gebhart/patrepeval huggingface dataset:
Association of a Homozygous Nonsense Mutation in the ABCA4 (ABCR) Gene with Cone-Rod Dystrophy Phenotype in an Italian Family (2004)

Genetic variation in the ABCA4 (ABCR) gene has been associated with several distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), retinitis pigmentosa (RP) and age-related macular degeneration. The current model of genotype/phenotype association suggests that patients harboring deleterious mutations in both ABCR alleles would develop RP-like retinal pathology. Here we describe ABCA4-associated phenotypes, including a proband with a homozygous nonsense mutation in a family from Southern Italy. The proband had been originally diagnosed with STGD. Ophthalmologic examination included kinetic perimetry, electrophysiological studies and fluorescein angiography. DNA of the affected individual and family members was analyzed for variants in all 50 exons of the ABCA4 gene by screening on the ABCR400 microarray. A homozygous nonsense mutation 2971G>T (G991X) was detected in a patient initially diagnosed with STGD based on funduscopic evidence, including bull's eye depigmentation of the fovea and flecks at the posterior pole extending to the mid-peripheral retina. Since this novel nucleotide substitution results in a truncated, nonfunctional, ABCA4 protein, the patient was examined in-depth for the severity of the disease phenotype. Indeed, subsequent electrophysiological studies determined severely reduced cone amplitude as compared to the rod amplitude, suggesting the diagnosis of CRD. ABCR400 microarray is an efficient tool for determining causal genetic variation, including new mutations. A homozygous protein-truncating mutation in ABCA4 can cause a phenotype ranging from STGD to CRD as diagnosed at an early stage of the disease. Only a combination of comprehensive genotype/phenotype correlation studies will determine the proper diagnosis and prognosis of ABCA4-associated pathology.
Enantioselective Synthesis of <i>anti</i>-1,2-Diamines by Cu-Catalyzed Reductive Couplings of Azadienes with Aldimines and Ketimines (2018)

Here we report highly efficient and chemoselective azadiene-imine reductive couplings catalyzed by (Ph-BPE)Cu-H that afford anti-1,2-diamines. In all cases, reactions take place with either aldimine or ketimine electrophiles to deliver a single diastereomer of product in >95:5 er. The products' diamines are easily differentiable, facilitating downstream synthesis.
Factor Analysis of the Einstein Neonatal Neurobehavioral Assessment Scale in Infants with Congenital Heart Disease and Healthy Controls (2022)

<b>Background:</b> Administration of the Einstein Neonatal Neurobehavioral Assessment Scale (ENNAS) can be time-consuming, and items can be highly correlated. We aimed to determine: (1) its factor analytic structure; (2) the validity of the factor structure; and (3) the associations of physiologic measures with factor scores. <b>Methods:</b> A factor analysis reduced 21 ENNAS items into 5 factors in 57 congenital heart disease (CHD) and 35 healthy infants. Multiple linear regressions examined the association of factor scores with group, gestational age, and physiologic variables. <b>Results:</b> 5-factor solution: 1 (Orienting Reflex), 2 (Extensor Axial Tone), 3 (Primitive Reflexes), 4 (Flexor Tone), 5 (Reflexive Tone Around Extremity Joints). Moderate to strong evidence supported: face, discriminant, and construct validity of these factors, with Factor 2 having the strongest. <b>Conclusions:</b> Components of Factor 2 may provide similar information about neonatal development, thus reducing the time for and burden of administration for researchers and clinicians.
Gut Organoid as a New Platform to Study Alginate and Chitosan Mediated PLGA Nanoparticles for Drug Delivery (2021)

Intestinal organoids can be used as an ex vivo epithelial model to study different drug delivery effects on epithelial cells' luminal surface. In this study, the impact of surface charge on the delivery of 5-ASA loaded PLGA nanoparticles into the lumen of organoids was investigated. Alginate and chitosan were used to coat the nanoparticles and provide negative and positive charges on the particles, respectively. The organoid growth and viability were not affected by the presence of either alginate- or chitosan-coated nanoparticles. It was shown that nanoparticles could be transported from the serosal side of the organoids to the lumen as the dye gradually accumulated in the lumen by day 2-3 after adding the nanoparticles to the Matrigel. By day 5, the dye was eliminated from the lumen of the organoids. It was concluded that the positively charged nanoparticles were more readily transported across the epithelium into the lumen. It may be attributed to the affinity of epithelial cells to the positive charge. Thus, the organoid can be utilized as an appropriate model to mimic the functions of the intestinal epithelium and can be used as a model to evaluate the benefits of nanoparticle-based drug delivery.
Computational Models in Electroencephalography (2021)

Abstract Computational models lie at the intersection of basic neuroscience and healthcare applications because they allow researchers to test hypotheses in silico and predict the outcome of experiments and interactions that are very hard to test in reality. Yet, what is meant by “computational model” is understood in many different ways by researchers in different fields of neuroscience and psychology, hindering communication and collaboration. In this review, we point out the state of the art of computational modeling in Electroencephalography (EEG) and outline how these models can be used to integrate findings from electrophysiology, network-level models, and behavior. On the one hand, computational models serve to investigate the mechanisms that generate brain activity, for example measured with EEG, such as the transient emergence of oscillations at different frequency bands and/or with different spatial topographies. On the other hand, computational models serve to design experiments and test hypotheses in silico. The final purpose of computational models of EEG is to obtain a comprehensive understanding of the mechanisms that underlie the EEG signal. This is crucial for an accurate interpretation of EEG measurements that may ultimately serve in the development of novel clinical applications.
Endodontic Approach and Periodontal Regenerative Therapy for a Mandibular Right Central Incisor Affected by a Perforation and Cemental Tear (2021)

A cemental tear involves complete or incomplete separation of the cementum on the root surface along the cementodentinal junction. Because a cemental tear can lead to periodontal breakdown and mimic endodontic and periodontal lesions, diagnosing clinical cases can be difficult and requires special examinations. A 72-year-old woman presented with a localized periodontal defect on the labial and interproximal surfaces of the mandibular right central incisor. Performing CBCT scans and a biopsy during periodontal surgery allowed definitive diagnosis of a cemental tear and perforation of the site. First, the perforation was repaired with endodontic therapy. Periodontal regenerative therapy using recombinant human fibroblast growth factor-2 (rhFGF-2) was then performed after removing granulomatous tissue and cementum fragments. Examination of the biopsy specimen showed bacterial colonies. This case showed successful clinical and radiographic outcomes at the 18-month follow-up.
Colloidal photonic crystal microchannel array with periodically modulated thickness (2002)

Here we report on the optical properties of a micrometer scale array of periodically modulated thickness colloidal crystals. A combination of soft-lithography, micromolding, and microfluidics techniques is employed to form rectangular microchannels that can impose a periodic modulation of the thickness of colloidal crystals grown within them. Correspondingly, a periodic fluctuation of the photonic band structure occurs at distances of the order of a few microns. Experimental evidence of this effect is obtained by optical microspectroscopy. Results are analyzed in terms of finite crystal size theoretical calculations.
Origins of u.s. Hispanics: Implications for Diabetes (1991)

The purpose of this article was to characterize the origins of the United States Hispanic population and discuss the implications of these origins in the context of diabetes risk. Particular attention was focused on the genetic origins of the three major U.S. Hispanic groups, i.e., Mexican Americans, Puerto Ricans, and Cubans. The U.S. Census figures provided basic demographic information. Genetic marker data for ancestral populations were taken from a review of the literature and compendia. Genetic marker data for the Puerto Rican and Cuban populations were extracted from the literature. Genetic markers determined on approximately 1000 randomly selected Mexican Americans from Starr County, Texas, were taken as representative of the Mexican-American population. The Hispanic population is the second largest and fastest growing minority in the U.S. Estimates of the Hispanic population in 1988 indicated some 19.4 million residents, of whom 62% were classified as Mexican, 13% as Puerto Rican, and the remaining 25% as Cubans and others. Various lines of evidence can be used to characterize the Hispanic population and its origins. These include ethnohistory, self-assessment of ancestry, surname distributions, speech and cultural characteristics, quantitative traits, and genetic structure. Genetic data were used to estimate the contribution of putative ancestral populations to the contemporary gene pool. For Mexican Americans, 31% of the contemporary gene pool is estimated to be Native American derived, whereas 61 and 8% are Spanish and African derived, respectively. In Puerto Rico, the percentage of contributions of Spanish, Native American, and African admixture to the population are 45, 18, and 37%, respectively. For Cuba, the parallel estimates are 62, 18, and 20%. The high frequency of Native American-derived genes in the contemporary Hispanic population predict a higher frequency of non-insulin-dependent diabetes mellitus (NIDDM) under the assumption that genes are important in NIDDM etiology. Our results are consistent with the finding of the significant role of genes in determining risk.
Positional cloning and characterization reveal the molecular basis for soybean maturity locus <i>E1</i> that regulates photoperiodic flowering (2012)

The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene (E1). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity.
Molecular changes in the expression of human colonic nutrient transporters during the transition from normality to malignancy (2002)

Healthy colonocytes derive 60-70% of their energy supply from short-chain fatty acids, particularly butyrate. Butyrate has profound effects on differentiation, proliferation and apoptosis of colonic epithelial cells by regulating expression of various genes associated with these processes. We have previously shown that butyrate is transported across the luminal membrane of the colonic epithelium via a monocarboxylate transporter, MCT1. In this paper, using immunohistochemistry and in situ hybridisation histochemistry, we have determined the profile of MCT1 protein and mRNA expression along the crypt to surface axis of healthy human colonic tissue. There is a gradient of MCT1 protein expression in the apical membrane of the cells along the crypt-surface axis rising to a peak in the surface epithelial cells. MCT1 mRNA is expressed along the crypt-surface axis and is most abundant in cells lining the crypt. Analysis of healthy colonic tissues and carcinomas using immunohistochemistry and Western blotting revealed a significant decline in the expression of MCT1 protein during transition from normality to malignancy. This was reflected in a corresponding reduction in MCT1 mRNA expression, as measured by Northern analysis. Carcinoma samples displaying reduced levels of MCT1 were found to express the high affinity glucose transporter, GLUT1, suggesting that there is a switch from butyrate to glucose as an energy source in colonic epithelia during transition to malignancy. The expression levels of MCT1 in association with GLUT1 could potentially be used as determinants of the malignant state of colonic tissue.
Photoluminescent Properties of AlAs/Al<sub>x</sub>Ga<sub>1-x</sub>As (x=0.5) Disordered Superlattices (1990)

The AlAs/Al 0.5 Ga 0.5 As disordered superlattice is fabricated, and its photoluminescent properties are compared with those of Al 0.76 Ga 0.24 As bulk alloy and the (AlAs) 2 (Al 0.5 Ga 0.5 As) 2 ordered superlattice. Their macroscopic AlAs compositions are almost the same, 0.75, but their microscopic structures are different. Among them, the AlAs/Al 0.5 Ga 0.5 As disordered superlattice exhibits the highest photoluminescent intensity at 4.2 K. A red shift is observed in a photoluminescent peak.
Three-Dimensional Profiling of Refractive Index Distribution inside Transparent Materials by Use of Nonresonant Four-Wave Mixing Microscopy (2008)

We propose that four-wave mixing (FWM) microscopy can be applied to three-dimensional mapping of refractive index (RI) structure inside transparent samples. We derive an analytical relationship between the RI and the intensity of the FWM signal that is due to nonresonant optical nonlinearity. By using the relationship, the RI profile can be directly and quantitatively obtained from the intensity distribution of the FWM signal. We experimentally demonstrate the RI profiling of a phase grating fabricated in a non-alkali glass.
JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES (2011)

The new program package JAGUC is a tool that bridges the gap between computational and biological sciences. It enables biologists to process large sequence data sets in order to infer biological meaning from hundreds of thousands of raw sequence data. JAGUC offers advantages over available tools which are further discussed in this manuscript.
No advantage of chemoradiotherapy over chemotherapy alone in elderly patients with localized low risk aggressive lymphoma: results of the LNH93-4 GELA study. (2005)

peer reviewed
Experiences building a communication‐oriented JavaOS (2000)

Mobile code makes it easier to maintain, debug, update, and customize a system. Active networks are one of the more interesting applications of mobile code: code is injected into the nodes of a network to customize the network's functionality, such as routing, and to add new features, such as special-purpose congestion control and filtering algorithms. The challenge is to develop a communication-oriented platform for such systems. We refer to mobile code targeted at low-level, communication-oriented systems like active networks as liquid software, the key distinction being that liquid software is focused on the efficient transfer of data, not high-performance computation. To this end, we have designed and implemented Joust, which consists of a complete re-implementation of the Java virtual machine (including both the runtime system and a just-in-time compiler), running on the Scout operating system (a configurable, communication-oriented OS). The result is a configurable, high-performance platform for running liquid software. We present the results of implementing two different applications of liquid software on Joust, including a prototype architecture for active networks. Copyright © 2000 John Wiley & Sons, Ltd.
Experience with the Modified Putterman Procedure (1988)

Results using our modification of the Putterman procedure are reported in 43 eyelids. The procedure is very effective in cases of minimal to moderate eyelid ptosis (3 mm or less) and in the presence of normal levator function. The patients, following a thorough clinical evaluation, are tested using 2.5% phenylephrine eyedrop solution, which acts as an extremely useful prognostic indicator. Depending on the degree of ptosis and the response to phenylephrine, 6 to 9 mm of combined Müller's muscle and conjunctiva is resected using a specially designed clamp under local or attended local anesthesia (no tarsal plate is resected). The incision is repaired using a running 6-0 Prolene horizontal mattress technique, and the ends are brought up through the skin and tied over the tarsal plate. In the treatment of 43 eyelids, with the exception of one slight overcorrection, there were no complications encountered with this simple procedure. Excellent results can be expected in properly selected patients, and recovery time is minimal. Our success in the last 4 years with this modified procedure allows us to strongly recommend it for the correction of mild to moderate ptosis when there is an acceptable response to phenylephrine.
A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings (2013)

Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.
Decomposition of SF<sub>6</sub>in an RF Plasma Environment (2002)

Sulfur hexafluoride (SFd)-contained gas is a common pollutant emitted during the etching process used in the semiconductor industry. This study demonstrated the application of radio-frequency (RF) plasma in the decomposition of SF6. The decomposition fraction of SF6 [etaSF6 (C(in)-C(out))/C(in) x 100%] and the mole fraction profile of the products were investigated as functions of input power and feed O2/SF6 ratio in an SiO2 reactor. The species detected in both SF6/Ar and SF6/O2/ Ar RF plasmas were SiF4, SO2, Fe2, SO2F2, SOF2, SOF4, S2F10, S2OF10, S2O2F10, and SF4. The results revealed that at 40 W, etaSF6 exceeded 99%, and the reaction products were almost all converted into stable compounds such as SiF4, SO2, and F2 with or without the addition of oxygen. Sulfur oxyfluorides such as SO2F2, SOF2, SOF4, S2OF10, and S2O2F10 were produced only below 40 W. The results of this work can be used to design a plasma/chemical system for online use in a series of a manufacturing process to treat SF6-containing exhaust gases.
Deposition of TiO <sub>2</sub> photocatalyst on polyethylene terephthalate or polyimide polymer films by reactive sputtering for flexible photocatalytic sheets (2019)

Abstract Polycrystalline anatase TiO 2 films were deposited by rf reactive magnetron sputtering on polyethylene terephthalate (PET) or polyimide (PI) films with different buffer layers, such as SiO 2 or Zn 2 SnO x (ZTO), between the TiO 2 film and the substrate. Such TiO 2 /(SiO 2 or ZTO)/(PET or PI) sheets with high transmittance in the visible region of light showed high photo-decomposition ability towards CH 3 CHO under UV irradiation by a black light centered at 352 nm. When SiO 2 was used as the buffer layer, a “nano-pore layer” was observed clearly over the full area of the polymer substrate close to the buffer layer after UV irradiation, whereas such degradation was suppressed drastically when ZTO was used as the buffer layer. Such photocatalytic sheets also demonstrated photo-induced hydrophilicity upon UV irradiation, with the contact angle to pure water becoming around 5° under UV irradiation. After additional deposition of SiO 2 on the outermost surface of the TiO 2 films by reactive sputtering under rather a high total gas pressure of 3.0 Pa, the photo-induced hydrophilicity was maintained for more than 98 days in the dark. Such three-layered SiO 2 /TiO 2 /ZTO films on PET or PI substrates could be promising flexible photocatalytic sheets that retain photo-induced hydrophilicity.
High-capacity Li2S–graphene oxide composite cathodes with stable cycling performance (2013)

With its high theoretical capacity of 1166 mA h g−1, Li2S is a promising prelithiated cathode material for applications such as vehicle electrification and grid energy storage. Herein, we demonstrate facile synthesis of Li2S–graphene oxide composites for use as high-capacity and stable-cycling Li2S cathodes. The wrapping of graphene oxide onto the surface of Li2S through favorable lithium–oxygen interactions helps to minimize the dissolution of intermediate polysulfides into the electrolyte during cycling, which is a major reason for rapid capacity decay. Using the Li2S–graphene oxide composites as a cathode material, we demonstrate a high discharge capacity of 782 mA h g−1 of Li2S (∼1122 mA h g−1 of S) with stable cycling performance over 150 charge–discharge cycles.