gebhart/patrepeval huggingface dataset:
Coral life history differences determine the refugium potential of a remote Caribbean reef (2016)

Abstract Remote populations can influence connectivity and may serve as refugia from climate change. Here, we investigated two reef-building corals ( Pseudodiploria strigosa and Orbicella franksi ) from the Flower Garden Banks (FGB) – the most isolated, high-latitude Caribbean reef system that retains high coral cover. We characterized coral size frequency distributions, quantified larval mortality rates and onset of competence, estimated larval production, and created detailed biophysical models incorporating these parameters to evaluate source-sink dynamics from 2009 to 2012. Mortality rates were similar across species but competency differed dramatically: P. strigosa was capable of metamorphosis within 2.5 days post fertilization (dpf), while O. franksi were not competent until &gt;20dpf and remained competent up to 120dpf Despite these differences, models demonstrated that larvae of both types were similarly successful in reseeding the FGB. Nevertheless, corals with shorter pelagic larval durations (PLD), such as P. strigosa , were highly isolated from the rest of the Caribbean, while long PLD corals, such as O. franksi , could export larvae to distant northern Caribbean reefs. These results suggest that FGB coral populations are self-sustaining and highlight the potential of long PLD corals, such as endangered Orbicella , to act as larval sources for other degraded Caribbean reefs.
The Impact of Bacteria Exposure on the Plasmonic Response of Silver\n Nanostructured Surfaces (2021)

Silver, especially in the form of nanostructures, is widely employed as an antimicrobial agent in a large range of commercial products. The origin of the biocidal mechanism has been elucidated in the last decades, and most likely originates from silver cation release due to oxidative dissolution followed by cellular uptake of silver ions, a process that causes a severe disruption of bacterial metabolism and eventually leads to eradication. Despite the large number of works dealing with the effects of nanosilver shape/size on the antibacterial mechanism and on the (bio)physical chemistry pathways that drive bacterial eradication, little effort has been devoted to the investigation of the silver NPs plasmon response upon interaction with bacteria. Here we present a detailed investigation of the bacteria-induced changes of the plasmon spectral and dynamical features after exposure to one of the most studied bacterial models, Escherichia Coli. Ultrafast pump-probe measurements indicate that the dramatic changes on particle size/shape and crystallinity, which stem from a bacteria-induced oxidative dissolution process, translate into a clear modification of the plasmon spectral and dynamical features. This study may open innovative new avenues in the field of biophysics of bio-responsive materials, with the aim of providing new and reliable biophysical signatures of the interaction of these materials with complex biological environments.
Identification of Erwinia stewartii by a ligase chain reaction assay (1994)

A PCR-coupled ligase chain reaction (LCR) assay was developed to distinguish the plant pathogenic bacterium Erwinia stewartii from other erwiniae. This new technique allows discrimination to the species level on the basis of a single-base-pair difference in the 16S rRNA gene which is unique to E. stewartii. Portions of the 16S rRNA genes of E. stewartii and the closely related Erwinia herbicola were sequenced. From comparison of the two 16S rRNA gene regions, two primer pairs were constructed such that only E. stewartii DNA gave a product in the LCR assay. The ligated product was separated from the radioactively labelled primers by denaturing polyacrylamide gel electrophoresis and visualized by autoradiography. Twenty-four different Erwinia species and strains were tested by PCR-coupled LCR to verify the specificity of the assay, and only E. stewartii strains gave a positive reaction. In addition, infected and healthy plant material was also assayed. E. stewartii was detected in infected plant material, even when large populations of epiphytic bacteria were present. No enrichment was necessary for detection of the pathogen in corn leaves. This assay has potential as a diagnostic technique for the detection of E. stewartii in infected plant and vector material.
Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function (2016)

Human haploinsufficiency of the transcription factor Tcf4 leads to a rare autism spectrum disorder called Pitt-Hopkins syndrome (PTHS), which is associated with severe language impairment and development delay. Here, we demonstrate that Tcf4 haploinsufficient mice have deficits in social interaction, ultrasonic vocalization, prepulse inhibition, and spatial and associative learning and memory. Despite learning deficits, Tcf4(+/-) mice have enhanced long-term potentiation in the CA1 area of the hippocampus. In translationally oriented studies, we found that small-molecule HDAC inhibitors normalized hippocampal LTP and memory recall. A comprehensive set of next-generation sequencing experiments of hippocampal mRNA and methylated DNA isolated from Tcf4-deficient and WT mice before or shortly after experiential learning, with or without administration of vorinostat, identified "memory-associated" genes modulated by HDAC inhibition and dysregulated by Tcf4 haploinsufficiency. Finally, we observed that Hdac2 isoform-selective knockdown was sufficient to rescue memory deficits in Tcf4(+/-) mice.
A CVS-Server Security Architecture — Concepts and Formal Analysis (2002)

We present a secure architecture of a CVS-server, its implementation (i.e. mainly its configuration) and its formal analysis. Our CVS-server is uses cvsauth, that provides protection of passwords and protection of some internal data of the CVS repository. In contrast to other (security oriented) CVS-architectures, our approach allows the CVS-server run on an open filesystem, i.e. a filesystem where users can have direct access both by CVS-commands and by standard UNIX/POSIX commands such as mv. For our secure architecture of the CVS-server, we provide a formal specification and security analysys. The latter is based on a refinement mapping high-level security requirements on the architecture on low-level security mechanisms on the UNIX/POSIX filesystem level. The purpose of the formal analysis of the secure CVS-server architecture is twofold: First, it is the bases for the specification of mutual security properties such as non-repudiation, authentication and access control for this architecture. Second, the mapping of the architecture on standard security implementation technology is described. Thus, our approach can be seen as a method to give a formal underpinning for the usually tricky business of system administrators.
Effect of low-shrinking composite on the bonding effectiveness of two adhesives in occlusal Class-I cavities (2012)

The purpose of this study was to evaluate if a low-shrinking composite can improve the bonding effectiveness of adhesives in highly constrained conditions. A low-shrinking composite ('els-extra low shrinkage', Saremco) was bonded in standardized occlusal Class-I cavities using a three-step ('cmf', Saremco) and a two-step etch-and-rinse adhesive ('XP Bond', Dentsply). Both adhesives were also combined with a conventional composite ('Z100', 3M ESPE). Half of the restored cavities were exposed to 20,000 thermo-cycles. 3-way ANOVA revealed a significant effect for the factors 'adhesive' and 'composite' (both p<0.0001), but not for 'thermo-cycling' (p=0.994). Significantly higher bond strengths were recorded for the low-shrinking composite than for the control composite, using either of the adhesives. The low-shrinking composite in combination with the three-step etch-and-rinse adhesive performed best in the high C-factor Class-I cavity. The two-step etch-and-rinse adhesive suffered strongly from polymerization-shrinkage stress, which could be partially restored by using the low-shrinking composite.
Wireless broadband technologies for regional and rural Australia (2008)

The deployment of wireless broadband networks to deliver high-speed broadband services to regional and rural Australia is increasingly being examined as a viable alternative to the deployment of wired technology. Whilst last-mile connectivity (i.e. the connection which links the enduser to the network backbone) can be very expensive for carriage service providers deploying wired technology, the deployment of wireless technologies, typically characterised by lower capital and operational costs, can provide a more effective solution to the connectivity problems presently experienced by these remote demographics...
Antiviral Drug Screen Identifies DNA-Damage Response Inhibitor as Potent Blocker of SARS-CoV-2 Replication. Garcia et al (2021)

Supplemental Items.
Imaging using a supercontinuum laser to assess tumors in patients with breast carcinoma (2016)

The supercontinuum laser light source has many advantages over other light sources, including broad spectral range. Transmission images of paired normal and malignant breast tissue samples from two patients were obtained using a Leukos supercontinuum (SC) laser light source with wavelengths in the second and third NIR optical windows and an IR- CCD InGaAs camera detector (Goodrich Sensors Inc. high response camera SU320KTSW-1.7RT with spectral response between 900 nm and 1,700 nm). Optical attenuation measurements at the four NIR optical windows were obtained from the samples.
Stereoselective [2 + 2] photodimerization: a viable strategy for the synthesis of enantiopure cyclobutane derivatives (2023)

The [2 + 2] photodimerization of cinnamic acid derivatives to afford enantiopure cyclobutanes has been investigated. The use of a chiral auxiliary represents a convenient and straightforward method to exert enantiocontrol on the reaction. By exploiting Evans oxazolidinones, the stereoselective light-driven cyclisation affords a functionalised cyclobutane ring with up to 99% enantiocontrol after removing the chiral auxiliary. In-flow experiments allowed us to improve further the efficiency of the methodology, leading to high conversion and excellent enantioselectivity.
Rational Choice in Experimental Markets (1986)

The theory of rational behavior has several different uses.(i) It is used at the most fundamental level of experimental methodology to induce preferences used as parameters in models.(ii) It appears repeatedly in experimentally successful mathematical models of complex phenomena such as speculation, bidding and signaling.(iii) It is used as a tool to generate ex-post models of results that are otherwise inexplicable.(iv) It has been used as a tool to succesfully design new institutions to solve specific problems.When tested directly the theory can be rejected.It is retained because neither an alternative theory nor an alternative general principle accomplishes so much.
High-speed operation of 1.5μm GaInAsP/InP optoelectronic integrated laser drivers (1988)

A 1.5μm-wavelength high-speed self-aligned constricted-mesa laser diode and an InP MESFET have been integrated monolithically without deterioration in the performance of either device, by using a gate projection process. A broad 3dB bandwidth of 6.6GHz was demonstrated for the first time.
Free form Optics Applications in Photovoltaic Concentration (2012)

Freeform surfaces are the key of the state-of-the-art nonimaging optics to solve the challenges in concentration photovoltaics. Different families (FK, XR, FRXI) will be presented, based on the SMS 3D design method and Köhler homogenization.
Evaluation of the Effect of Phytol on the Formation of PAHs in Cigarette Smoke (2010)

Abstract Phytol or (2E,7R,11R)-3,7,11,15-tetramethyl-2-hexadecen- 1-ol (MW = 296.53 a.u.), is naturally present in tobacco at levels around 100-150 µg/g dry leaf, where it is bound in the form of an ester to a porphyrine type group (known as chlorin) with several substituents and chelated to Mg 2+ ion, to form chlorophyll. This study evaluated the formation of PAHs when several levels of phytol up to ten times higher than typical phytol level were added on 3R4F cigarettes. The cigarettes were smoked under two different smoking conditions. One regimen (indicated as 35/60) used 35 mL puff volume, 2 s puff duration, each puff taken every 60 s, and in the other used 60 mL puff volume, 2 s puff duration, each puff taken every 30 s (indicated as 60/30). The increase in the PAHs level upon phytol addition was not significant. A statistical evaluation of the dependence of total PAHs and the added level of phytol showed that the hypothesis of a zero slope for the dependence line phytol/total PAHs cannot be rejected (with a p = 0.101 for 35/60 smoking and p = 0.626 for 60/30 smoking). Still, for 35/60 smoking conditions, an increase of about 14% in total levels of PAHs was noticed when the added phytol level was 1.5 mg phytol per cigarette. However, this PAHs increased level was not necessarily determined by the phytol addition, and can be caused by random procedural/analytical errors (as indicated by the statistical analysis) or by the modification of cigarettes during phytol addition. Also, the observed level is much lower than the expected 100% increase in the PAHs level, based on literature prediction. Intensive smoking did not show an increase in PAHs level at all. Flash pyrolysis of free phytol and of chlorophyll a provided results that indicated that phytol bound in chlorophyll is not likely to generate different PAHs level compared to free phytol. Thus, phytol has been shown not to be a significant contributor/ precursor to the PAHs formation in cigarette smoke.
Technologies for Next Generation Silicon Photonics (2016)

We have demonstrated technologies for ultra high bandwidth silicon photonics. These include multi-mode communications multiplexing enabling bandwidth scaling and back-end integration with new materials such as graphene for ultra high speed devices.
Current status of targeted microbubbles in diagnostic molecular imaging of pancreatic cancer (2020)

Pancreatic ductal adenocarcinoma (PDAC) is often associated with a poor prognosis due to silent onset, resistance to therapies, and rapid spreading. Most patients are ineligible for curable surgery as they present with advanced disease at the time of diagnosis. Present diagnostic methods relying on anatomical changes have various limitations including difficulty to discriminate between benign and malignant conditions, invasiveness, the ambiguity of imaging results, or the inability to detect molecular biomarkers of PDAC initiation and progression. Therefore, new imaging technologies with high sensitivity and specificity are critically needed for accurately detecting PDAC and noninvasively characterizing molecular features driving its pathogenesis. Contrast enhanced targeted ultrasound (CETUS) is an upcoming molecular imaging modality that specifically addresses these issues. Unlike anatomical imaging modalities such as CT and MRI, molecular imaging using CETUS is promising for early and accurate detection of PDAC. The use of molecularly targeted microbubbles that bind to neovascular targets can enhance the ultrasound signal specifically from malignant PDAC tissues. This review discusses the current state of diagnostic imaging modalities for pancreatic cancer and places a special focus on ultrasound targeted-microbubble technology together with its clinical translatability for PDAC detection.
Identification of Dermatophyte and Non-Dermatophyte Agents in Onychomycosis by PCR and DNA Sequencing—A Retrospective Comparison of Diagnostic Tools (2022)

Rapid and reliable fungal identification is crucial to delineate infectious diseases, and to establish appropriate treatment for onychomycosis. Compared to conventional diagnostic methods, molecular techniques are faster and feature higher accuracy in fungal identification. However, in current clinical practice, molecular mycology is not widely available, and its practical applicability is still under discussion. This study summarizes the results of 16,094 consecutive nail specimens with clinical suspicion of onychomycosis. We performed PCR/sequencing on all primary nail specimens for which conventional mycological diagnostics remained inconclusive. In specimens with a positive direct microscopy but negative or contaminated culture, molecular mycology proved superior and specified a fungal agent in 65% (587/898). In 75% (443/587), the identified pathogen was a dermatophyte. Positive cultures for dermatophytes, yeasts and non-dermatophyte molds (NDMs) were concordant with primary-specimen-DNA PCR/sequencing in 83% (10/12), 34% (22/65) and 45% (76/169), respectively. Among NDMs, agreement was high for <i>Fusarium</i> spp. (32/40; 80%), but low for <i>Penicillium</i> spp. (5/25; 20%) and <i>Alternaria</i> spp. (1/20; 5%). This study underlines the improvement in diagnostic yield by fungal primary-specimen-DNA PCR/sequencing in the event of a negative or contaminated culture, as well as its significance for the diagnosis of dermatophyte and non-dermatophyte onychomycosis. Molecular mycology methods like PCR and DNA sequencing should complement conventional diagnostics in cases of equivocal findings, suspected NDM onychomycosis or treatment-resistant nail pathologies.
Integrated optic waveguides in gallium lanthanum sulfide glass for mid-IR applications (2017)

Chalcogenide integrated optic (IO) waveguides operating in the mid-wave infrared (MWIR) are of interest for a variety of applications. They are potentially useful in compact MWIR laser sources for applications such as gas sensing and infrared countermeasures. Most work on chalcogenide integrated optics to date, however, has focused on arsenic sulfide, As<sub>2</sub>S<sub>3</sub>, or glasses with similar compositions. These glasses are known to suffer from a host of photo-induced effects including photo-darkening, photo-induced crystallization, and low optical damage thresholds. Furthermore, they can typically accept only low concentration of rare earth dopants without clustering or crystallization. Gallium lanthanum sulfide (GLS) is an alternative chalcogenide glass with great potential for use in IO devices operating in the MWIR. Like As<sub>2</sub>S<sub>3</sub>, GLS exhibits a large transparency window in the MWIR and high optical nonlinearity, but it does not suffer from the same type of photo-induced effects. High rare earth dopant concentrations without clustering are possible in GLS because rare earth ions substitute for lanthanum ions in the glass matrix. IO waveguides have previously been fabricated in GLS by several methods. Formerly, it was hypothesized that patterning GLS via reactive ion etching (RIE) was impossible do the presence of lanthanum and rare earth dopant ions, but we present results for GLS waveguides fabricated via RIE. In addition, we demonstrate 2.7 &mu;m emission from Er<sup>3+</sup>-doped GLS waveguides resulting from erbium’s <sup>4</sup>I<sub>11/2</sub>&rarr;<sup>4</sup>I<sub>13/2</sub> transition.
Effects of short-term chemical ablation of glucagon signalling by peptide-based glucagon receptor antagonists on insulin secretion and glucose homeostasis in mice (2013)

Glucagon is a hormone with important effects on blood glucose regulation. This study has utilized the stable glucagon receptor antagonists, desHis¹Pro⁴Glu⁹-glucagon and desHis¹Pro⁴Glu⁹(Lys¹²PAL)-glucagon, to evaluate the effects of sustained inhibition of glucagon receptor signalling in normal mice. Twice-daily injection of either analogue for 10 days had no effect on food intake, body weight and non-fasting plasma glucose concentrations. However, insulin levels were significantly raised (p<0.05 to p<0.01) from day 3 onwards in desHis¹Pro⁴Glu⁹-glucagon mice. After 10 days, glucose tolerance was improved (p<0.05) in desHis¹Pro⁴Glu⁹-glucagon treated mice. Glucose-mediated insulin secretion and circulating cholesterol levels were significantly (p<0.05 to p<0.01) decreased in both treatment groups. Importantly, the effects of glucagon to increase blood glucose and insulin concentrations were still annulled on day 10. Insulin sensitivity was almost identical in all groups of mice at the end of the study. In addition, no changes in pancreatic insulin and glucagon content or islet morphology were observed in either treatment group. Finally, acute injection of desHis¹Pro⁴Glu⁹-glucagon followed by a 24-h fast in treatment naïve mice was not associated with any hypoglycaemic episodes. These data indicate that peptide-based glucagon receptor antagonists represent safe and effective treatment options for type 2 diabetes.
Progress in Non-Cd Quantum Dot Development for Lighting Applications (2012)

During the past few years there has been a significant progress in adapting the properties of non-Cd quantum dots (QDs) for lighting applications. It includes synthesis of novel materials, improvement of quantum efficiency and thermal stability, and most importantly, manufacturability on a scale large enough to meet the needs of the lighting industry. In this paper, we review the characteristics of three most mature non-Cd QD material systems, InP, CuInS2 and doped ZnS/ZnSe, from the perspective of lighting applications. Of these three systems, the InP-based QDs with core/shell structure are now available with quantum efficiency (QE) comparable to the best performing CdSe QDs, and in quantities large enough to meet the lighting needs. The CuInS2 QDs have also emerged as another non-toxic alternative to CdSe QDs but they need significant development to be comparable to InP and CdSe QDs.
Insulin Action and Insulin Resistance in Noninsulin-Dependent Diabetes Mellitus (1997)

Noninsulin-dependent diabetes mellitus (NIDDM) is a complex metabolic disorder of heterogenous etiology (1–5). There is clearly a strong hereditary component to the disease, but the exact genetic abnormalities are likely to differ among different population groups (6–8). In addition, NIDDM is likely to be multigenic, in that more than one discrete gene defect may exist within a given patient to lead esventually to the NIDDM phenotype. Thus, from a genetic point of view, NIDDM is heterogenous and polygenic, making identification of diabetes genes particularly difficult. Numerous biochemical abnormalities have been identified in NIDDM, and the relative contribution of different physiologic or cellular defects differs among different patient groups (6,7). Regardless of the exact pathophysiologic sequence in a particular patient, once full-blown fasting hyperglycemia develops, a characteristic set of metabolic derangements can be identified in the great majority of patients with NIDDM. The major metabolic abnormalities in NIDDM are summarized in Fig. 1, which depicts the final common pathophysiologic state in a typical NIDDM patient (1). It comprises abnormalities in the pancreatic islets, the liver, and the peripheral insulin target tissues.