gebhart/patrepeval huggingface dataset:
Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles (2020)

Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infections. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. <i>cbsA</i> was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular <i>Xanthomonas</i> to cause vascular blight, while <i>cbsA</i> mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that <i>cbsA</i> was lost in multiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.
Development of a Miniaturized Hollow-Waveguide Gas Correlation Radiometer for Trace Gas Measurements in the Martian Atmosphere (2012)

We present preliminary results in the development of a miniaturized gas correlation radiometer (GCR) for column trace gas measurements in the Martian atmosphere. The GCR is designed as an orbiting instrument capable of mapping multiple trace gases and identifying active regions on the Mars surface.
A Strategy for Rapid, High-Confidence Protein Identification (1997)

A procedure is described for rapid, high-confidence identification of proteins using matrix-assisted laser desorption/ionization tandem ion trap mass spectrometry in conjunction with a genome database searching strategy. The procedure involves excision of copper-stained bands or spots from electrophoretic gels, in-gel trypsin digestion of the proteins, single-stage mass spectrometric analysis of the resultant mixture of tryptic peptides, followed by tandem ion trap mass spectrometric analysis of selected individual peptides, and database searching of the relevant genomic database using the program PepFrag. The scheme provides sensitive, real-time protein identification as well as facile identification of modifications. A single operator can unambiguously identify 5-10 proteins/day from an organism whose genome is known at a level of > 0.5 pmol of protein loaded on a gel. The utility of the technique was demonstrated by the identification and characterization of a band from a human HTLV-I preparation and 11 different proteins from a yeast RNA polymerase II C-terminal repeat domain-affinity preparation. The technology has great potential for postgenome biological science, where it promises to facilitate the dissection and anatomy of macromolecular assemblages, the definition of disease state markers, and the investigation of protein targets in biological processes such as the cell cycle and signal transduction.
Synthetic Bistability and Differentiation in Yeast (2019)

Engineered systems that control cellular differentiation and pattern formation are essential for applications like tissue engineering, biomaterial fabrication, and synthetic ecosystems. Synthetic circuits that can take on multiple states have been made to engineer multicellular systems. However, how to use these states to drive interesting cellular behavior remains challenging. Here, we present a cellular differentiation program involving a novel synthetic bistable switch coupled to an antibiotic resistance gene that affects growth in yeast ( S. cerevisiae). The switch is composed of a positive feedback loop involving a novel transcription factor and can be switched ON and OFF via two different transient inducer inputs. By further coupling the bistable switch with an antibiotic resistance gene, we obtained a growth differentiation circuit, where yeast cells can be switched to stable HIGH or LOW growth rate states via transient inducer inputs. This work demonstrates a rationally designed and experimentally validated cellular differentiation behavior in yeast.
Assessment of Diabetes-Related Distress (1995)

These findings suggest that the PAID, a brief, easy-to-administer instrument, may be valuable in assessing psychosocial adjustment to diabetes. In addition to high internal reliability, the consistent pattern of correlational findings indicates that the PAID is tapping into relevant aspects of emotional distress and that its particular feature, the measurement of diabetes-related emotional distress, is uniquely associated with diabetes-relevant outcomes. These data are also consistent with the hypothesis that diabetes-related emotional distress, separate from general emotional distress, is an independent and major contributor to poor adherence. Given that the study was limited to female patients using insulin, further examination of the clinical usefulness of the PAID will need to focus on more heterogeneous samples.
Specification-centered robustness (2011)

In addition to being correct, a system should be robust, that is, it should behave reasonably even after receiving unexpected inputs. In this paper, we summarize two formal notions of robustness that we have introduced previously for reactive systems. One of the notions is based on assigning costs for failures on a user-provided notion of incorrect transitions in a specification. Here, we define a system to be robust if a finite number of incorrect inputs does not lead to an infinite number of incorrect outputs. We also give a more refined notion of robustness that aims to minimize the ratio of output failures to input failures. The second notion is aimed at liveness. In contrast to the previous notion, it has no concept of recovery from an error. Instead, it compares the ratio of the number of liveness constraints that the system violates to the number of liveness constraints that the environment violates.
Probing the Exit Channel of the OH + CH3OH → H2O + CH3O Reaction by Photodetachment of CH3O–(H2O) (2021)

Transition state dynamics of bimolecular reactions can be probed by photodetachment of a precursor anion when the Franck-Condon region of the corresponding neutral potential energy surface is near a saddle point. In this study, photodetachment of anions at <i>m</i>/<i>z</i> = 49 enabled investigation of the exit channel of the OH + CH<sub>3</sub>OH → H<sub>2</sub>O + CH<sub>3</sub>O reaction using photoelectron-photofragment coincidence spectroscopy. High-level coupled-cluster calculations of the stationary points on the anion surface show that the methoxide-water cluster CH<sub>3</sub>O<sup>-</sup>(H<sub>2</sub>O) is the stable minimum on the anion surface. Photodetachment at a 3.20 eV photon energy leads to long-lived H<sub>2</sub>O(CH<sub>3</sub>O) complexes and H<sub>2</sub>O + CH<sub>3</sub>O products consistent with both direct dissociative photodetachment and resonance mediated processes on the neutral surface. The partitioning of total kinetic energy in the system indicates that water stretch and bend excitation is induced in dissociative photodetachment and evidence for long-lived complexes consistent with vibrational Feshbach resonances is reported.
Teaching invention, innovation, and entrepreneurship to Northern Nevada high school science and math teachers (2002)

The economic history of the United States is replete with examples of inventors and small business innovators making major contributions. From the late 18/sup th/ Century to the present time, major technical advancements have been made as a result of individual inventors, innovators and entrepreneurs working independently of large industrial corporations and government laboratories. It is alarming to note however, just how little is being taught in this country about subjects relating to inventing, innovating and being an entrepreneur. This paper describes a special class that was designed and taught to a group of Northern Nevada high school math and science teachers. The class time was spread over a three day period and the topics covered were all related to invention, innovation and entrepreneurship. The final afternoon was devoted to developing methods, techniques and curriculum for the high school teachers to consider for use in their own classes.
Electronic Activation during Nanoparticle Exsolution for Enhanced Activity at Elevated Temperature (2023)

Nanoparticle (NP) exsolution from perovskite-based oxides matrix upon reduction has emerged as an ideal platform for designing highly active catalysts for energy and environmental applications. However, the mechanism of how the material characteristics impacts the activity is still ambiguous. In this work, taking Pr<sub>0.4</sub>Sr<sub>0.6</sub>Co<sub>0.2</sub>Fe<sub>0.7</sub>Nb<sub>0.1</sub>O<sub>3</sub> thin film as the model system, we demonstrate the critical impact of the exsolution process on the local surface electronic structure. Combining advanced microscopic and spectroscopic techniques, particularly scanning tunneling microscopy/spectroscopy and synchrotron-based near ambient X-ray photoelectron spectroscopy, we find that the band gaps of both the oxide matrix and exsolved NP decrease during exsolution. Such changes are attributed to the defect state within the forbidden band introduced by oxygen vacancies and the charge transfer across the NP/matrix interface. Both the electronic activations of oxide matrix and the exsolved NP phase lead to good electrocatalytic activity toward the fuel oxidation reaction at elevated temperature.
Differences in health-related quality of life between HIV-positive and HIV-negative people in Zambia and South Africa: a cross-sectional baseline survey of the HPTN 071 (PopART) trial (2017)

National Institute of Allergy and Infectious Diseases, National Institute on Drug Abuse, National Institute of Mental Health, President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, the Bill & Melinda Gates Foundation.
Architectural Principles of Uniform Resource Name Resolution (1998)

This document addresses the issues of the discovery of URN (Uniform Resource Name) resolver services that in turn will directly translate URNs into URLs (Uniform Resource Locators) and URCs (Uniform Resource Characteristics).The document falls into three major parts, the assumptions underlying the work, the guidelines in order to be a viable Resolver Discovery Service or RDS, and a framework for designing RDSs.The guidelines fall into three principle areas: evolvability, usability, and security and privacy.An RDS that is compliant with the framework will not necessarily be compliant with the guidelines.Compliance with the guidelines will need to be validated separately.
Equivalent Linear Programming Formulations for Robust Trajectory Planning Under Input Dependent Uncertainties (2022)

We consider the problem of optimal trajectory planning for discrete-time linear dynamical systems with bounded uncertainty in the inputs. In particular, we consider uncertainty in the form of control disturbance with bounds that are proportional to the nominal control and exogenous disturbance that lies in a known polytope. We show that robust linear inequality state constraints on such systems can be equivalently reformulated as deterministic linear inequality constraints, hence the robust trajectory problem can be solved without conservatism within the specified uncertainty bounds. Furthermore, the resulting problems are convex optimization problems that can be solved efficiently to global optimality. To this end, we first utilize duality theory of convex optimization to formulate the robust trajectory planning problem as a deterministic optimization problem with some bilinear constraints (Lemma (1)). Then we observe that the bilinear constraints can be replaced by linear ones by finding a closed-form solution of the optimization problem over one of the two variables in the bilinear terms (Lemma (2)). These two lemmas are our main contributions, which together lead to Theorem (1), which allows the deterministic linear reformulation which renders our problem tractable. We then demonstrate our method via numerical simulations on a simple example problem.
Phytochrome and Seed Germination. IV. Action of Light Sources With Different Spectral Energy Distribution on the Germination of Tomato Seeds (1968)

Germination of tomato seeds exposed to a single, saturating irradiation from light sources of different spectral energy distribution seems to be dependent upon the photostationary P(FR)/P(R) ratio established by the irradiation. Germination of tomato seeds exposed to prolonged irradiations from the same light sources does not seem to be controlled solely by the P(FR)/P(R) ratio induced and maintained by the irradiation.
Further Studies on the Chromogenic Substrate Assay Method for Bacterial Endotoxins Using Horseshoe Crab (Tachypleus tridentatus) Hemocyte Lysate1 (1982)

Basic studies on the chromogenic substrate method for the assay of bacterial endotoxins were performed using Tachypleus hemocyte lysate. From the substrate specificity studies, Tachypleus clotting enzyme was found to prefer tripeptidyl- p -nitroanilide (pNA) having glycine and leucine (valine) in the P2 and P3 positions, and the apparent Km values for these peptidyl-pNA's were in the order of 10 −5 M. Coagulogen, a natural substrate of the clotting enzyme, competitively inhibited the amidase-catalyzed hydrolysis of Tos-Ile-Glu-Gly-Arg-pNA with a K1 of 3.8 × 10 −6 M, indicating that the amidase activity is due to catalytic action of the clotting enzyme. Using the chromogenic substrate, the optimal conditions for the endotoxin-induced activation of the latent amidase in Tachypleus hemocyte lysate was examined. As a result, it was shown that the following points should be taken into consideration for the assaying of endotoxins; (1) the endotoxin-induced amidase activity in the lysate occurs optimally at pH 8.0 and at 40°C, (2) the induction requires Mg 2+ , (3) the endotoxin-induced amidase activity is unstable on prolonged incubation, (4) the sensitivity of the lysate to endotoxin is highly dependent upon its protein concentration, and (5) the latent amidase activity in the lysate is induced by a variety of endotoxin preparations with considerable differences in reactivity. In conclusion, the chromogenic substrate method using Tachypleus hemocyte lysate is valuable for the detection and quantitation of bacterial endotoxins, and under certain conditions the method is fifty-times more sensitive than the Limulus gelation test.
Splicing mutation in human hereditary analbuminemia. (1988)

We have identified a structural defect in the serum albumin gene in human analbuminemia. Sequence determination of 1.1 kilobases (kb) of the 5' regulatory region and of 6 kb across exonic regions revealed a single AG-to-GG mutation within the 3' splice site of intron 6 in the defective gene of an analbuminemic individual. In an in vitro assay on the RNA transcript this mutation causes a defect in splicing of the intron 6 sequence and in subsequent ligation of the exon 6-exon 7 sequences. Using polymerase-amplified genomic DNA and allele-specific oligodeoxynucleotide probes, we have also shown that the sequence of this intron 6/exon 7 splice junction is normal in a different, unrelated analbuminemic individual. Analbuminemia in humans is therefore the result of one of multiple defects in our genome.
Poster 235: Surgical Management of Patellar Instability in Adolescents with High Grade Trochlear Dysplasia (2022)

Objectives: High-grade trochlear dysplasia (HGTD) has previously been identified as a risk factor for failure of surgical management of patellofemoral instability (PFI). However, limited data exists on the influence of the type of surgical procedure performed on postoperative outcomes in these patients. The purpose of this study was to identify the rates of failure of primary PFI surgery in patients with HGTD compared to those without HGTD and to assess the effect of the type of surgery on recurrent instability and return to OR. Methods: We retrospectively reviewed patients aged ≤19 years who underwent primary surgery for PFI at our institution between 2008 and 2017. Patients underwent procedures including medial retinacular plication (MRP), medial patellofemoral ligament reconstruction (MPFLR), tibial tubercle osteotomy (TTO), or combined procedures. We excluded patients with incomplete imaging data, BMI &gt;30kg/m 2 , those that underwent surgery for fixation of a chondral fracture &gt;1cm, and patients with a diagnosis of syndromic disorder. Trochlear dysplasia was evaluated based on pre-operative MRI. Patients were divided between those that had HGTD and those without HGTD. Comparisons were made between the two groups and logistic regression analysis was utilized to determine if surgery category was associated with rate of recurrence in the HGTD patients. Results: Three-hundred three patients, average age 15.1 years, underwent primary surgical stabilization for PFI with median follow up time of 3.0 years. Forty-nine percent (149/303) of the cohort had HGTD. Demographics were comparable between HGTD groups (Table 1). When compared to the patients without HGTD, patients with HGTD showed similar rates of recurrent instability, return to the OR for instability, and return to the OR for other reasons. Looking at patients with just HGTD, there was a significant association between surgery type and outcomes (Table 2). HGTD patients who underwent MPFLR had a 63% decrease in the odds of experiencing recurrent instability compared to those undergoing MRP (OR=0.37; p=0.03). Similarly, the TTO surgery group had an 80% decrease in the odds of experiencing recurrent instability compared to patients undergoing MRP (OR=0.20; p=0.002). Conclusions: While adolescents with PFI and HGTD overall have similar results after surgical stabilization, there is a significant effect of the type of surgery performed. Patients with HGTD that underwent MRP had significantly more instability and return to the OR for instability surgeries than patients that underwent other procedures. Based on this data, adolescents with PFI and HGTD should be considered for more powerful surgeries to limit the risk of recurrence or return to the OR. [Table: see text][Table: see text]
Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements (2017)

We developed a flow cytometry-based method to purify P. tetraurelia nuclei to high purity and provided quality control with flow cell imaging and high throughput DNA sequencing. We identified 61 germline transposable elements including the first Paramecium retrotransposons. This approach paves the way to sequence the germline genomes of P. aurelia sibling species for future comparative genomic studies.
Near‐Infrared Chemical Imaging as a Process Analytical Tool (2005)

This chapter contains sections titled: The process analytical technology (PAT) initiative The role of near-infrared chemical imaging (NIR-CI) in the pharmaceutical industry The development of imaging spectroscopy Chemical imaging principles PAT applications Processing case study one: Estimating ‘abundance’ of sample components Processing case study two: Determining blend homogeneity through statistical analysis Final thoughts Acknowledgements
Ion Pairs of 5,5-dimethyl-2-(2-hydroxy-3,5-disulfophenylhydrazo)cyclohexane-1,3-dione with Cationic Surface-Active Substances as Analytical Reagent for Determination of Copper(II) (2010)

A new organic reagent, 5,5-dimethyl-2-(2-hydroxy-3,5-disulfophenylhydrazo)сyclo-hexane-1,3-dione (H2L), was synthesized by azo coupling of diazonium salts of 2-hydroxy-3,5-disulfoaniline with dimedone. The dissociation constants of H2L were determined by potentiometric titration, being pK 1 = 5.90 ± 0.03 and pK 2 = 9.67 ± 0.04. The interaction in systems of H2L and cationic surface-active substances (CSAS), cetylpyridinium chloride (CPCl), cetylpyridinium bromide (CPBr), or cetyltrimethylammonium bromide (CTABr) was studied in the presence and absence of Cu(II). It was found that the detection limit of Cu(II) using H2L–CSAS pairs decreases in accord with the stability of associates H2L(CPCl)2 > H2L(CPBr)2 > H2L(CTABr)2 and their copper(II) complexes Cu[(HL)(CPCl)2]2 > Cu[(HL)(CPBr)2]2 > Cu[(HL)(CTABr)2]2. The effects of foreign ions and masking substances on the complexation were studied and showed that the reaction of Cu(II) with H2L in the presence of CSAS is more selective. Based on these observations, a procedure for the spectrophotometric determination of copper(II) in soils polluted by oil, seawater, igneous rock, and nickel-based alloys was developed.
CETS (2010)

Temporal memory safety errors, such as dangling pointer dereferences and double frees, are a prevalent source of software bugs in unmanaged languages such as C. Existing schemes that attempt to retrofit temporal safety for such languages have high runtime overheads and/or are incomplete, thereby limiting their effectiveness as debugging aids. This paper presents CETS, a compile-time transformation for detecting all violations of temporal safety in C programs. Inspired by existing approaches, CETS maintains a unique identifier with each object, associates this metadata with the pointers in a disjoint metadata space to retain memory layout compatibility, and checks that the object is still allocated on pointer dereferences. A formal proof shows that this is sufficient to provide temporal safety even in the presence of arbitrary casts if the program contains no spatial safety violations. Our CETS prototype employs both temporal check removal optimizations and traditional compiler optimizations to achieve a runtime overhead of just 48% on average. When combined with a spatial-checking system, the average overall overhead is 116% for complete memory safety
Supplementary Figure 6 from Sef Downregulation by Ras Causes MEK1/2 to Become Aberrantly Nuclear Localized Leading to Polyploidy and Neoplastic Transformation (2023)

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Tyrosinaemia II (1984)

Four cases of tyrosinaemia type II (Richner-Hanhart syndrome) are reported. This syndrome consists of corneal erosions, palmar and plantar hyperkeratoses, and sometimes mental retardation. Presentation with photophobia and dendritic corneal ulceration or circumscribed palmoplantar keratoderma should alert the physician to the possible diagnosis of tyrosinaemia II. Early diagnosis is important, as the clinical picture can be modified by dietary restriction.