gebhart/patrepeval huggingface dataset:
Assessment of whole brain white matter integrity in youths and young adults with a family history of substance‐use disorders (2014)

Individuals with a family history of substance use disorders (FH+) are at a greater risk of developing substance use disorders than their peers with no such family histories (FH-) and this vulnerability is proportional to the number of affected relatives (FH density). The risk for developing substance use disorders peaks during adolescence to early adulthood in the general population, and that is thought to be related to delayed maturation of frontocortical and frontostriatal functional circuits. We hypothesized that FH+ youth and young adults have impaired myelination of frontocortical and frontostriatal white matter tracts. We examined fractional anisotropy (FA) data in 80 FH+ and 34 FH- youths (12.9 ± 1.0 years) and in 25 FH+ and 30 FH- young adults (24.3 ± 3.4 years). FH+ youths had lower FA values in both frontocortical and frontostriatal tracts as well as parietocortical tracts including the anterior, superior and posterior corona radiata and the superior frontal-occipital fasciculus. Moreover, FA values in these tracts were negatively correlated with FH density. FH+ adults had lower FA values in two frontocortical tracts: the genu of the corpus callosum and anterior corona radiata and also significant negative correlations between FA and FH density in these same tracts. In both groups, lower FA values corresponded to higher radial diffusivity suggesting reduced axonal myelination. We interpreted our findings as evidence for impaired myelination of frontal white matter that was proportional to FH density. Our data suggest that deficits may partially resolve with age, paralleling an age-related decline in risk for developing substance use disorders.
ChemInform Abstract: Small‐Molecule Quadruplex‐Targeted Drug Discovery (2014)

Abstract Review: 112 refs.
Numerical Simulation of the Vibro-Acoustic Behavior of a Vehicle under Operating Conditions (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Currently the numerical simulations of the vibro-acoustic behavior of vehicles are built considering only major structures, such as its basic structure (body in white), doors, dashboard etc. To take into account the contribution of other components (such as trims, seats, sound insulation etc.) to the overall response of the model, the average characteristics of these materials are inserted globally in this model. However, for more correlated models is necessary to consider local characteristics of these components.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This work presents the numerical procedure for simulating the effect of the structural damping of viscoelastic coatings and the acoustic absorption of the trims such that its effects can be considered in the model of the full vehicle.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The operating forces applied to the model were estimated from the laboratory and road tests using the SPC/TPA technique. Furthermore, the model enables the subjective evaluation of the noise from the auralization/synthesis based on numerical frequency response functions and road test data.&lt;/div&gt;&lt;/div&gt;
Identification of a Classical Mutant in the Industrial HostAspergillus nigerby Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites (2015)

The asexual filamentous fungus Aspergillus niger is an important industrial cell factory for citric acid production. In this study, we genetically characterized a UV-generated A. niger mutant that was originally isolated as a nonacidifying mutant, which is a desirable trait for industrial enzyme production. Physiological analysis showed that this mutant did not secrete large amounts of citric acid and oxalic acid, thus explaining the nonacidifying phenotype. As traditional complementation approaches to characterize the mutant genotype were unsuccessful, we used bulk segregant analysis in combination with high-throughput genome sequencing to identify the mutation responsible for the nonacidifying phenotype. Since A. niger has no sexual cycle, parasexual genetics was used to generate haploid segregants derived from diploids by loss of whole chromosomes. We found that the nonacidifying phenotype was caused by a point mutation in the laeA gene. LaeA encodes a putative methyltransferase-domain protein, which we show here to be required for citric acid production in an A. niger lab strain (N402) and in other citric acid production strains. The unexpected link between LaeA and citric acid production could provide new insights into the transcriptional control mechanisms related to citric acid production in A. niger. Interestingly, the secondary metabolite profile of a ΔlaeA strain differed from the wild-type strain, showing both decreased and increased metabolite levels, indicating that LaeA is also involved in regulating the production of secondary metabolites. Finally, we show that our systems genetics approach is a powerful tool to identify trait mutations.
Four Novel Mutations, Including the First Gross Deletion in TCF1, identified in HNF4a, GCK and TCF1 in Patients with MODY in Israel (2007)

Maturity onset diabetes of the young (MODY) is characterized by a primary defect in insulin secretion with non-ketotic hyperglycemia, monogenic autosomal dominant mode of inheritance, age at onset less than 25 years, and lack of autoantibodies. The aim of this study was to characterize the genetic basis of MODY in different ethnic groups in the Israeli population. Fifty-nine unrelated Israeli patients with MODY were assessed for mutations in the three common MODY genes: hepatocyte nuclear factor (HNF)-4alpha, glucokinase (GCK), and transcription factor 1 (TCF1). Overall, 11 mutations in 12 unrelated families were found (20.3% of patients), for a relative frequency of 1.7% for MODY1, 8.5% for MODY2, and 10.1% for MODY3. Four mutations were novel, including the first gross deletion ever described in the TCF1 gene. The low overall mutation frequency found here may suggest the involvement of other, yet unidentified, genes in the etiology of MODY in Israel.
Graphene-based flexible and wearable electronics (2018)

Graphene with an exceptional combination of electronic, optical and outstanding mechanical features has been proved to lead a completely different kind of 2-D electronics. The most exciting feature of graphene is its ultra-thin thickness, that can be conformally contacted to any kind of rough surface without losing much of its transparency and conductivity. Graphene has been explored demonstrating various prototype flexible electronic applications, however, its potentiality has been proven wherever transparent conductive electrodes (TCEs) are needed in a flexible, stretchable format. Graphene-based TCEs in flexible electronic applications showed greatly superior performance over their conventionally available competitor indium tin oxide (ITO). Moreover, enormous applications have been emerging, especially in wearable devices that can be potentially used in our daily life as well as in biomedical areas. However, the production of high-quality, defect-free large area graphene is still a challenge and the main hurdle in the commercialization of flexible and wearable products. The objective of the present review paper is to summarize the progress made so far in graphene-based flexible and wearable applications. The current developments including challenges and future perspectives are also highlighted.
Hydrogen-implanted SeGe alloys as optical recording media (1988)

Thin films of Se(x)Ge(1-x) have been used as optical recording media for x values of 0.33, 0.5, and 0.67. An investigation of the effect of hydrogen implantation into thin films of this material on optical recording parameters has been performed in the range from 10(14) to 10(16) ions/cm(2). Parameters such as writing energy and contrast ratio were mainly studied. Pulsed holography was also achieved.
Transcriptional Glucose Signaling through The Glucose Response Element Is Mediated by the Pentose Phosphate Pathway (1996)

Glucose catabolism induces the expression of the L-type pyruvate kinase (L-PK) gene through the glucose response element (GIRE). The metabolic pathway used by glucose after its phosphorylation to glucose 6-phosphate by glucokinase to induce L-PK gene expression in hepatocytes remains unknown. The sugar alcohol xylitol is metabolized to xylulose 5-phosphate, an intermediate of the nonoxidative branch of the pentose phosphate pathway. In this study, we demonstrated that xylitol at low concentration (O.5 mM) induced the expression of the L-PK/CAT construct in glucose-responsive mhAT3F hepatoma cells at the same level as 20 mM glucose, while it did not affect intracellular concentration of glucose 6-phosphate significantly. The effect of xylitol on the induction of the L-PK gene expression was noncumulative with that of glucose since 20 mM glucose plus 5 mM xylitol induced the expression of the L-PK/CAT construct similarly to 20 mM glucose alone. In hepatocytes in primary culture, 5 mM xylitol induced accumulation of the L-PK mRNA even in the absence of insulin. Furthermore, the response to xylitol as well as glucose required the presence of a functional GIRE. It can be assumed from these results that glucose induces the expression of the L-PK gene through the nonoxidative branch of the pentose phosphate pathway. The effect of xylitol at low concentration suggests that the glucose signal to the transcriptional machinery is mediated by xylulose 5-phosphate.
Yeast Reveal a ‘Druggable’ Rsp5/Nedd4 Network That Ameliorates α-Synuclein Toxicity in Neurons (2013)

α-Synuclein (α-syn) is a small lipid-binding protein implicated in several neurodegenerative diseases, including Parkinson’s disease, whose pathobiology is conserved from yeast to man. There are no therapies targeting these underlying cellular pathologies, or indeed those of any major neurodegenerative disease. Using unbiased phenotypic screens as an alternative to target-based approaches, we discovered an N-aryl benzimidazole (NAB) that strongly and selectively protected diverse cell types from α-syn toxicity. Three chemical genetic screens in wild-type yeast cells established that NAB promoted endosomal transport events dependent on the E3 ubiquitin ligase Rsp5/Nedd4. These same steps were perturbed by α-syn itself. Thus, NAB identifies a druggable node in the biology of α-syn that can correct multiple aspects of its underlying pathology, including dysfunctional endosomal and endoplasmic reticulum–to-Golgi vesicle trafficking.
Structure-Based De Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations (2021)

Recently, molecular generation models based on deep learning have attracted significant attention in drug discovery. However, most existing molecular generation models have a serious limitation in the context of drug design wherein they do not sufficiently consider the effect of the three-dimensional (3D) structure of the target protein in the generation process. In this study, we developed a new deep learning-based molecular generator, SBMolGen, that integrates a recurrent neural network, a Monte Carlo tree search, and docking simulations. The results of an evaluation using four target proteins (two kinases and two G protein-coupled receptors) showed that the generated molecules had a better binding affinity score (docking score) than the known active compounds, and they possessed a broader chemical space distribution. SBMolGen not only generates novel binding active molecules but also presents 3D docking poses with target proteins, which will be useful in subsequent drug design.
Method and apparatus for measuring film spectral properties (2023)

Film spectral properties are measured by projecting chopped monochromatic light onto a luminescent film sample deposited on a substrate, and coupling through use of immersion oil the reflection of light therefrom to a light detector.
Comparison of Image Normalization Techniques for Rectal Cancer Segmentation in Multi-Center Data: Initial results (2023)

We evaluated the influence of normalization (setting mean and standard deviation, histogram matching and percentiles) on the segmentation of rectal cancer on multimodal images when operating on multicenter data as part of a Radiomics pipeline. We used two different networks for segmentation. When training and evaluating on all data or data from a single center, normalization did not play a significant role. In contrast, when training on one center and evaluating on all others, it did play a major role. Best results are obtained by normalization using percentiles. Fixing the mean and standard deviation did not work well.
Advanced Ultrashort Pulse Fiber Lasers (2011)

New developments in femtosecond fiber-lasers include ultrabroad coherent supercontinuum generation, power levels up to 80W, at 120fs and 150MHz of an Yb-fiber laser and sub-100fs Tm-fiber-systems. Those sources are CEO-phase stabilized for advanced frequency comb applications.
Diagnosis of Choroidal Disease With Deep Learning-Based Image Enhancement and Volumetric Quantification of Optical Coherence Tomography (2022)

This novel analysis can be applied retrospectively to existing OCT datasets, and it represents a significant advance toward the automated diagnosis of choroidal pathologies based on observations and quantifications of the vasculature.
Reduction of EGF receptor synthesis by antisense RNA vectors (1986)

An association has been observed between squamous cell carcinomas and elevated EGF receptor levels. The approach taken here to analyze this problem was to construct vectors which express antisense RNA for the EGF receptor. The plasmid vector used was derived from pSV2-neo, which is readily selectable. Three EGF receptor cDNA fragments, a 5'-, a middle and a 3'-region were tested for differences in efficiency as antisense RNA. The results suggest that the 5'-fragment was the most efficient.
Carbon nanotube-based hybrid hole-transporting material and selective contact for high efficiency perovskite solar cells (2015)

Hybrid hole-transporting material and selective contact for perovskite solar cells was manufactured by industrially viable materials and methods.
Efficient Low-Driving-Voltage Blue Phosphorescent Homojunction Organic Light-Emitting Devices (2011)

A blue phosphorescent p–i–n homojunction organic light-emitting device with a low driving voltage was demonstrated using 4,6-bis[3-(carbazol-9-yl)phenyl] pyrimidine (46DCzPPm) as the bipolar host material and iridium(III) bis[4,6-(difluorophenyl)pyridinato-N,C2'] picolinate as the blue triplet emitter. The device incorporated an n-doping electron-transport layer consisting of Cs2CO3-doped 46DCzPPm and a p-doping hole-transport layer consisting of MoO3-doped 46DCzPPm. A maximum external quantum efficiency of 10.2% and a power efficiency of 27.8 lm W-1 were obtained. At 100 cd m-2, the efficiencies were 9.1% and 21.5 lm W-1, and even at 1000 cd m-2, the efficiencies remained at 7.0% and 12.8 lm W-1, respectively, with an extremely low driving voltage of 3.9 V.
pH-Degradable Mannosylated Nanogels for Dendritic Cell Targeting (2016)

We report on the design of glycosylated nanogels via core-cross-linking of amphiphilic non-water-soluble block copolymers composed of an acetylated glycosylated block and a pentafluorophenyl (PFP) activated ester block prepared by reversible addition-fragmentation (RAFT) polymerization. Self-assembly, pH-sensitive core-cross-linking, and removal of remaining PFP esters and protecting groups are achieved in one pot and yield fully hydrated sub-100 nm nanogels. Using cell subsets that exhibit high and low expression of the mannose receptor (MR) under conditions that suppress active endocytosis, we show that mannosylated but not galactosylated nanogels can efficiently target the MR that is expressed on the cell surface of primary dendritic cells (DCs). These nanogels hold promise for immunological applications involving DCs and macrophage subsets.
Etching, Insertion, and Abstraction Reactions of Atomic Deuterium with Amorphous Silicon Hydride Films (1997)

We report structural and kinetic studies of the reactions of hydride species in Si thin films with atomic deuterium (Dat). Infrared (IR) spectroscopy is used to obtain Si−H bonding information, and direct recoiling methods are used to measure reaction rates. Two kinds of films are prepared by filament-assisted growth from Si2H6 and are characterized by IR spectroscopy. A film containing only monohydride hydrogen is grown at 200 °C, and a polymer containing tri-, di-, and monohydride is grown at −110 °C. Rates of H abstraction by Dat, and of Dat insertion into Si−Si bonds, are reported. The abstraction rate of H by Dat in both films is similar to the abstraction rate on H-terminated crystal Si surfaces. The insertion rate into Si−Si bonds in both films is about one-tenth the rate of abstraction. A qualitative study of the etching reaction of Dat with the polymeric film is reported, and a strong temperature dependence is observed.
A Distributed Algorithm for Adaptive Traffic Lights Control in Wireless Sensor Networks (2012)

In this paper, we address the problem of controlling traffic lights at an intersection with a wireless sensor network. We propose a wireless sensor network architecture that does not depend on a centralized coordinator and we separate logically this distributed network into 4 levels of hierarchy. On this architecture, we define and evaluate through simulation a phases selection algorithm that decides dynamically of the movements composing the next phase and of the duration of this phase. Simulation results show that this algorithm, if properly tuned, has the capacity to reduce average waiting time at an intersection, while avoiding starvation for multiple load levels.
Security of smart distribution grids: Data integrity attacks on integrated volt/VAR control and countermeasures (2014)

We examine the feasibility of an attack on the measurements that will be used by integrated volt-var control (VVC) in future smart power distribution systems. The analysis is performed under a variety of assumptions of adversary capability regarding knowledge of details of the VVC algorithm used, system topology, access to actual measurements, and ability to corrupt measurements. The adversary also faces an optimization problem, which is to maximize adverse impact while remaining stealthy. This is achieved by first identifying sets of measurements that can be jointly but stealthily corrupted. Then, the maximal impact of such data corruption is computed for the case where the operator is unaware of the attack and directly applies the configuration from the integrated VVC. Furthermore, since the attacker is constrained to remaining stealthy, we consider a game-theoretic framework where the operator chooses settings to maximize observability and constrain the adversary action space.
Cycle-oriented distributed preconfiguration: ring-like speed with mesh-like capacity for self-planning network restoration (2002)

Cycle-oriented preconfiguration of spare capacity is a new idea for the design and operation of mesh-restorable networks. It offers a sought-after goal: to retain the capacity-efficiency of a mesh-restorable network, while approaching the speed of line-switched self-healing rings. We show that through a strategy of pre-failure cross-connection between the spare links of a mesh network, it is possible to achieve 100% restoration with little, if any, additional spare capacity than in a mesh network. In addition, we find that this strategy requires the operation of only two cross-connections per restoration path. Although spares are connected into cycles, the method is different than self-healing rings because each preconfigured cycle contributes to the restoration of more failure scenarios than can a ring. Additionally, two restoration paths may be obtained from each pre-formed cycle, whereas a ring only yields one restoration path for each failure it addresses. We give an optimal design formulation and results for preconfiguration of spare capacity and describe a distributed self-organizing protocol through which a network can continually approximate the optimal preconfiguration state.
Wasserstein Task Embedding for Measuring Task Similarities (2022)

Measuring similarities between different tasks is critical in a broad spectrum of machine learning problems, including transfer, multi-task, continual, and meta-learning. Most current approaches to measuring task similarities are architecture-dependent: 1) relying on pre-trained models, or 2) training networks on tasks and using forward transfer as a proxy for task similarity. In this paper, we leverage the optimal transport theory and define a novel task embedding for supervised classification that is model-agnostic, training-free, and capable of handling (partially) disjoint label sets. In short, given a dataset with ground-truth labels, we perform a label embedding through multi-dimensional scaling and concatenate dataset samples with their corresponding label embeddings. Then, we define the distance between two datasets as the 2-Wasserstein distance between their updated samples. Lastly, we leverage the 2-Wasserstein embedding framework to embed tasks into a vector space in which the Euclidean distance between the embedded points approximates the proposed 2-Wasserstein distance between tasks. We show that the proposed embedding leads to a significantly faster comparison of tasks compared to related approaches like the Optimal Transport Dataset Distance (OTDD). Furthermore, we demonstrate the effectiveness of our proposed embedding through various numerical experiments and show statistically significant correlations between our proposed distance and the forward and backward transfer between tasks.
Gene Response to Stress in the Asian Citrus Psyllid (Hemiptera: Psyllidae) (2010)

The Asian citrus psyllid, Diaphorina citri, is a vector of the phloem-inhabiting bacterium Candidatus Liberibacter asiaticus, a pathogen associated with the economically important citrus disease known as huanglongbing. Knowledge of the molecular genetics of D. citri and other insects provides insights into the basic biology of insects. For example, insects can be subjected to stressful conditions and then screened to determine if the conditions promote specific genetic responses. Such information, by identifying critical genetic responses linked to survival, can then be used in the development of genetic tools and in novel management strategies aimed at reducing psyllids populations. In this study, transcriptional responses of D. citri adults against 3 stress factors were investigated: physical wounding, heat stress, and exposure to low doses of the insecticide imidacloprid. No measureable transcriptional activity was observed for genes (cyp, gst, CuZn-SOD, hsc70, or hsp90), which, in other insects, have been shown to respond to either physical wounding, heat stress, or exposure to insecticides. However, increased transcriptional activity of a heat-shock gene, hsp70, was found in adult psyllids exposed to 42°C, although 6 h of exposure to this temperature was lethal to psyllids. These results suggest that hsp70 may play a role in response to heat stress of D. citri. Summer temperatures can exceed 37°C in Florida, Texas and California areas where the psyllids now occurs. Natural temperature fluctuations and gradual increases provide enough time for psyllids to acclimate to hot summer temperatures. We propose that the development of a method to disrupt gene expression, such as hsp70, may be applicable for future strategies to suppress psyllids populations.
Formation of porous metal oxides via sol–gel type hydrolysis of metal alkoxide complexes modified with organic templates (1992)

Hybrid organic/inorganic network polymers were formed via the reaction of polyacrylic acid (Mw= 2000 u) with tin(IV), titanium(IV) and silicon(IV) alkoxides and subsequent hydrolysis to form mesoporous materials. The polyacrylate template was removed by subsequent treatment with nitric acid to produce microporous inorganic hydrous metal oxides.