gebhart/patrepeval huggingface dataset:
Optimization of equilibrium carbon dioxide methane reforming parameters by the Gibbs free energy minimization method (2012)

The thermodynamic equilibrium in the carbon dioxide conversion of methane is studied by Gibbs energy minimization. The curves that represent the dependences of the degree of coke formation, the content of methane and carbon dioxide in syngas, and the syngas module on the CO2/CH4 mole ratio in the initial mixture and on temperature at various pressures, are plotted. The regions in which the CO2/CH4 mole ratio is optimal for carbon dioxide conversion and no coke formation occurs, and which are characterized by a minimal content of methane and carbon dioxide in syngas, are revealed.
Cross-domain security of cyber-physical systems (2017)

The interaction between the cyber domain and the physical domain components and processes can be leveraged to enhance the security of the cyber-physical system. In order to do so, we must first analyze various cyber domain and physical domain information flows, and characterize the relation between them using model functions. In this paper, we present a notion of cross-domain security of cyber-physical systems, whereby we present a security analysis framework that can be used for generating novel cross-domain attack models, attack detection methods, etc. We demonstrate how information flows such as discrete domain signal flows and continuous domain energy flows in the cyber and physical domain can be used to generate model functions using data-driven estimation, and use this model functions for performing various cross-domain security analysis. We also demonstrate the practical applicability of the cross-domain security analysis framework using the cyber-physical manufacturing system as a case study.
Monitoring Pharmacologically Induced Immunosuppression by Immune Repertoire Sequencing to Detect Acute Allograft Rejection in Heart Transplant Patients: A Proof-of-Concept Diagnostic Accuracy Study (2015)

&lt;div&gt;&lt;p&gt;Background&lt;/p&gt;&lt;p&gt;It remains difficult to predict and to measure the efficacy of pharmacological immunosuppression. We hypothesized that measuring the B-cell repertoire would enable assessment of the overall level of immunosuppression after heart transplantation.&lt;/p&gt;&lt;p&gt;Methods and Findings&lt;/p&gt;&lt;p&gt;In this proof-of-concept study, we implemented a molecular-barcode-based immune repertoire sequencing assay that sensitively and accurately measures the isotype and clonal composition of the circulating B cell repertoire. We used this assay to measure the temporal response of the B cell repertoire to immunosuppression after heart transplantation. We selected a subset of 12 participants from a larger prospective cohort study (&lt;a href="http://ClinicalTrials.gov" target="_blank"&gt;ClinicalTrials.gov&lt;/a&gt; NCT01985412) that is ongoing at Stanford Medical Center and for which enrollment started in March 2010. This subset of 12 participants was selected to represent post-heart-transplant events, with and without acute rejection (six participants with moderate-to-severe rejection and six without). We analyzed 130 samples from these patients, with an average follow-up period of 15 mo. Immune repertoire sequencing enables the measurement of a patient’s net state of immunosuppression (correlation with tacrolimus level, &lt;i&gt;r&lt;/i&gt; = −0.867, 95% CI −0.968 to −0.523, &lt;i&gt;p&lt;/i&gt; = 0.0014), as well as the diagnosis of acute allograft rejection, which is preceded by increased immune activity with a sensitivity of 71.4% (95% CI 30.3% to 94.9%) and a specificity of 82.0% (95% CI 72.1% to 89.1%) (cell-free donor-derived DNA as noninvasive gold standard). To illustrate the potential of immune repertoire sequencing to monitor atypical post-transplant trajectories, we analyzed two more patients, one with chronic infections and one with amyloidosis. A larger, prospective study will be needed to validate the power of immune repertoire sequencing to predict rejection events, as this proof-of-concept study is limited to a small number of patients who were selected based on several criteria including the availability of a large number of samples and the absence or presence of rejection events.&lt;/p&gt;&lt;p&gt;Conclusions&lt;/p&gt;&lt;p&gt;If confirmed in larger, prospective studies, the method described here has potential applications in the tailored management of post-transplant immunosuppression and, more broadly, as a method for assessing the overall activity of the immune system.&lt;/p&gt;&lt;/div&gt;
ChemInform Abstract: Fluorous Boc (FBoc) Carbamates: New Amine Protecting Groups for Use in Fluorous Synthesis. (2001)

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.
Pancreatic Insulinomas in Multiple Endocrine Neoplasia, Type I Knockout Mice Can Develop in the Absence of Chromosome Instability or Microsatellite Instability (2004)

Multiple endocrine neoplasia, type I (MEN1) is an inherited cancer syndrome characterized by tumors arising primarily in endocrine tissues. The responsible gene acts as a tumor suppressor, and tumors in affected heterozygous individuals occur after inactivation of the wild-type allele. Previous studies have shown that Men1 knockout mice develop multiple pancreatic insulinomas, but this occurs many months after loss of both copies of the Men1 gene. These studies imply that loss of Men1 is not alone sufficient for tumor formation and that additional somatic genetic changes are most likely essential for tumorigenesis. The usual expectation is that such mutations would arise either by a chromosomal instability or microsatellite instability mechanism. In a study of more then a dozen such tumors, using the techniques of array-based comparative genomic hybridization, fluorescent in situ hybridization, loss of heterozygosity analysis using multiple microsatellite markers across the genome, and real time PCR to assess DNA copy number, it appears that many of these full-blown clonal adenomas remain remarkably euploid. Furthermore, the loss of the wild-type Men1 allele in heterozygous Men1 mice occurs by loss and reduplication of the entire mutant-bearing chromosome. Thus, the somatic genetic changes that are postulated to lead to tumorigenesis in a mouse model of MEN1 must be unusually subtle, occurring at either the nucleotide level or through epigenetic mechanisms.
Influence of the MIIF index on operation of multi-infeed HVDC systems (2011)

The Multi-infeed Interaction Factor (MIIF) is an important index for quantifying the interaction between the converters of a Multi-infeed (MI) HVDC transmission system. Using an analytical formulation of power flow, the impact of ac and dc side system parameters on the MIIF is analyzed. The analysis is conducted using a two-infeed HVDC test system derived from the CIGRE HVDC Benchmark model. Results show that the ac grid effective short ratios at the MI converters, length of the tie line connecting the converter ac buses, and the power flow distribution in the ac network are the main factors affecting the MIIF value. The magnitude of the voltage drop at the converter bus does not influence the MIIF value.
Acid-Base Balance with Different Capd Solutions (1996)

Our objective is to investigate transperitoneal buffer fluxes with solution containing lactate and bicarbonate, and to compare the final effect on body base balance of the two solutions. One hundred and four exchanges, using different dwell times, were performed in 52 stable continuous ambulatory peritoneal dialysis (CAPD) patients. Dialysate effluent lactate and bicarbonate and volumes were measured. Net dialytic base gain was calculated. Patients' acid-base status and plasma lactate were determined. In lactate-buffer CAPD solution, lactate concentration in dialysate effluent inversely correlated with length of dwell time, but did not correlate with plasma lactate concentration and net ultrafiltration. Bicarbonate concentration in dialysate effluent correlated with plasma bicarbonate and dwell time but not with ultrafiltration. The arithmetic sum of the lactate gain and bicarbonate loss yielded the net dialytic base gain. Ultrafiltration was the most important factor affecting net dialytic base gain. A previous study demonstrated that in patients using a bicarbonate-buffered solution the net bicarbonate gain is a function of dwell time, ultrafiltration, and plasma bicarbonate. By combining the predicted data of the dialytic base gain with the calculated metabolic acid production, an approximate body base balance could be obtained with both lactate- and bicarbonate-buffered CAPD solutions. The body base balance in CAPD patients is self-regulated by the feedback between plasma bicarbonate concentration and dialytic base gain. The level of plasma bicarbonate is determined by the dialytic base gain and the metabolic acid production. This can explain the large interpatient variability in acid-base correction. Bicarbonate-buffered CAPD solution is equal to lactate solution in correcting acid-base disorders of CAPD patients.
Direct Patterning of Nanometer-Scale Structures on Insulating Substrates with Variable Pressure Electron Beam Lithography (VP-eBL) (2005)

using conventional eBL resists and processing. As a result of this capability, VP-eBL may be useful for patterning on substrates such as sapphire, MgO and polymers with potential applications in optoelectronics and flexible electronics. In addition, further characterization of the VP-eBL process may provide insight into the mechanisms electron scattering and charge-balance in the VPSEM.
Optimisation of Protein Extraction from Medicinal Cannabis Mature Buds for Bottom-Up Proteomics (2019)

Medicinal cannabis is used to relieve the symptoms of certain medical conditions, such as epilepsy. Cannabis is a controlled substance and until recently was illegal in many jurisdictions. Consequently, the study of this plant has been restricted. Proteomics studies on <i>Cannabis sativa</i> reported so far have been primarily based on plant organs and tissues other than buds, such as roots, hypocotyl, leaves, hempseeds and flour. As far as we know, no optimisation of protein extraction from cannabis reproductive tissues has been attempted. Therefore, we set out to assess different protein extraction methods followed by mass spectrometry-based proteomics to recover, separate and identify the proteins of the reproductive organs of medicinal cannabis, apical buds and isolated trichomes. Database search following shotgun proteomics was limited to protein sequences from <i>C. sativa</i> and closely related species available from UniprotKB. Our results demonstrate that a buffer containing the chaotrope reagent guanidine hydrochloride recovers many more proteins than a urea-based buffer. In combination with a precipitation with trichloroacetic acid, such buffer proved optimum to identify proteins using a trypsin digestion followed by nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) analyses. This is validated by focusing on enzymes involved in the phytocannabinoid pathway.
Novel Eukaryotic Lineages Inferred from Small-Subunit rRNA Analyses of Oxygen-Depleted Marine Environments (2003)

Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes.
Evaluation of Kinect Depth Sensor for Use in Mobile Robotics (2011)

To autonomously navigate through unstructured environment mobile robots rely mainly on vision systems. Commonly used are stereo vision, laser and infrared sensors. This paper deals with an evaluation of the Kinect depth sensor and compares it with stereo vision. Also the depth resolution, the accuracy and the repeatability have been determined throughout several experiments based on the SDK of Code Laboratories (CL) for Windows 7. Our experimental results show that the Kinect has a maximum depth resolution of 1.3[mm/color value] and a maximum accuracy of 0.02%. Also, depth density has been assessed and compared to stereo vision images, concluding several benefits the Kinect brings to the field of mobile robotics. Finally, suggestions are being made for several applications for use in mobile robotics
Characterization of digital-micromirror device-based infrared scene projector (2005)

A test procedure is developed for an infrared laser scene projector, and applied to a projection system that we develop based on digital micromirror technology. The intended use will be for simulation and target training. Resolution and noise are significant parameters for target perception models of infrared imaging systems. System resolution is normally measured as the modulation transfer function (MTF), and its noise modeled through an appropriate signal standard deviation metric. We compare MTF measurements for both mid-wave (MWIR) and long-wave IR (LWIR) bands for an infrared laser scene projector based on the digital micromirror device (DMD). Moreover, we use two complimentary models to characterize imaging camera noise. This provides a quantitative image-quality criterion of system performance.
Transmission of RZ-DQPSK over 6500 km with 0.66 bit/s/Hz spectral efficiency (2004)

Transmission of 12.5 Gbit/s RZ-DQPSK signals over 6500 km with different channel spacings is presented. We demonstrate the feasibility of trans-oceanic transmission using DQPSK in DWDM systems with up to 0.66 bit/s/Hz spectral efficiency. Introduction: Differential quadrature phase shift keying (DQPSK) has recently been suggested as a suitable modulation format for optical communication systems (1). With DQPSK, two bits are transmitted for every symbol, thus the symbol rate and the bandwidth of all electronic and electro-optical components can be halved compared to a binary system. This leads to improved dispersion tolerance and allows for closer channel spacing in wavelength division multiplexing (WDM) systems, and very high spectral efficiency have been obtained in recent experiments (2-4). As differential binary phase shift keying (DBPSK), DQPSK also benefits from a 3 dB improved sensitivity when balanced detection is used. Here, we present a transmission experiment over transoceanic distances using optical DQPSK modulation format with a return-to-zero waveform (RZ-DQPSK). In a 64 channel WDM system experiment, we transmit 12.5 Gbit/s RZ-DQPSK signals over a distance of 6500 km. We investigate channel spacings ranging from 133 to 15 GHz, achieving a maximum spectral efficiency of 0.66 bit/s/Hz, and demonstrate that DQPSK is well suited for dense WDM (DWDM) applications. Experiment: The experimental set-up is illustrated in Fig. 1. In the transmitter, we had a total number of 64 continuous wave (CW) lasers spaced 66 GHz, divided into two groups of odd and even channels. The odd numbered lasers were modulated with a 12.5 Gbit/s information rate (or 6.25 Gbit/s symbol rate) RZ-DQPSK signal. First, a Mach Zehnder (MZ) modulator driven with a 2Vπ data signal (Data1) was used to generate a DBPSK signal. Then, a phase modulator (PM) driven with a ½Vπ data signal (Data2) applied a 90o phase modulation to generate a DQPSK signal. Finally, a MZ driven with a Vπ clock signal was used to generate the RZ waveform. The Data1 and Data2 signals were pre-coded so that a pseudo random bit sequence (PRBS) was obtained at the receiver. Depending on the sign of the 45° phase offset in the demodulator, the received pattern was a 2 15 -1 PRBS or an inverted 2 15 -1 PRBS. Even numbered channels were modulated with a 6.25 Gbit/s RZ-DBPSK with a data pattern different from the odd channels. As 6.25 Gbit/s RZ-DBPSK has the same pulse-shape and similar spectrum as 12.5 Gbit/s RZ-DQPSK, the inter-channel cross-talk was not significantly affected by this simplification. The amplifier chain was 465 km long and consisted of 11 fibre spans made of large effective area fiber with a dispersion of 20 ps/nm/km (D+), and inverse dispersion fibre (IDF) with dispersion of -40 ps/nm/km. The average span length was 45 km, and the respective lengths of the D+ and IDF fibres had been adjusted to get a dispersion map with good dispersion and dispersion slope compensation. To reach longer distances, the fibre link was inserted in a re-circulating loop.
Cryogenic process simulation (1994)

Combining accurate fluid property databases with a commercial equation-solving software package running on a desktop computer allows simulation of cryogenic processes without extensive computer programming. Computer simulation can be a powerful tool for process development or optimization. Most engineering simulations to date have required extensive programming skills in languages such as Fortran, Pascal, etc. Authors of simulation code have also usually been responsible for choosing and writing the particular solution algorithm. This paper describes a method of simulating cryogenic processes with a commercial software package on a desktop personal computer that does not require these traditional programming tasks. Applications include modeling of cryogenic refrigerators, heat exchangers, vapor-cooled power leads, vapor pressure thermometers, and various other engineering problems.
Huperzine‐A administration recovers rat ovary function after sympathetic stress (2020)

Chronic cold stress affects ovarian morphology and impairs fertility in rats. It causes an ovarian polycystic ovary (PCOS)-like phenotype, which resembles PCOS in women. The mechanism of cold stress action involves increased ovarian noradrenaline (NA) levels, which remain elevated after cessation of cold stress. By contrast, ovarian acetylcholine (ACh) levels are only transiently elevated and returned to control levels after a 28-day post stress period. Because ACh can exert trophic actions in the ovary, we hypothesised that a sustained elevation of ovarian ACh levels by intraovarian exposure to the ACh-esterase blocker huperzine-A (Hup-A) may interfere with cold stress-induced ovarian changes. This possibility was examined in female Sprague-Dawley rats exposed to cold stress (4°C for 3 h day<sup>-1</sup> for 28 days), followed by a 28-day period without stress. To elevate ACh, in a second group Hup-A was delivered into the ovary of cold stress-exposed rats. A third group was not exposed to cold stress. As expected, cold stress elevated ovarian NA, reduced the number of corpora lutea and increased the number of follicular cysts. It increased plasma testosterone and oestradiol but decreased plasma levels of progesterone. In the Hup-A group, ovarian levels of both, NA and ACh, were elevated, there were fewer cysts and normal testosterone and oestradiol plasma levels were found. However, progesterone levels remained low. Most likely, low progesterone was associated with impaired mating behaviour and low pregnancy rate. We propose that elevated intraovarian levels of ACh are involved in the rescue of ovarian function, opening a target to control ovarian diseases affecting follicular development.
Application of an Annealed Neural Network to a Timetabling Problem (1996)

In this paper, we use an annealed neural network to solve a timetabling problem with contiguity and availability constraints. A novel feature of the problem is that it may not be possible to satisfy the complete set of scheduling requirements, forcing the network to exhibit selection capability. We formulate the problem in a manner consistent with neural computation, describe our implementation of the annealed neural network, and report computational results for a series of randomly-generated problems. Solution quality varies depending on the size and difficulty of the problem, as well as on the values of the penalty parameters used to weight the various constraints.
Bulk and single cell transcriptomic analysis of different dementia types in human hippocampus (2022)

Abstract Background Alzheimer’s disease (AD) is characterized by cognitive deterioration and extracellular amyloid beta deposits and neurofibrillary tangles in the brain. These may occur in tandem with markers of Lewy body (LB) and vascular dementia (VaD). Studying bulk and single‐cell expression profiles for these disorders may identify factors shared between and unique to AD and other dementias. Method Bulk RNA‐sequencing was performed using 210 human postmortem hippocampal region samples obtained from brains donated to the BU Alzheimer Disease Research Center. After quality checks (QC), 191 samples classified as AD+LB (n=43), AD+VaD (n=54), AD alone (n=73), and controls (n=17) were included in the study. Analysis of expression differences between each of these AD groups and controls was performed using limma software with models including covariates for age, sex, RNA quality, plate, and two surrogate variables to adjust for unknown variation. Weighted gene co‐expression network analysis (WGCNA) was used to identify clusters of co‐expressed genes. Additionally, high quality single‐nuclei RNA sequencing data (snRNA‐seq) was obtained from 8 of the 210 hippocampal samples with an average of 6000 cells detected per sample and 1800 genes per cell after QC. This snRNA‐seq data was integrated with the bulk data using Scissor to identify cell populations positively and negatively associated with AD. Result 481 genes were differentially expressed between AD cases and controls. Upregulated genes in AD subjects were enriched for cilia function and morphological development and downregulated genes in AD subjects were enriched for mitochondrial energy production. A WGCNA module strongly associated with ciliary function was found to be overrepresented in AD (and especially AD+VaD) samples compared to controls. Multiple brain cell types were detected from our snRNA‐seq data. Of these, a subpopulation of ependymal cells related to the ciliary WGCNA module was positively associated with AD status. Conclusion Our results suggest that different sets of co‐expressed genes in hippocampus distinguish AD brains with and without pathological hallmarks related to other forms of dementia, and brains without AD pathology. This study also provides preliminary evidence for the involvement of ependymal cell populations in AD