gebhart/patrepeval huggingface dataset:
Genetic and environmental factors for hyperhomocysteinaemia and its clinical implications in Parkinson's disease. (2009)

Elevated homocysteine (Hcy) plasma levels are caused by genetic and environmental factors. Polymorphisms of Hcy metabolizing enzyme genes may result in its plasma increase. Experimental and clinical studies have shown the possible role of hyperhomocysteinaemia in pathogenesis of Parkinson's disease (PD), Alzheimer's disease and vascular disorders. The results of clinical studies in PD generally do not support the theoretical hypotheses, and animal studies remain controversial. A major environmental factor responsible for Hcy increase in PD seems to be levodopa therapy. Its metabolism results in Hcy increase and may be reduced with folate and vitamins B6, B12 supplementation or inhibition of catechol-O-methyltransferase (COMT) activity. Therefore, the potential harmful role of Hcy may be diminished in PD patients with vascular comorbidities. Further studies are needed to establish the real role of Hcy for PD and other neurological disorders. The paper summarizes the current knowledge on the genetic and environmental factors responsible for Hcy increase in PD.
The search for the universal probe card solution (2002)

Epoxy Ring, Cobra, and other new products are evaluated against the demand for high pin count, high frequency, high temperature, multi-DUT, long life, etc. There doesn't appear to be a single universal solution, but rather each technology provides a usable response to the growing wafer test requirements. However, the climate is right for creativity and innovation to meet the challenges of the future.
Probabilistic system-on-a-chip architectures (2007)

Parameter variations, noise susceptibility, and increasing energy dissipation of cmos devices have been recognized as major challenges in circuit and microarchitecture design in the nanometer regime. Among these, parameter variations and noise susceptibility are increasingly causing cmos devices to behave in an “unreliable” or “probabilistic” manner. To address these challenges, a shift in design paradigm from current-day deterministic designs to “statistical” or “probabilistic” designs is deemed inevitable. To respond to this need, in this article, we introduce and study an entirely novel family of probabilistic architectures: the probabilistic system-on-a-chip (psoc). psoc architectures are based on cmos devices rendered probabilistic due to noise, referred to as probabilistic CMOS or PCMOS devices. We demonstrate that in addition to harnessing the probabilistic behavior of pcmos devices, psoc architectures yield significant improvements, both in energy consumed as well as performance in the context of probabilistic or randomized applications with broad utility. All of our application and architectural savings are quantified using the product of the energy and performance, denoted (energy × performance): The pcmos-based gains are as high as a substantial multiplicative factor of over 560 when compared to a competing energy-efficient cmos-based realization. Our architectural design is application specific and involves navigating design space spanning the algorithm (application), its architecture (psoc), and the probabilistic technology (pcmos).
Ion implantation in compound semiconductors for high-performance electronic devices (1996)

Advanced electronic devices based on compound semiconductors often make use of selective area ion implantation doping or isolation. The implantation processing becomes more complex as the device dimensions are reduced and more complex material systems are employed. The authors review several applications of ion implantation to high performance junction field effect transistors (JFETs) and heterostructure field effect transistors (HFETs) that are based on compound semiconductors, including: GaAs, AlGaAs, InGaP, and AlGaSb.
Depth-range extension with folding technique for SPAD-based TOF LIDAR systems (2014)

Direct Time-of-Flight (D-ToF) sensors can be implemented combining Single-Photon Avalanche Diodes (SPAD) with Time-to-Digital Converters (TDCs). Such an architecture exhibits an intrinsic distance range limitation due to the TDC range, which is fixed by the TDC resolution and number of bits. Up to now it was not possible to extend this range without redesigning the TDC. In this work we propose a method to overcome this limitation thanks to a folding measuring technique. In our implementation the TDC is based on a ring-oscillator; the TDC starts when a photon is detected and stops when an external Stop signal is provided. As the number of bits is limited, the TDC restarts from 0 after reaching the final value (folding). In this paper, we show that it is possible to arbitrary extend the maximum detectable distance through repeated measurements by modifying the timing of the “stop” signal in multiples of the TDC's maximum range.
Fluoxetine in relapse prevention of PTSD (2003)

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Isolation and composition of inositolphosphorylceramide-type sphingolipids of hyphal forms of Candida albicans (1996)

Hyphal forms of the human pathogen Candida albicans have been found to contain substantial quantities of phosphosphingolipids. These lipids were fractionated into three classes by normal-phase high-performance liquid chromatography. The first class contained equimolar amounts of phosphorus, inositol, phytosphingosines, and fatty acids; their composition and chromatographic behavior suggest that these compounds are inositolphosphorylceramides. The second class contained equimolar amounts of phosphorus, mannosylinositol, phytosphingosines, and fatty acids; their composition and chromatographic behavior indicate that these compounds are mannosylinositolphosphorylceramides. The third class of compounds contained phosphorus, mannosylinositol, inositol, phytosphingosines, and fatty acids in a molar ratio of 2:1:1:1:1; their composition and chromatographic behavior indicate that these compounds are mannosyldiinositolphosphorylceramides. Molecular species in each class differ in the composition of long chain bases and fatty acids; the most abundant long chain bases were C18 and C20 phytosphingosines, and the most abundant fatty acids were hydroxy and nonhydroxy C24-26. The array of sphingolipids in C. albicans is similar to that of Saccharomyces cerevisiae. Sphingolipids have been shown to be essential in S. cerevisiae, thus these lipids, which are not present in animals, offer a potentially unique target for antifungal chemotherapy against C. albicans.
An interference suppressor for CW and narrow-band signals using filter bank on CDMA communications (2002)

A novel digital interference suppression method based on Fourier transform has been proposed. Since the frequency power spectrum of CW and narrow band interference signals are larger than that of the spread-spectrum signal, these interference signals can be reduced by limiting the signal level in the frequency domain. The proposed method is composed of FDM/TDM transform using a filter bank and an amplitude limiter adjusted to the spectrum of the spread-spectrum signal. The received signals are divided into separate narrow frequency bands in real time using a frequency function and the amplitude of these signals is limited. This signal processing reduces the interference signals. This paper describes the principle design of the transform circuit and explains the optimum limiting technique. In particular, the proposed digital processing model is compared with the analog processing model which has already been reported. In addition, the adjustment level of the amplitude limiter for the DS and FH spread-spectrum signal is shown. Finally, the improvement in interference suppression using FFT and the optimum limiting limiter is demonstrated with measured the eye pattern of the correlated signal. The performance of this suppressor is shown by measuring the bit error rate in the presence of CW interference signals and Gaussian noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Continuous query processing in data streams using duality of data and queries (2006)

Recent data stream systems such as TelegraphCQ have employed the well-known property of duality between data and queries. In these systems, query processing methods are classified into two dual categories -- data-initiative and query-initiative -- depending on whether query processing is initiated by selecting a data element or a query. Although the duality property has been widely recognized, previous data stream systems do not fully take advantages of this property since they use the two dual methods independently: data-initiative methods only for continuous queries and query-initiative methods only for ad-hoc queries. We contend that continuous query processing can be better optimized by adopting an approach that integrates the two dual methods. Our primary contribution is based on the observation that spatial join is a powerful tool for achieving this objective. In this paper, we first present a new viewpoint of transforming the continuous query processing problem to a multi-dimensional spatial join problem. We then present a continuous query processing algorithm based on spatial join, which we name Spatial Join CQ. This algorithm processes continuous queries by finding the pairs of overlapping regions from a set of data elements and a set of queries, both defined as regions in the multi-dimensional space. The algorithm achieves the advantages of the two dual methods simultaneously. Experimental results show that the proposed algorithm outperforms earlier algorithms by up to 36 times for simple selection continuous queries and by up to 7 times for sliding window join queries.
Spatial and temporal variations of microbial community in a mixed plug‐flow loop reactor fed with dairy manure (2014)

Mixed plug-flow loop reactor (MPFLR) has been widely adopted by the US dairy farms to convert cattle manure to biogas. However, the microbiome in MPFLR digesters remains unexplored. In this study, the microbiome in a MPFLR digester operated on a mega-dairy farm was examined thrice over a 2 month period. Within 23 days of retention time, 55-70% of total manure solid was digested. Except for a few minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of the digester and over time. Metagenomic analysis showed that although with some temporal variations, the bacterial community was rather stable spatially in the digester. The methanogenic community was also stable both spatially and temporally in the digester. Among methanogens, genus Methanosaeta dominated in the digester. Quantitative polymerase chain reaction (qPCR) analysis and metagenomic analysis yielded different relative abundance of individual genera of methanogens, especially for Methanobacterium, which was predominant based on qPCR analysis but undetectable by metagenomics. Collectively, the results showed that only small microbial and chemical gradients existed within the digester, and the digestion process occurred similarly throughout the MPFLR digester. The findings of this study may help improve the operation and design of this type of manure digesters.
Engineering <i>Escherichia coli</i> into a Protein Delivery System for Mammalian Cells (2015)

Many Gram-negative pathogens encode type 3 secretion systems, sophisticated nanomachines that deliver proteins directly into the cytoplasm of mammalian cells. These systems present attractive opportunities for therapeutic protein delivery applications; however, their utility has been limited by their inherent pathogenicity. Here, we report the reengineering of a laboratory strain of Escherichia coli with a tunable type 3 secretion system that can efficiently deliver heterologous proteins into mammalian cells, thereby circumventing the need for virulence attenuation. We first introduced a 31 kB region of Shigella flexneri DNA that encodes all of the information needed to form the secretion nanomachine onto a plasmid that can be directly propagated within E. coli or integrated into the E. coli chromosome. To provide flexible control over type 3 secretion and protein delivery, we generated plasmids expressing master regulators of the type 3 system from either constitutive or inducible promoters. We then constructed a Gateway-compatible plasmid library of type 3 secretion sequences to enable rapid screening and identification of sequences that do not perturb function when fused to heterologous protein substrates and optimized their delivery into mammalian cells. Combining these elements, we found that coordinated expression of the type 3 secretion system and modified target protein substrates produces a nonpathogenic strain that expresses, secretes, and delivers heterologous proteins into mammalian cells. This reengineered system thus provides a highly flexible protein delivery platform with potential for future therapeutic applications.
Mouse vimentin: structural relationship to fos, jun, CREB and tpr. (1990)

We have isolated and characterized mouse cDNA clones representing the entire coding region of vimentin. RNA blot analysis of different stages during development has revealed differential control in the expression of vimentin mRNA in the different tissues studied. The nucleotide sequence extends 1800 base pairs and contains the 466 amino acid mouse vimentin polypeptide chain, flanked by 90 base pairs 5' and 312 base pairs 3' untranslated region. Conformational analysis of the deduced amino acid sequence was used to localize the three known structural domains: a non-alpha-helical N-terminal head of 81 residues, a rod-like domain of 330 residues arising from three alpha-helices, and a non-alpha-helical C-terminal domain of 55 residues. Amino acid sequence comparisons with other species revealed high sequence conservation of mouse vimentin to hamster (98.7%), human (96%), and chicken (88%) protein. Computer sequence analysis also revealed domains of significant homology between different alpha helical regions of vimentin and the DNA binding-leucine zipper domain of several proto-oncogenes and transcription regulators. Specifically, 50-70% structural similarity was observed between the basic domain of the DNA binding region of the nuclear proto-oncogene products c-fos and its related antigen fra-1, c-jun and the cAMP-responsive DNA binding protein CREB, with part of the N-terminal half region of helix 1b of vimentin. When the leucine zipper domains of all these proteins were compared to vimentin, at least two different regions of similarity in the vimentin molecule were found reaching up to 53% for jun, 60% for fos, and 76% for CREB. Further analysis revealed several domains of significant similarity (50%) between all alpha-helices of the rod domain of vimentin and the N-terminal (approximately 210 residues) activation domain tpr of the oncogenic raf.
Fast GC-PFPD system for field analysis of chemical warfare agents (2000)

A fast gas chromatograph (GC) equipped with a pulsed-flame photometric detector (PFPD) was designed and built with the intention of facilitating field analysis of the full range of chemical warfare agents (CWA). This GC-PFPD system was tested with five organophosphorus and organosulfur CWA simulants that cover the volatility range of common CWA. Fast repetitive analysis was demonstrated with a cycle time as short as 30 s, combined with very low detection limits of 20 ng/m3 for organophosphorus CWA simulants and 200 ng/m3 for organosulfur compounds. With a longer analysis time of 80 s, a 3-ng/m3 detection limit was demonstrated for DMMP. In the GC-PFPD system, the separation power of each of these techniques is orthogonal and independent; thus, this hyphenated combination is characterized by a very low false-alarm rate, combined with CWA identification capability at the molecular level. The large improvement in system selectivity is demonstrated in the direct analysis of a low level of triethylphosphate in the headspace of diesel fuel without any interference. The system inlet was heated and the sample path was inert without any metal, enabling fast response time and low detection limits for a low volatility agent such as VX. The same fast GC-PFPD system could also be quickly and easily switched to a continuous sampling “sniff” mode of operation with 2-s response time. Alternatively, it could be operated in a novel mode of thermally modulated inlet (TMI) that provided intermediate results between those of GC and “sniff” in terms of the trade-off of response time and performance. The fast GC-PFPD system is also characterized by low average hydrogen consumption (about 4 ml/min), small size, and low weight. No attempt was made to complete the system in terms of portable control electronics. The advantages and unique features of this system, as well as the importance of CWA identification at the molecular level, are discussed. © 2000 John Wiley & Sons, Inc. Field Analyt Chem Technol 4: 170–194, 2000
Semiclassical Dynamics of Electron Wave Packet States with Phase Vortices (2007)

We consider semiclassical higher-order wave packet solutions of the Schrödinger equation with phase vortices. The vortex line is aligned with the propagation direction, and the wave packet carries a well-defined orbital angular momentum (OAM) variant Planck's over 2pil (l is the vortex strength) along its main linear momentum. The probability current coils around the momentum in such OAM states of electrons. In an electric field, these states evolve like massless particles with spin l. The magnetic-monopole Berry curvature appears in momentum space, which results in a spin-orbit-type interaction and a Berry/Magnus transverse force acting on the wave packet. This brings about the OAM Hall effect. In a magnetic field, there is a Zeeman interaction, which, can lead to more complicated dynamics.
Spectrally Selective Nanocomposite Textile for Outdoor Personal Cooling (2018)

Outdoor heat stress poses a serious public health threat and curtails industrial labor supply and productivity, thus adversely impacting the wellness and economy of the entire society. With climate change, there will be more intense and frequent heat waves that further present a grand challenge for sustainability. However, an efficient and economical method that can provide localized outdoor cooling of the human body without intensive energy input is lacking. Here, a novel spectrally selective nanocomposite textile for radiative outdoor cooling using zinc oxide nanoparticle-embedded polyethylene is demonstrated. By reflecting more than 90% solar irradiance and selectively transmitting out human body thermal radiation, this textile can enable simulated skin to avoid overheating by 5-13 °C compared to normal textile like cotton under peak daylight condition. Owing to its superior passive cooling capability and compatibility with large-scale production, this radiative outdoor cooling textile is promising to widely benefit the sustainability of society in many aspects spanning from health to economy.
Identification of the aromatase inhibitor letrozole in urine by gas chromatography/mass spectrometry (2005)

Letrozole (1-(bis-(4-cyanophenyl)methyl)-1,2,4-triazole) is used therapeutically as a non-steroidal aromatase inhibitor (Femara) to treat hormone-sensitive breast cancer in postmenopausal women. For doping purposes it may be used to counteract the adverse effects of an extensive abuse of anabolic androgenic steroids (gynaecomastia) and to increase the testosterone concentration by stimulation of the testosterone biosynthesis. The use of aromatase inhibitors has been prohibited by IOC/WADA regulations for male and female athletes since September 2001 and January 2005, respectively. Spot urine samples from women suffering from metastatic breast cancer and being treated with letrozole were collected and analysed to develop/optimise the detection system for metabolites of letrozole to allow the identification of athletes who do not comply with the internationally prohibited use of this cancer drug. The assay was based on gas chromatography/mass spectrometry (GC/MS) and the main metabolite of letrozole (bis-4-cyanophenylmethanol) was identified by comparison of its mass spectrum and retention time with that of a bis-4-cyanophenylmethanol reference. The full-scan spectrum, diagnostic ions and a validation of the method for the analysis of bis-4-cyanophenylmethanol are presented.
Synaptic Plasticity and AMPA Receptor Trafficking (2003)

Alterations in neuronal activity can elicit long-lasting changes in the strength of synaptic transmission at excitatory synapses and, as a consequence, may underlie many forms of experience-dependent plasticity, including learning and memory. The best-characterized forms of such synaptic plasticity are the long-term depression (LTD) and long-term potentiation (LTP) observed at excitatory synapses in the CA1 region of the hippocampus. It is now well accepted that the trafficking of AMPA receptors to and away from the synaptic plasma membrane plays an essential role in both LTP and LTD, respectively. Here we review current models of AMPA receptor trafficking and how this trafficking may be regulated at the molecular level in order to produce the observed changes in synaptic strength. We also review recent work from our lab suggesting that synaptic plasticity in the mesolimbic dopamine system may contribute importantly to the neural adaptations elicited by drugs of abuse.
Iterative Microarray and RNA Interference–Based Interrogation of the Src-Induced Invasive Phenotype (2005)

Src kinase has long been recognized as a factor in the progression of colorectal cancer and seems to play a specific role in the development of the metastatic phenotype. In spite of numerous studies conducted to elucidate the exact role of Src in cancer progression, downstream targets of Src remain poorly understood. Gene expression profiling has permitted the identification of large sets of genes that may be functionally interrelated but it is often unclear as to which molecular pathways they belong. Here we have developed an iterative approach to experimentally reconstruct a network of gene activity regulated by Src and contributing to the invasive phenotype. Our strategy uses a combination of phenotypic anchoring of gene expression profiles and loss-of-function screening by way of RNA-mediated interference. Using a panel of human colon cancer cell lines exhibiting differential Src-specific activity and invasivity, we identify the first two levels of gene transcription responsible for the invasive phenotype, where first-tier genes are controlled by Src activity and the second-tier genes are under the influence of the first tier. Specifically, perturbation of first-tier gene activity by either pharmacologic inhibition of Src or RNA-mediated interference-directed knockdown leads to a loss of invasivity and decline of second-tier gene activity. The targeting of first-tier genes may be bypassed altogether because knockdown of second-tier genes led to a similar loss of invasive potential. In this manner, numerous members of a "transcriptional cascade" pathway for metastatic activity have been identified and functionally validated.
Thresholding using two-dimensional histogram and fuzzy entropy principle (2000)

This paper presents a thresholding approach by performing fuzzy partition on a two-dimensional (2-D) histogram based on fuzzy relation and maximum fuzzy entropy principle. The experiments with various gray level and color images have demonstrated that the proposed approach outperforms the 2-D nonfuzzy approach and the one dimensional (1-D) fuzzy partition approach.