. The power factor at the utility end is controllable. By using matrix converters for power conversion bulky capacitors are eliminated from the drive.
Numerical Study on the Effectiveness of Grouting Reinforcement on the Large Heaving Floor of the Deep Retained Goaf-Side Gateroad: A Case Study in China (2018)

To study the effectiveness of grouting reinforcement on a large heaving floor of the retained goaf-side gateroad (RGSG) at a 900 m depth in the Zhuji coal mine, a numerical model involving strain softening constitutive material was built. First, the simulated deformations of the RGSG were compared with field data to verify the reliability of the numerical model. Then, the dynamic distribution of the stress in the RGSG floor was examined to reveal the mechanism of floor heave. Finally, grouting reinforcement was proposed to control the RGSG floor, and the corresponding effectiveness was verified by improving the rock mechanics of the floor strata based on the results of numerical uniaxial compressive tests. The results demonstrated that a fairly good match was achieved between the field and numerical data, and the proposed FLAC3D (Fast Lagrangian Analysis of Continua) numerical model was an effective approach to study the stability of the deep RGSG. A variation of the ratio between horizontal stress to vertical stress in the floor strata was the root cause of floor heave in the deep RGSG. Ideally, the floor heave could be reduced by 41%, 62%, and 79% when the floor strata of 1 m depth were reinforced with grouting schemes I, II, and III, respectively.
The Genomic, Epigenomic, and Psychosocial Characteristics of Long-Term Survivors of Ovarian Cancer (2015)

Abstract : Ovarian cancer (OC) remains a major health problem in the United Sates (US). In 2012, there will be an estimated 22,280 cases of epithelial OC (EOC) resulting in 15,500 deaths. While the median survival of OC patients has improved over the last two decades, the vast majority of patients suffer relapse and develop chemo-resistant disease. The overall survival of patients suffering from OC has not changed appreciably over the last three decades. Despite these dismal statistics, there is a minority of OC patients who are long-term (LT) survivors (10 years).This includes a subset of advanced stage (15 ) and a higher proportion of early-stage disease (75 ). Unfortunately, there is little genomic or biologic characterization of these tumors, or patient reported outcomes that characterize LT survivors. The clinical importance of identifying subsets of patients who may or may not benefit from therapy, and understanding the biology of their tumors, is significant both from a patient survival and quality of life (QOL) standpoint. The characterization of LT survivors of advanced stage OC will potentially identify molecular and clinical pathways that can be targeted to help women who have shorter survivals. Further, careful characterization of these patients, including their initial and longitudinal health-related QOL reports, their response to treatments, and their tumors will provide significant measures of prognostic factors. Accurate identification of women with high-grade, early stage OC who will recur will allow for tailoring therapy to only those who will benefit. Thus, the systematic molecular and patient-reported outcomes evaluation of LT survivors of OC (both early and advanced stage) will yield data, which can significantly impact the management of OC patients.
Gene Editing, Gene Therapy, and Cell Xenotransplantation: Cell Transplantation Across Species (2017)

Genetic modification of large animals, pigs in particular, has come a long way during the last decade. These modifications can help minimize immunological and physiological incompatibilities between porcine and human cells, thus allowing for better tolerance and function of xenocells.
Variability in Wound Care Recommendations Following Dermatologic Procedures (2019)

The instructions provided in dermatology patient handouts are highly variable, with various topical agents being recommended for wound healing. Topical antibiotics are not indicated for prophylaxis in clean dermatologic procedures but are still widely used. Greater efforts should be made to ensure that patients receive consistent and evidence-based wound care guidance.
Effects of boundary conditions on cyclic thermal strains of clay and sand (2017)

The thermal oedometer has been widely adopted to determine soil deformation under heating and cooling. Very often an oedometer ring made of steel is used to confine a soil specimen laterally. To investigate and quantify the effects of boundary conditions (i.e. thermal expansion and contraction) of an oedometer ring on soil thermal strains, steel and invar rings were adopted for comparisons. The former has a linear thermal expansion coefficient (TEC) of 1·5 × 10 −5 m/(m °C), which is within the typical range of 5 × 10 −6 to 3·5 × 10 −5 m/(m °C) for soil skeletons. The linear TEC of the latter is 5·0 × 10 −7 m/(m °C), which is substantially smaller than those of soils. Axial strains of saturated normally consolidated clay and loose sand subjected to thermal cycles were measured in these two types of oedometer rings. The accumulated plastic strains of clay and sand measured in the steel ring were 32 and 11% larger than those measured in the invar ring, respectively. As expected, the expansion and contraction of the steel ring itself resulted in additional soil deformation during thermal cycles. It was also found that a popular equation, which assumes that the soil volume remains constant during the expansion and contraction of the odometer ring, overestimates the influence of boundary conditions on the incremental axial strain of soil by more than threefold.
Supplementary Table 1 from Cellular Targets of Gefitinib (2023)

Supplementary Table 1 from Cellular Targets of Gefitinib
Reply (2005)

We thank Stanley Shaldon for his critical comments on our introductory paragraph about the history of home haemodialysis.We have furthermore been informed by Christopher Blagg that they started their home haemodialysis program in Seattle also in 1964 (personal communication).We are in no position to judge whose claims about the history of home haemodialysis are true and whose are not.As a matter of fact, two of us weren't even born in 1961.
The Effects of Threading, Infection Time, and Multiple-Attacker Collaboration on Malware Propagation (2009)

Self-propagating malware spreads over the network quickly and automatically. Malware propagation should be modeled accurately for fast detection and defense. State-of-the-art malware propagation models fail to consider a number of issues. First, the malware can scan a host for multiple vulnerabilities on multiple ports. Second, the vulnerability scanning can be done by multiple threads concurrently. Third, the exploitation of vulnerabilities and the infection of vulnerable hosts cannot be done instantly. Fourth, the malware propagation can start from multiple places in the network rather than a single release point. Finally, the malware copies can collaborate with each other to cause much more damage. Little was done to understand the effects of multi-port scanning, multi-threading, infection time, multiple starting points, and collaboration (MMIMC) on malware propagation. This research quantitatively measures the effects of MMIMC on infected hosts. We employ the Fibonacci number sequence (FNS)to model the effects of infection time. We derive the shift property, which illustrates that different malware initialization scan be represented by shifting their propagations on the time axis. We prove the linear property, which shows that the effects of multiple-attacker collaboration can be represented by linear combinations of individual attacks. Experimental results show that the above issues significantly affect malware propagation and verify our analysis.
Development of a polymer-based gas sensor - humidity and CO2 sensitivity (2009)

A low cost polymer-based gas sensor array for volatile odor detection and identification is being investigated for grain storage application. These sensors are found sensitive to changes in humidity, a common factor in any environment, and a variable parameter in grain storage facilities. The humidity caused resistance variations are investigated for twelve composite polymer films as the sensing materials of odor detectors. Significant variation in humidity sensitivity is found amongst the investigated polymers. Understanding of polymer-based odor sensor response due to humidity is needed to enable compensation for humidity induced variability in sensor measurements. In addition to humidity, the polymer-based sensors are shown sensitive to CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , a released component due to the grain deterioration. The sensitivity of odor detectors are examined at different CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> concentration levels, showing remarkable sensor responses. The performed measurements are indicating that polymer-based sensors suffer from ambient temperature dependency. To overcome this drawback, a new sensor structure is being proposed. This device utilizes a thin SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> platform to be fabricated on silicon wafer. A thin layer of titanium is used to effectively heat and maintain a constant temperature throughout the detector reactive area. Therefore this structure may eliminate sensor response shifts caused by ambient temperature variations.
Translational approaches to obsessive‐compulsive disorder: from animal models to clinical treatment (2011)

Obsessive-compulsive disorder (OCD) is characterized by obsessions (intrusive thoughts) and compulsions (repetitive ritualistic behaviours) leading to functional impairment. Accumulating evidence links these conditions with underlying dysregulation of fronto-striatal circuitry and monoamine systems. These abnormalities represent key targets for existing and novel treatment interventions. However, the brain bases of these conditions and treatment mechanisms are still not fully elucidated. Animal models simulating the behavioural and clinical manifestations of the disorder show great potential for augmenting our understanding of the pathophysiology and treatment of OCD. This paper provides an overview of what is known about OCD from several perspectives. We begin by describing the clinical features of OCD and the criteria used to assess the validity of animal models of symptomatology; namely, face validity (phenomenological similarity between inducing conditions and specific symptoms of the human phenomenon), predictive validity (similarity in response to treatment) and construct validity (similarity in underlying physiological or psychological mechanisms). We then survey animal models of OC spectrum conditions within this framework, focusing on (i) ethological models; (ii) genetic and pharmacological models; and (iii) neurobehavioural models. We also discuss their advantages and shortcomings in relation to their capacity to identify potentially efficacious new compounds. It is of interest that there has been rather little evidence of 'false alarms' for therapeutic drug effects in OCD models which actually fail in the clinic. While it is more difficult to model obsessive cognition than compulsive behaviour in experimental animals, it is feasible to infer cognitive inflexibility in certain animal paradigms. Finally, key future neurobiological and treatment research areas are highlighted.
Nonpolar AlxGa1−xN/AlyGa1−yN multiple quantum wells on GaN nanowire for UV emission (2022)

Nonpolar m-plane AlGaN offers the advantage of polarization-free multiple quantum wells (MQWs) for ultraviolet (UV) emission and can be achieved on the sidewalls of selective area grown GaN nanowires. We reveal that the growth of AlGaN on GaN nanowires by metal organic chemical vapor deposition (MOCVD) is driven by vapor-phase diffusion, and consequently puts a limit on the pitch of nanowire array due to shadowing effect. An insight into the difficulty of achieving metal-polar AlGaN nanowire by selective area growth (SAG) in MOCVD is also provided and can be attributed to the strong tendency to form pyramidal structure due to a very small growth rate of { $$10\bar 11$$ } semipolar planes compared to (0001) c-plane. The nonpolar m-plane sidewalls of GaN nanowires obtained via SAG provides an excellent platform for growth of nonpolar AlGaN MQWs. UV emission from m-plane AlxGa1−xN/AlyGa1−yN MQWs grown on sidewalls of dislocation-free GaN nanowire is demonstrated in the wavelength range of 318–343 nm.
Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer (2015)

Diseases caused by multidrug-resistant bacteria are taking an important toll with respect to human morbidity and mortality. The most relevant antibiotic resistance genes come to human pathogens carried by plasmids, mainly using conjugation as a transmission mechanism. Here, we identified and characterized a series of compounds that were active against several plasmid groups of clinical relevance, in a wide variety of bacterial hosts. These inhibitors might be used for fighting antibiotic-resistance dissemination by inhibiting conjugation. Potential inhibitors could be used in specific settings (e.g., farm, fish factory, or even clinical settings) to investigate their effect in the eradication of undesired resistances.
Computational modeling and analysis of a flow in a storage room (2002)

When a radioactive material gas is accidentally released with a room, the present of the hazardous gas will directly affect the people safety inside. In this study, the flow field and gas dispersion in a ventilated tritium storage room at Los Alamos National Laboratory was simulated using CFX-5.5, a commercially available CFD package using a finite volume methodology. CFD models provide a simultaneously numerical solution of continuity, Navier-Stokes, and energy equations for a flow field geometry with specified boundary conditions. CFX-5 uses a coupled solver, which solves the hydrodynamic equations (for u, v, w, p) as a single system. This reduces the number of iterations required for convergence to a steady state, and to a transient analysis solution for each time step in time-dependant gas dispersion as well.
AAL5 at a Gigabit for a Kilobuck (1994)

We present a novel LAN that has been designed to meet three criteria: it should be low cost, support standard protocols, and provide high performance. The LAN interconnects many workstations in a ring topology with a link rate of 1 Gbit/s. The packet format is the same as that of a B-ISDN cell except that our packets can have arbitrary length. The network also provides hardware support for ATM Adaptation Layer 5 as weIl as TCP/IP. We have implemented the ring network and we describe a network interface card which provides hardware support for critical functions such as calculating checksums. This card is used in conjunction with a second card that supports a single-copy implementation of the TCP/IP protocols. The application-to-application throughput has been measured at rates in excess of 200 Mbit/s between two workstations.
Vaccine efficacy against Ontario isolates of infectious bronchitis virus. (2009)

Infectious bronchitis (IB) is an economically important viral disease with worldwide distribution. Every country with an intensive poultry industry has infectious bronchitis virus (IBV). The virus rapidly spreads from bird to bird through horizontal transmission by aerosol or ingestion. Sentinel bird studies were carried out in southern Ontario and IBV has been isolated from layer flocks. Genetic analysis of the S1 region of the strains showed that they were not vaccine related. The pathogenicity of selected Ontario variants of IBV isolates was studied and the subsequent work was to determine the degree of protection against field isolates provided by a commonly used vaccine MILDVAC-Ma5 in Ontario. The protection was evaluated by challenging immunized chickens with the respiratory (IBV-ON1) and nephropathogenic (IBV-ON4) viruses. The mean vaccine efficacy for IBV-ON1 was 66.7% indicating that a Massachusetts serotype vaccine would provide some protection against IBV field isolates.
Effect of General Microdialysis-Induced Depletion on Extracellular Dopamine (1996)

Continuous sampling by microdialysis induces a general depletion of all low molecular weight materials around the microdialysis probe. The effect of this depletion on the estimation of extracellular dopamine (DA) concentration was evaluated for various degrees of depletion. The basal level of DA in the striatum of male Wistar rats was estimated by the zero net flux method at six different flow rates ranging form 0.3 to 1.6 microL/min. The extracellular DA concentrations in the striatum of male rats measured by this method were found not to differ significantly from one flow rate to another (p > 0.05) with a mean of 6.5 nM +/- 0.11. These finding suggest that the estimation of extracellular dopamine by quantitative microdialysis is independent of the flow rate and that the depletion of other extracellular substances around the probe has no effect on the determination of the extracellular concentration of dopamine.
Predictive Control Strategy Based on Extreme Learning Machine for Path-Tracking of Autonomous Mobile Robot (2014)

In this paper, we propose a novel nonlinear predictive control strategy based on an extreme learning machine to address the path-tracking control problem of wheeled mobile robots in the presence external disturbances. The hybrid chaotic optimization algorithm (HCOA), which can avoid being trapped in local minima and improve convergence in dealing with the large space and high-dimension optimization problems, is used to perform real-time nonlinear minimization of the cost function of a mobile robot to enhance the control accuracy. The proposed improved bidirectional extreme learning machine is employed to model the mobile robot plant and estimate future plant output. The experimental results of tracking the automation mobile robot indicate that the proposed controller can provide more accuracy and faster tracking performance than traditional neural network predictive controllers.
Image segmentation for image-based dietary assessment: A comparative study (2013)

There is a health crisis in the US related to diet that is further exacerbated by our aging population and sedentary lifestyles. Six of the ten leading causes of death in the United States can be directly linked to diet. Dietary assessment, the process of determining what someone eats during the course of a day, is essential for understanding the link between diet and health. We are developing imaging based tools to automatically obtain accurate estimates of what foods a user consumes. Accurate food segmentation is essential for identifying food items and estimating food portion sizes. In this paper, we present a quantitative evaluation of automatic image segmentation methods for food image analysis used for dietary assessment. The experiments indicate that local variation is more suitable for food image segmentation in general dietary assessment studies where the food images acquired have complex background.
Heparin Fails to Inhibit the Proliferation of Human Vascular Smooth Muscle Cells in the Presence of Human Serum (1998)

The proliferation of vascular smooth muscle cells (VSMC) plays a significant part in both the developing atherosclerotic lesion and in restenosis. Heparin has been widely reported to inhibit the growth of VSMC in culture and intimal VSMC in some animal models of vascular hyperplasia. Clinical trials with heparin, however, have failed to inhibit restenosis following angioplasty. Bovine serum is normally used as a growth supplement in in vitro VSMC growth assays. We have compared the effects of human serum with those of bovine serum on the cellular response to heparin in human VSMC culture. While heparin inhibited the proliferation of human VSMC in the presence of bovine serum, it was totally ineffective in the presence of human serum. These observations were consistent over a wide range of serum and VSMC samples. Experiments utilizing neutralizing antibodies to a number of growth factors showed that cells in either serum were similarly dependent on platelet-derived growth factor for proliferation. In contrast, proliferation in the presence of bovine serum was shown to be dependent on extracellular basic fibroblast growth factor, whereas that in human serum was not. Direct binding of [3H]-heparin to VSMC was significantly reduced in the presence of human serum compared with bovine serum, and the former contained twice the concentration of heparin-binding factors of the latter. Removal of heparin-binding factors from either serum type significantly reduced the proliferation potential. Fractionation of heparin-binding factors from human serum showed that the major growth-promoting activity, together with heparin resistance, was contained within a fraction excluded by a 100,000 molecular weight membrane. We conclude that the mechanism of resistance to heparin in human serum is likely to be due to a combination of differential growth factor binding and interference with heparin interaction with cellular receptors by a high molecular weight heparin-binding factor. This phenomenon may significantly contribute to the lack of success of heparin as an antirestenotic agent in clinical trials.