gebhart/patrepeval huggingface dataset:
Genetic and biochemical basis for alternative routes of tocotrienol biosynthesis for enhanced vitamin<scp>E</scp>antioxidant production (2012)

Vitamin E tocotrienol synthesis in monocots requires homogentisate geranylgeranyl transferase (HGGT), which catalyzes the condensation of homogentisate and the unsaturated C20 isoprenoid geranylgeranyl diphosphate (GGDP). By contrast, vitamin E tocopherol synthesis is mediated by homogentisate phytyltransferase (HPT), which condenses homogentisate and the saturated C20 isoprenoid phytyl diphosphate (PDP). An HGGT-independent pathway for tocotrienol synthesis has also been shown to occur by de-regulation of homogentisate synthesis. In this paper, the basis for this pathway and its impact on vitamin E production when combined with HGGT are explored. An Arabidopsis line was initially developed that accumulates tocotrienols and homogentisate by co-expression of Arabidopsis hydroxyphenylpyruvate dioxygenase (HPPD) and Escherichia coli bi-functional chorismate mutase/prephenate dehydrogenase (TyrA). When crossed into the vte2-1 HPT null mutant, tocotrienol production was lost, indicating that HPT catalyzes tocotrienol synthesis in HPPD/TyrA-expressing plants by atypical use of GGDP as a substrate. Consistent with this, recombinant Arabidopsis HPT preferentially catalyzed in vitro production of the tocotrienol precursor geranylgeranyl benzoquinol only when presented with high molar ratios of GGDP:PDP. In addition, tocotrienol levels were highest in early growth stages in HPPD/TyrA lines, but decreased strongly relative to tocopherols during later growth stages when PDP is known to accumulate. Collectively, these results indicate that HPPD/TyrA-induced tocotrienol production requires HPT and occurs upon enrichment of GGDP relative to PDP in prenyl diphosphate pools. Finally, combined expression of HPPD/TyrA and HGGT in Arabidopsis leaves and seeds resulted in large additive increases in vitamin E production, indicating that homogentisate concentrations limit HGGT-catalyzed tocotrienol synthesis.
Optical Fibre-Based Photon Sources for Quantum Information Applications (2013)

We describe progress in the development of photon sources based on optical fibres, including recent results of promising applications for these sources, such as in-line entanglement generation, entanglement swapping and two-colour quantum metrology.
The Influence of Noise, Vibration, Cycle Paths, and Period of Day on Stress Experienced by Cyclists (2018)

Urban and transport planners need to assess the stressful conditions experienced by cyclists, considering that highly stressful situations can discourage people from cycling as a transport mode. Therefore, this study has two objectives: (1) to present a method for monitoring stress and other environmental factors along cycling routes using smart sensors; and (2) to analyze the influence of noise, vibration, presence of cycle paths, and the period of the day on stress experienced by cyclists. Data were collected in the city of São Carlos, Brazil, using stress and noise sensors, accelerometers, and Global Positioning System (GPS). Primarily, heat maps generated from the data made it possible to identify critical points of stress along the routes. In addition, the results of a logistic regression model were analyzed to identify the influence of the studied variables on stress. Although high levels of noise increased the odds of experiencing stress by 4%, very uncomfortable vibrations increased the odds by 14%, and the presence of cycle paths reduced the odds by 8%, an analysis of p-values and odds ratio confidence intervals shows, with a 95% confidence level, that only the period of the day influenced stress, as confirmed by the data. In this case, the odds of having stress increased by 24% in the afternoon rush hour compared to the morning rush hour.
Impact of a Transposon Insertion in <i>phzF2</i> on the Specialized Metabolite Production and Interkingdom Interactions of Pseudomonas aeruginosa (2014)

In microbiology, gene disruption and subsequent experiments often center on phenotypic changes caused by one class of specialized metabolites (quorum sensors, virulence factors, or natural products), disregarding global downstream metabolic effects. With the recent development of mass spectrometry-based methods and technologies for microbial metabolomics investigations, it is now possible to visualize global production of diverse classes of microbial specialized metabolites simultaneously. Using imaging mass spectrometry (IMS) applied to the analysis of microbiology experiments, we can observe the effects of mutations, knockouts, insertions, and complementation on the interactive metabolome. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the impact on specialized metabolite production of a transposon insertion into a Pseudomonas aeruginosa phenazine biosynthetic gene, phzF2. The disruption of phenazine biosynthesis led to broad changes in specialized metabolite production, including loss of pyoverdine production. This shift in specialized metabolite production significantly alters the metabolic outcome of an interaction with Aspergillus fumigatus by influencing triacetylfusarinine production.
Unravelling Small-Polaron Transport in Metal Oxide Photoelectrodes (2016)

Transition-metal oxides are a promising class of semiconductors for the oxidation of water, a process that underpins both photoelectrochemical water splitting and carbon dioxide reduction. However, these materials are limited by very slow charge transport. This is because, unlike conventional semiconductors, material aspects of metal oxides favor the formation of slow-moving, self-trapped charge carriers: small polarons. In this Perspective, we seek to highlight the salient features of small-polaron transport in metal oxides, offer guidelines for their experimental characterization, and examine recent transport studies of two prototypical oxide photoanodes: tungsten-doped monoclinic bismuth vanadate (W:BiVO4) and titanium-doped hematite (Ti:α-Fe2O3). Analysis shows that conduction in both materials is well-described by the adiabatic small-polaron model, with electron drift mobility (distinct from the Hall mobility) values on the order of 10(-4) and 10(-2) cm(2) V(-1) s(-1), respectively. Future directions to build a full picture of charge transport in this family of materials are discussed.
Human-based nanocomposite cryogels for hemostatic and wound healing applications (2019)

In trauma surgery, a fast and effective hemostatic agent is crucial to prevent death. The current used hemostatic sponges are highly effective in stopping the hemorrhages, however they have a limited stability, shape memory, and biological functionality to induce an efficient regenerative healing after injury. Blood derivatives have attracted great attention as an inexpensive milieu of bioactive molecules (e.g., growth factors, cytokines), self-assembling scaffolding proteins (e.g., fibrinogen, fibronectin, vitronectin), and antimicrobial peptides (e.g., platelet factor-4) that have the ability to enhance angiogenesis, stem cell recruitment, and tissue regeneration. Among those, platelet lysate (PL) has attracted great attention as a milieu of supra-physiological doses of biomolecules that can be easily standardized. However, the current PL scaffolds showed limited stability and weak mechanical strength, which severely limits its performance as a bioinstructive and hemostatic biomaterial. Herein, we propose the use of aldehyde-functionalized CNC (a-CNC) that will be crosslinked through reversible Schiff base bonds established with the amine groups of PL proteins to produce a stable hemostatic cryogel for wound healing applications.
Flexible energy storage devices based on nanomaterials (2016)

Flexible electronics in mobile environments such as those encountered in wearable devices also require energy sources. Ideally the energy source, typically batteries and supercapacitors, should also be flexible and have the same form factor as the electronic system. This has given rise to a new paradigm of flexible energy storage devices. The requirement for flexibility imposes limits on thickness of the component parts of a battery or supercapacitor. As a result the current collectors, electrode layers and the electrolytes all have to be thin enough and not crack or disintegrate under repeated cycles of flexing to the specified minimum arc diameter, typically 1 - 5 cm. In order to achieve sufficient reaction surface/volume in thin film form to have the required energy/power capacity nanomaterial formulations of the electrode become essential. The electrolyte requirements for a flexible energy storage device are particularly challenging. Hermetic sealing of a liquid electrolyte in a flexible package is never ideal. This leads to loss of electrolyte and performance over unacceptable short times. Solid electrolytes are therefore preferred, but they have higher resistance than their liquid counterparts and lead to a loss in performance. Recent developments in flexible batteries. Flexible primary and secondary batteries based on aqueous electrolytes being researched by the authors are introduced. Nanomaterial enhanced solid electrolytes for flexible Zn-MnO2 batteries are also introduced.
Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors (2020)

Although human endogenous retroviruses (HERVs) represent a substantial proportion of the human genome and some HERVs, such as HERV-K(HML-2), are reported to be involved in neurological disorders, little is known about their biological function. We report that RNA from an HERV-K(HML-2) envelope gene region binds to and activates human Toll-like receptor (TLR) 8, as well as murine Tlr7, expressed in neurons and microglia, thereby causing neurodegeneration. HERV-K(HML-2) RNA introduced into the cerebrospinal fluid (CSF) of either C57BL/6 wild-type mice or APPPS1 mice, a mouse model for Alzheimer's disease (AD), resulted in neurodegeneration and microglia accumulation. Tlr7-deficient mice were protected against neurodegenerative effects but were resensitized toward HERV-K(HML-2) RNA when neurons ectopically expressed murine Tlr7 or human TLR8. Transcriptome data sets of human AD brain samples revealed a distinct correlation of upregulated HERV-K(HML-2) and TLR8 RNA expression. HERV-K(HML-2) RNA was detectable more frequently in CSF from individuals with AD compared with controls. Our data establish HERV-K(HML-2) RNA as an endogenous ligand for species-specific TLRs 7/8 and imply a functional contribution of human endogenous retroviral transcripts to neurodegenerative processes, such as AD.
IC‐P‐085: Early pathological changes due to Alzheimer's disease are detected by graph theoretical measures of functional connectivity (2013)

Alzheimer's disease (AD) is the most common cause of dementia and has a long prodromal phase. During this period, amyloid and tau pathology accumulate and exerts their pathological effects. Resting state functional connectivity MRI (rs-fcMRI) has demonstrated that brain networks degrade during symptomatic disease. However, the global character of changes in brain networks remains incompletely understood. Further, it is unclear to what extent these degradations exist prior to symptom onset. In this study, we investigated graph theory metrics of functional integration (clustering coefficient), functional segregation (path length), and functional distinctness (modularity) in participants as a function of clinical disease severity. Further, we assessed if these graph metrics were affected in cognitively normal participants with cerebrospinal fluid evidence of disease. Participants were evaluated using the clinical dementia rating CDR scale (205 were CDR0, 90 were CDR0.5, and 31 were CDR1). We further subdivided CDR0 individuals based on CSF analysis (132 subjects had no evidence of amyloid or tau pathology and 59 had evidence of either amyloid pathology or both amyloid and tau pathology). Each participant underwent rs-fcMRI scans that were preprocessed using standard techniques. Graph theoretical metrics were analyzed relative to cognitive or pathological status. Both clustering coefficient and modularity, but not path length, were reduced in AD. Cognitively normal participants who harbored early AD biomarker pathology also showed reduced clustering coefficient and modularity, suggesting that these individuals demonstrated brain changes similar to symptomatic AD, but to a lesser degree. Our data also demonstrate that AD causes widespread neural dysfunction and that this dysfunction is present before symptom onset. Specifically, we show that the brain becomes less integrated during the course of AD. The loss of modularity may reflect the loss of distinct resting-state structure previously observed in AD. Finally, these changes appear to be present in presymptomatic AD, though to a lesser degree.
FINN-L: Library Extensions and Design Trade-off Analysis for Variable Precision LSTM Networks on FPGAs (2018)

It is well known that many types of artificial neural networks, including recurrent networks, can achieve a high classification accuracy even with low-precision weights and activations. The reduction in precision generally yields much more efficient hardware implementations in regards to hardware cost, memory requirements, energy, and achievable throughput. In this paper, we present the first systematic exploration of this design space as a function of precision for Bidirectional Long Short-Term Memory (BiLSTM) neural network. Specifically, we include an in-depth investigation of precision vs. accuracy using a fully hardware-aware training flow, where during training quantization of all aspects of the network including weights, input, output and in-memory cell activations are taken into consideration. In addition, hardware resource cost, power consumption and throughput scalability are explored as a function of precision for FPGA-based implementations of BiLSTM, and multiple approaches of parallelizing the hardware. We provide the first open source HLS library extension of FINN for parameterizable hardware architectures of LSTM layers on FPGAs which offers full precision flexibility and allows for parameterizable performance scaling offering different levels of parallelism within the architecture. Based on this library, we present an FPGA-based accelerator for BiLSTM neural network designed for optical character recognition, along with numerous other experimental proof points for a Zynq UltraScale+ XCZU7EV MPSoC within the given design space.
Conductive atomic force microscopy studies of thin SiO2 layer degradation (2006)

The dielectric degradation of ultrathin (∼2nm) silicon dioxide (SiO2) layers has been investigated by constant and ramped voltage stresses with the conductive atomic force microscopy (CAFM). CAFM imaging shows clearly the lateral degradation propagation and its saturation. Current-voltage characteristics, performed at nanometer scale, show the trap creation rate in function of the stress condition. The critical trap density has been found.
Generalizability and reproducibility of functional connectivity in autism (2019)

Overall, functional connectivity features predictive of autism demonstrated limited generalizability across sites, with consistent results only for large samples. Different types of functional connectivity features do not consistently predict different symptoms of autism. Rather, specific features that predict autism symptoms are distributed across feature types.
Determining the Overall Impact of Interruptions During Online Testing (2014)

With an increase in the number of online tests, interruptions during testing due to unexpected technical issues seem unavoidable. For example, interruptions occurred during several recent state tests. When interruptions occur, it is important to determine the extent of their impact on the examinees’ scores. There is a lack of research on this topic due to the novelty of the problem. This article is an attempt to fill that void. Several methods, primarily based on propensity score matching, linear regression, and item response theory, were suggested to determine the overall impact of the interruptions on the examinees’ scores. A realistic simulation study shows that the suggested methods have satisfactory Type I error rate and power. Then the methods were applied to data from the Indiana Statewide Testing for Educational Progress‐Plus (ISTEP+) test that experienced interruptions in 2013. The results indicate that the interruptions did not have a significant overall impact on the student scores for the ISTEP+ test.
ChemInform Abstract: Electron Spin Echo Envelope Modulation Studies of Cu2+ Interactions with Framework Al in Dehydrated X, Y, and A Zeolites. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 5 from Inhibition of NF-κB–Mediated Signaling by the Cyclin-Dependent Kinase Inhibitor CR8 Overcomes Prosurvival Stimuli to Induce Apoptosis in Chronic Lymphocytic Leukemia Cells (2023)

&lt;p&gt;PDF file - 96K, CR8 induces CLL cell apoptosis in a caspase-dependent manner.&lt;/p&gt;
Serotonin Transporter Null Mutation and Sexual Behavior in Female Rats: 5-HT1A Receptor Desensitization (2010)

The absence (-/-) or reduced (+/-) expression of SERT does not affect basal sexual activity in female rats in a paced mating situation. The data indicate a desensitized 5-HT1A receptor in the SERT-/-, but not in the SERT+/- females. Under normal basal conditions, desensitized 5-HT1A receptors apparently do not play a role in female sexual behavior of the SERT-/-. However, upon activation of the 5-HT1A receptor in "normal" females (SERT+/+ and SERT+/-), a hyposexual behavior is induced.
Silver nitrate and adenine sulphate induced high regeneration frequency in the recalcitrant plant<i>Cosmos bipinnatus</i>using cotyledon explants (2017)

Plant regeneration ability was studied in the medicinal-ornamental plant, Cosmos bipinnatus ‘Sonata white’, which is a dicotyledonous recalcitrant plant to shoot induction. Cotyledons were used as sources of explants to investigate plant regeneration. High frequency of direct shoot induction was obtained when BA (5 mg/l) and AgNO3 (5 mg/l) were used in combination with 20 mg/l adenine sulphate (73.8%) in Murashige and Skoog (MS) medium. The highest shoot number per explant (5.7) was induced on MS medium supplemented with 5 mg/l BA, 5 mg/l AgNO3, and 40 mg/l adenine. Eight week-old shoots were transferred to root induction media containing MS and half-strength MS medium with different concentration of IBA. The highest rate of root induction (70.8%) was obtained on half-strength MS medium with 1.5 mg/l IBA within four weeks. The plantlets were transferred to pot and kept in the greenhouse condition. Seventy percent of the plantlets successfully acclimatised.Abbreviations: BA, 6-benzylaminopurine; IBA, Indole-3-butyric acid; MS, Murashige and Skoog; PGRs, plant growth regulators.
Formation of ring-shaped lateral meniscus following anterior cruciate ligament reconstruction (2017)

This is the first case in the literature of inter-horn bridge formation involved in ring-shaped lateral meniscus following ACL reconstruction.
The Effects of Aggregation on Electronic and Optical Properties of Oligothiophene Particles (2012)

Solution processing of oligothiophene molecules is shown to produce a range of particles with distinct morphologies. Once isolated on a substrate, the optical and electronic properties of individual particles were studied. From polarized scanning confocal microscopy experiments, distinct particles that are identifiable by shape were shown to have similar emission spectra except in regard to the 0-0 vibronic band intensity. This suppression of the 0-0 vibronic band correlates to the amount of energetic disorder present in a weakly coupled H-aggregate. The studied particles ranged from moderate to almost complete suppression of the 0-0 vibronic band when compared to the emission spectrum of the isolated molecule in solution. All particles were found to have a high degree of geometric order (molecular alignment) as observed from the fluorescence dichroism (FD) values of around 0.7-0.8 for all the studied morphologies. The structural and electronic properties of the particles were investigated with Kelvin probe force microscopy (KPFM) to measure the local contact potential (LCP) difference, a quantity that is closely related to the differences in intermolecular charge distribution between the oligothiophene particles. The LCP was found to vary by as much as 70 mV between different oligothiophene particles and a trend was observed that correlated the LCP changes with the amount of energetic disorder present, as signified by the suppression of the 0-0 vibronic peak in the emission spectra. Combined polarized scanning confocal microscopy studies, along with KPFM measurements, help to provide fundamental insights into the role of morphology, molecular packing, and intermolecular charge distributions in oligiothiophene particles.
Call admission control schemes guaranteeing the frame and call level QoSs in CDMA cellular networks (2004)

CDMA systems have a trade-off relationship between the frame error rate (FER) and the number of accepted users. Therefore, the call admission control (CAC) scheme is essential for guaranteeing the FER below the required value, which is the measure of the quality of service (QoS) in the frame level. In cellular networks, the dropping probability of handoff calls is another critical measure for QoS in the call level. There has been, nevertheless, little concern for CAC schemes guaranteeing these QoS requirements simultaneously in the CDMA cellular networks. In this paper, we propose CAC that track the time-varying capacity of CDMA systems by estimating the distribution of the total received power at a base station, thereby realizing the bandwidth reservation scheme to meet the QoS requirement for handoff calls in the call level.
Proteomic and Transcriptomic Analyses of the Hippocampus and Cortex in SUDEP and High-Risk SUDEP Cases (2020)

Abstract Sudden unexpected death in epilepsy (SUDEP) is the leading type of epilepsy-related death. Severely depressed brain activity in these cases may impair respiration, arousal, and protective reflexes, occurring as a prolonged postictal generalized EEG suppression (PGES) and resulting in a high-risk for SUDEP. In autopsy hippocampus and cortex, we observed no proteomic differences between SUDEP and epilepsy cases, contrasting our previously reported robust differences between epilepsy and controls. Transcriptomics in hippocampus and cortex from surgical epilepsy cases segregated by PGES identified 55 differentially expressed genes (37 protein-coding, 15 lncRNAs, three pending) in hippocampus. Overall, the SUDEP proteome and high-risk SUDEP transcriptome largely reflected other epilepsy cases in the brain regions analyzed, consistent with diverse epilepsy syndromes and comorbidities associated with SUDEP. Thus, studies with larger cohorts and different epilepsy syndromes, as well as additional anatomic regions may identify molecular mechanisms of SUDEP.