gebhart/patrepeval huggingface dataset:
Poly(3-Hydroxybutyrate) Degradation in Ralstonia eutropha H16 Is Mediated Stereoselectively to (S)-3-Hydroxybutyryl Coenzyme A (CoA) via Crotonyl-CoA (2013)

Degradation of poly(3-hydroxybutyrate) (PHB) by the thiolytic activity of the PHB depolymerase PhaZ1 from Ralstonia eutropha H16 was analyzed in the presence of different phasins. An Escherichia coli strain was constructed that harbored the genes for PHB synthesis (phaCAB), the phasin PhaP1, and the PHB depolymerase PhaZ1. PHB was isolated in the native form (nPHB) from this recombinant E. coli strain, and the in vitro degradation of the polyester was examined. Degradation resulted in the formation of the expected 3-hydroxybutyryl coenzyme A (3HB-CoA) and in the formation of a second product, which occurred in significantly higher concentrations than 3HB-CoA. This second product was identified by liquid chromatography mass spectrometry (LC-MS) as crotonyl-CoA. Replacement of PhaP1 by PhaP2 or PhaP4 resulted in a lower degradation rate, whereas the absence of the phasins prevented the degradation of nPHB by the PHB depolymerase PhaZ1 almost completely. In addition, the in vitro degradation of nPHB granules isolated from R. eutropha H16 (wild type) and from the R. eutropha ΔphaP1 and ΔphaP1-4 deletion mutants was examined. In contrast to the results obtained with nPHB granules isolated from E. coli, degradation of nPHB granules isolated from the wild type of R. eutropha yielded high concentrations of 3HB-CoA and low concentrations of crotonyl-CoA. The degradation of nPHB granules isolated from the ΔphaP1 and ΔphaP1-4 deletion mutants of R. eutropha was significantly reduced in comparison to that of nPHB granules isolated from wild-type R. eutropha. Stereochemical analyses of 3HB-CoA revealed that the (R) stereoisomer was collected after degradation of granules isolated from E. coli, whereas the (S) stereoisomer was collected after degradation of granules isolated from R. eutropha. Based on these results, a newly observed mechanism in the degradation pathway for PHB in R. eutropha is proposed which is connected by crotonyl-CoA to the β-oxidation cycle. According to this model, the NADPH-dependent synthesis of PHB with (R)-3HB-CoA as the intermediate and the PHB degradation yielding (S)-3HB-CoA, which is further converted in an NAD-dependent reaction, are separated.
Diethylamino/methylphosphonium-methylide und ihre Bis(cyclopentadienyI)zirconium(IV)-Komplexe / Diethylamino/methylphosphonium-methylides and their Bis(cyclopentadienyl)zirconium(IV) Complexes (1985)

(1a- The diethylamino/methylphosphines Me n (NEt 2 ) 3-n P c) with n = 0, 1, or 2 have been synthesized from PCl 3 or MePCl 2 , respectively. Addition of methyliodide gave the phosphonium salts Me n (NEt 2 ) 4-n P + I - (2a- c) with n = 1 , 2 , or 3. These salts were converted into the corresponding ylides Me n (NEt 2 ) 3-n P=CH 2 (3a- c) with n = 0, 1, or 2. The products are reactive, colorless, distillable liquids, freely soluble in non-polar solvents. - (C 5 H 5 ) 2 ZrCl 2 when treated with 3b afforded two isomeric products with chelating or monodentate vlide coordination, respectively: (C 5 H 5 ) 2 ZrCl(CH 2 ) 2 P(NEt 2 ) 2 (4) and (C 5 H 5 ) 2 ZrClCH=P(NEt 2 ) 2 Me (5). In an analogous reaction. 3a gave a dinuclear complex [(C 5 H 5 ) 2 ZrCP(NEt 2 )Me 2 ] 2 (6) whereas no well-defined material could be obtained with the bulky trisamino ylide 3c. All compounds were characterized by their 1 H. 13 C, and 31 P NMR spectra.
Metabolomic profiling of patients with high gradient aortic stenosis undergoing transcatheter aortic valve replacement (2020)

Metabolic profiling identified significant and reversible changes in circulating metabolites of patients with AS. The correlation of circulating metabolites with clinical parameters supports the use of these data to identify novel diagnostic as well as prognostic markers for disease screening, pathophysiological studies as well as patient surveillance.
Diagnosis of Advanced Gastric Cancer (2013)

In Korea, gastric cancer is the most common cancer and the third leading cause of death from cancer. But recently, as a consequence of more accurate diagnostic and therapeutic strategies, mortality rate has decreased. The overall survival of patients with gastric cancer has increased markedly in Korea, due to the virtue of Korean National Cancer Screening Program. Nowadays, more than half of the patients are diagnosed as early gastric cancer. However, the survival of patients with advanced gastric carcinoma has not improved yet. Early detection of and treatment for AGC may improve outcomes, above and beyond the lead-time bias, in patients who have asymptomatic disease and a good performance status. Endoscopy ensures the most accurate diagnosis of gastric adenocarcinoma, while CT can be used to assess local and distant diseases. Endoscopy is the most useful method for securing the diagnosis of gastric adenocarcinoma and CT is also useful to assess local and distant diseases. PET imaging seems to have limited capacity detecting early gastric carcinomas. But PET/CT images of metastatic or advanced gastric adenocarcinoma can visualize primary tumors and also identify distant metastasis of solid organs with a high detection rate. (Korean J Helicobacter Up Gastrointest
Writing buried optical waveguides: Contrasts in ultrafast and ultraviolet lasers (2002)

Ultrafast lasers and deep-ultraviolet F2 lasers present stark contrasts in driving multi-photon and single-photon interactions within transparent glasses. Low-loss single mode waveguides and simple photonic components were formed with a 50-fs Ti:Sapphire laser and a 157-nm 15-ns F2 laser inside the bulk of fused silica. Laser interactions were confined by large NA optics within a small ∼8-μm diameter focal volume and scanned with precision motion stages to shape 3-dimensional photonic structures. Refractive index changes of up to 0.01 were induced with the ultrafast laser at a high scanning speed of several hundred microns per second and 100-kHz repetition rate. Weaker refractive index changes of 0.0005 were generated by the F2 laser, owing to a lower 100-Hz repetition rate and weaker absorption in the focal volume. The laser-generated waveguides offer high transmission of ∼1 dB/cm, are transparent to light in the visible and infrared spectrum, and can support multi-mode guiding with low insertion loss into optical fibers. The paper will present examples of fabricating simple three-dimensional photonic components.
Forensic Applications of Nitrogen and Oxygen Isotopes in Tracing Nitrate Sources in Urban Environments (2002)

Ground and surface waters in urban areas are susceptible to nitrate contamination from septic systems, leaking sewer lines, and fertilizer applications. Source identification is a primary step toward a successful remediation plan in affected areas. In this respect, nitrogen and oxygen isotope ratios of nitrate, in conjunction with hydrologic data and water chemistry, have proven valuable in urban studies from Austin, Texas, and Tacoma, Washington. In Austin, stream water was sampled during stremflow and baseflow conditions to assess surface and subsurface sources of nitrate, respectively. In Tacoma, well waters were sampled in adjacent sewered and un-sewered areas to determine if locally high nitrate concentrations were caused by septic systems in the un-sewered areas. In both studies, sewage was identified as a nitrate source and mixing between sewage and other sources of nitrate was apparent. In addition to source identification, combined nitrogen and oxygen isotopes were important in determining the significance of denitrification, which can complicate source assessment by reducing nitrate concentrations and increasing i 15 N values. The two studies illustrate the value of nitrogen and oxygen isotopes of nitrate for forensic applications in urba areas.
Shape computation of closed elastica under external forces (2014)

This paper deals with a computation method for calculating a largely deformed shape of a closed elastica subject to external forces. The computation method considered here utilizes a dimensionless discrete elastica model discretized by a multi-link approximation, and employs the shooting method for solving boundary-value problems of a closed elastica. Validity of the computation is confirmed by comparing a real shape of a closed elastica subject to external forces and a corresponding simulated one. Numerical stability of the computation is also discussed.
A dual colour fluorescence in situ hybridization (FISH) assay for identifying the zoonotic malaria parasite Plasmodium knowlesi with a potential application for the specific diagnosis of knowlesi malaria in peripheral-level laboratories of Southeast Asia (2017)

To our knowledge, this is the first description of a FISH assay for P. knowlesi that is potentially useful for diagnosing infections in remote laboratories in endemic countries.
47‐3: High Efficiency and High PPI AMOLED with Cavity Tuned by Inkjet Printed Hole Injection Layer (2018)

A low‐cost AMOLED with 10µm sub‐pixel width is fabricated without using a FMM. Solution hole injection layers were printed on a TFT array panel to replace multiple thicknesses of ITO commonly used for cavity tuning, resulting in a new process with low cost and high pixel density. The panel using inkjet‐printed hole injection layer achieved the same performance as a panel using ITO only. The panel achieved a high NTSC ratio of 95.6% coverage and a reflectivity of ambient light lower than 6%, thanks to a precise alignment of AMOLED sub‐pixels and a RGB color filter rather than a circular polarizer.
Non-rigid Stereo-motion (2007)

Using a calibrated stereo pair is a common and practical solution to obtain reliable 3-D reconstructions. In its simpler formulation, once the stereo rig is calibrated, the depth of points in the image is estimated by applying triangulation In order to obtain accurate depth estimates, the cameras are usually separated from each other by a significant baseline thus creating widely spaced observations of the same object. The disadvantage of this configuration though, is that having a wide baseline makes the matching of features between pairs of views a more challenging problem. On the other hand, the task of computing temporal tracks from single camera sequences is relatively easier since the images are closely spaced in time. As a drawback, disparities may be insufficient to obtain a reliable depth estimation and, as a result, longer sequences are needed to infer the 3-D structure. Particularly, in the case of non-rigid structure, a sufficient overall rigid motion is necessary to allow the algorithms to estimate the reconstruction parameters correctly. Hence, a question of relevant interest is the feasibility of an approach that efficiently fuses the positive aspects of both methods. The problem of recovering 3-D structure using a stereo-rig moving in time or a stereo rig looking at a moving object has been defined for the rigid case as the stereo-motion problem (Waxman & Duncan, 1998; Following a similar direction, we introduce a multi-camera motion model that is able to deal with a timevarying shape and we present a linear solution based on the factorization framework that is subsequently optimized with a non-linear procedure. Schematically, the chapter is structured as follows. The inference of 3-D structure from an image sequence (single camera case) is introduced in Section 2, focusing particularly on the case of a deforming body. The next section will show how the presented framework, based on a factorization solution of the problem, can be consistently extended to the case of multiple cameras viewing a deforming body and a linear solution to the problem will be as well provided. Section 3 introduces a non-linear optimization strategy to refine the linear solution obtained with the previous method and Section 4 will validate the presented approaches with experimental tests on synthetic and real deforming bodies. Finally we present further considerations over the presented framework and its future extensions.
A Combined Digital and Biomarker Diagnostic Aid for Mood Disorders (the Delta Trial): Protocol for an Observational Study (Preprint) (2020)

<sec> <title>BACKGROUND</title> Mood disorders affect hundreds of millions of people worldwide, imposing a substantial medical and economic burden. Existing diagnostic methods for mood disorders often result in a delay until accurate diagnosis, exacerbating the challenges of these disorders. Advances in digital tools for psychiatry and understanding the biological basis of mood disorders offer the potential for novel diagnostic methods that facilitate early and accurate diagnosis of patients. </sec> <sec> <title>OBJECTIVE</title> The Delta Trial was launched to develop an algorithm-based diagnostic aid combining symptom data and proteomic biomarkers to reduce the misdiagnosis of bipolar disorder (BD) as a major depressive disorder (MDD) and achieve more accurate and earlier MDD diagnosis. </sec> <sec> <title>METHODS</title> Participants for this ethically approved trial were recruited through the internet, mainly through Facebook advertising. Participants were then screened for eligibility, consented to participate, and completed an adaptive digital questionnaire that was designed and created for the trial on a purpose-built digital platform. A subset of these participants was selected to provide dried blood spot (DBS) samples and undertake a World Health Organization World Mental Health Composite International Diagnostic Interview (CIDI). Inclusion and exclusion criteria were chosen to maximize the safety of a trial population that was both relevant to the trial objectives and generalizable. To provide statistical power and validation sets for the primary and secondary objectives, 840 participants were required to complete the digital questionnaire, submit DBS samples, and undertake a CIDI. </sec> <sec> <title>RESULTS</title> The Delta Trial is now complete. More than 3200 participants completed the digital questionnaire, 924 of whom also submitted DBS samples and a CIDI, whereas a total of 1780 participants completed a 6-month follow-up questionnaire and 1542 completed a 12-month follow-up questionnaire. The analysis of the trial data is now underway. </sec> <sec> <title>CONCLUSIONS</title> If a diagnostic aid is able to improve the diagnosis of BD and MDD, it may enable earlier treatment for patients with mood disorders. </sec> <sec> <title>INTERNATIONAL REGISTERED REPORT</title> DERR1-10.2196/18453 </sec>
Factor X Deficiency and Systemic Amyloidosis (1977)

The association of an isolated acquired factor X (Stuart-factor) deficiency and systemic acquired amyloidosis has been sporadically reported over the last 15 years,1 , 2 and over two thirds of the patients with acquired factor X deficiency have systemic amyloidosis. These facts suggest that an important relation exists between the two entities. In view of the isolated nature of the factor X deficiency it does not appear reasonable to implicate hepatocellular destruction by amyloid infiltrates as the causative mechanism, since most patients with acquired factor X deficiency have normal levels of other coagulation factors known to be of hepatocellular origin. In addition, . . .
Open absorption cycle for combined dehumidification, water heating, and evaporative cooling (2023)

An absorption cycle system, which permits water heating, dehumidifying, and/or evaporative cooling, includes a desorber, absorber, heat exchanger, and, optionally, an evaporator, is constructed to heat a process water that is plumbed through the absorber, heat exchanger, and condenser. In the absence or isolation of the evaporator, the system can dehumidify ambient air to the absorber. The water vapor released by evaporative cooling at the evaporator can be provided to the absorber in a controlled manner to simultaneously maintain a desired humidity while cooling the air ambient by the evaporator. The absorption cycle system can be housed within a single unit or can be compartmentalized.
Changes in Skin, Salivary, and Urinary pH as Indicators of Anxiety Level in Humans (1985)

ABSTRACT In this study, an examination was made of the levels of skin, salivary, and urinary pH associated with changes in anxiety level. Thirty‐two normal women (20–25 yrs old) were the subjects in the study. Anxiety was measured by using the Anxiety State Behavioral Scale of Chorot and Sandin, the Eight State Questionnaire of Cattell et al., a self‐report rating scale, a behavioral index (motoric expression), and the Trait Anxiety Questionnaire S‐R of Sandin and Chorot. Personality was measured by the EPI of Eysenck and Eysenck. Dependent variables were measured in three experimental conditions (Baseline I vs. Oral Examination vs. Baseline II). The results showed that: 1) During the stress condition, a highly significant increase in anxiety (A‐state) occurred. 2) During the stress situation statistically significant reductions in the skin, salivary, and urinary pH were produced. 3) There was a statistically significant correlation between the change in pH and the level of A‐state as measured during the stress period. The change in pH was greater in subjects with a high A‐state than in those having a low A‐state. In conclusion, it appears that skin, salivary, and urinary pH may serve as physiological indicators of anxiety level.
Immunoglobulin M antibody titers in the diagnosis of Legionnaires disease (1982)

The purpose of this study was to determine whether measurement of immunoglobulin M (IgM) antibodies against Legionella pneumophila serogroup 1 can aid in the diagnosis of Legionnaires disease. On the basis of measurements of antibody levels in 1,942 control sera, we used an IgM titer of 1:256, observed in 2.3% of the controls, as presumptive evidence of Legionnaires disease. Measurement of IgM titers permitted us to presumptively or definitively diagnose Legionnaires disease in 13 of 34 patients earlier than we would have if only IgG titers had been measured. Of the 13 patients, 5 were diagnosed serologically only by IgM antibody determination. IgM titers were presumptively diagnostic in week 1 of clinical symptoms in 4 of the 13 patients. We conclude that conjugates used for antilegionella indirect fluorescent-antibody tests should be capable of detecting IgM antibodies so that the value of serological results in diagnosing and managing Legionnaires disease will be maximized.
The pathogenesis of Campylobacter jejuni-mediated enteritis. (2001)

Campylobacter jejuni, a gram-negative spiral shaped bacterium, is a frequent cause of gastrointestinal food-borne illness in humans throughout the world. Illness with C. jejuni ranges from mild to severe diarrheal disease. This article focuses on Campylobacter virulence determinants and their potential role in the development of C. jejuni-mediated enteritis. A model is presented that diagrams the interactions of C. jejuni with the intestinal epithelium. Additional work to identify and characterize C. jejuni virulence determinants is certain to provide novel insights into the diversity of strategies employed by bacterial pathogens to cause disease.
<title>Three-dimensional laser radar with APD arrays</title> (2001)

MIT Lincoln Laboratory is actively developing laser and detector technologies that make it possible to build a 3D laser radar with several attractive features, including capture of an entire 3D image on a single laser pulse, tens of thousands of pixels, few-centimeter range resolution, and small size, weight, and power requirements. The laser technology is base don diode-pumped solid-state microchip lasers that are passively Q-switched. The detector technology is based on Lincoln-built arrays of avalanche photodiodes operating in the Geiger mode, with integrated timing circuitry for each pixel. The advantage of these technologies is that they offer the potential for small, compact, rugged, high-performance systems which are critical for many applications.
Effects of Medium Supplements on Proliferation, Differentiation Potential, and In Vitro Expansion of Mesenchymal Stem Cells (2012)

Mesenchymal stem cells (MSCs) possess great potential for use in regenerative medicine. However, their clinical application may be limited by the ability to expand their cell numbers in vitro while maintaining their differential potentials and stem cell properties. Thus the aim of this study was to test the effect of a range of medium supplements on MSC self-renewal and differentiation potential. Cells were cultured until confluent and subcultured continuously until reaching senescence. Medium supplementation with fibroblast growth factor (FGF)-2, platelet-derived growth factor (PDGF)-BB, ascorbic acid (AA), and epidermal growth factor (EGF) both increased proliferation rate and markedly increased number of cell doublings before reaching senescence, with a greater than 1,000-fold increase in total cell numbers for AA, FGF-2, and PDGF-BB compared with control cultures. Long-term culture was associated with loss of osteogenic/adipocytic differentiation potential, particularly with FGF-2 supplementation but also with AA, EGF, and PDGF-BB. In addition FGF-2 resulted in reduction in expression of CD146 and alkaline phosphatase, but this was partially reversible on removal of the supplement. Cells expressed surface markers including CD146, CD105, CD44, CD90, and CD71 by flow cytometry throughout, and expression of these putative stem cell markers persisted even after loss of differentiation potentials. Overall, medium supplementation with FGF-2, AA, EGF, and PDGF-BB greatly enhanced the total in vitro expansion capacity of MSC cultures, although differentiation potentials were lost prior to reaching senescence. Loss of differentiation potential was not reflected by changes in stem cell surface marker expression.
Embedded tutorial: formal equivalence checking between system-level models and RTL (2005)

A rigorous system-level model (SLM) for a hardware design project is extremely important, often critical. Such a functional model not only defines the architect's ideas but also builds a precise foundation for both hardware designers and verification engineers. The key uses of SLMs are: architecture validation; performance modeling and architectural trade-off; platforms for software development and verification; and functional reference model. In this tutorial, we discuss how to formally verify sequential equivalence between SLMs and RTL, for both timed and untimed models. First, we provide a formal definition of the sequential equivalence. Then we discuss various formal verification technology that enables such practice in real designs.
Measuring clinical competence of medical students (1978)

Evidence of clinical competence for medical students entering the clinical clerkships at the University of Kansas College of Health Sciences is established by passing two different examinations: a 100 item multiple choice examination and a videotaped history and physical examination by each student of a simulated patient, being rated by that patient and two examiners. In 1976 the class of 196 medical students took an average 1.85 written examinations per student. With 70% or better constituting a passing score, 30.6% passed on the first attempt, 55.6% the second, 11.2% the third and 2.5% the fourth. Each student passed the televised practical examination and had the opportunity to review his or her videotape with a critiqued data base and the examiners' and simulated patient's evaluations in hand. Correlation coefficients for all 196 students between scores of written examinations, medicine tutors, examiners and professional patients revealed weak but significant correlations between the assessments of examiners and medical tutors and assessments of examiners and written examination scores, but not between other evaluations. This scheme of proof of competence appears to be objective and direct, and serves the convenience of both students and teaching staff.