gebhart/patrepeval huggingface dataset:
mapman : a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes (2004)

MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.
Synthesis and Magnetic Properties of Colloidal MnPt3 Nanocrystals (2006)

The colloidal synthesis and magnetic properties of MnPt(3) nanocrystals are reported. The nanocrystal size depended on the Mn reactant used, but the Mn:Pt stoichiometry was always 1:3. As synthesized, the nanocrystals are compositionally disordered with the face-centered cubic (fcc) A1 phase. Annealing at 580 degrees C changed the MnPt(3) crystal structure to the compositionally ordered L1(2) phase (AuCu(3) structure) with higher magnetocrystalline anisotropy. Magnetization measurements showed that the A1 nanocrystals are paramagnetic and the L1(2) MnPt(3) nanocrystals are superparamagnetic.
PSIII-16 Evaluating the impact of group stunning on physiological parameters of pigs in a small abattoir (2019)

Abstract Small abattoirs commonly process pigs and sheep in a handling system designed for cattle. Smaller species are usually stunned in groups in the cattle shackling area in front of the stun box. The purpose of this study was to determine the effects of stun order on physiological parameters in pigs. A total of 148 barrows and gilts were stunned in 29 groups of four to five pigs with seven control pigs. All pigs were moved together into the stunning pen and stunned one at a time with a handheld penetrating captive bolt stunner and immediately shackled and processed. The average time from pen entrance to the final stun was 22 minutes. To act as a control, one pig was moved into the pen individually and stunned after the same elapsed time as the groups. Blood lactate and glucose concentration were measured in exsanguination blood using hand-held analyzers. A one-way ANOVA was used to determine the effect of stun order on blood metabolite concentration. Pigs stunned first had significantly greater lactate than the last pigs stunned (P &amp;lt; 0.01). Stun order did not have a significant effect on blood glucose concentration (P = 0.43). The control pigs had significantly lower lactate than the first pig stunned (P = 0.04). Greater blood lactate concentrations in the first pig may be due to handling into the stunning pen prior to the first stun. Handler interaction may have resulted in an increase in certain behaviors such as turning back and squealing which further caused the first pigs to have increased lactate.
Hippocampal ripples signal contextually-mediated episodic recall (2021)

High-frequency oscillatory events, termed ripples, represent synchrony of neural activity in the brain. Recent evidence suggests medial temporal lobe (MTL) ripples support memory retrieval. However, it is unclear if ripples signal the reinstatement of episodic memories. Analyzing electrophysiological MTL recordings from 219 neurosurgical participants performing episodic recall tasks, we find that the rate of hippocampal ripples rises just prior to the free recall of recently-formed memories. This pre-recall ripple effect (PRE) is stronger in the CA1 and dentate gyrus (DG) subfields of hippocampus than neighboring MTL regions entorhinal and parahippocampal cortex. The PRE is also stronger prior to the retrieval of temporally and semantically clustered as compared with unclustered recalls, indicating the involvement of ripples in contextual reinstatement, which is a hallmark of episodic memory. One sentence summary High frequency human hippocampal ripples occur prior to those memories most likely retrieved via episodic mechanisms.
Acquisition systems and decoding algorithms of peripheral neural signals for prosthetic applications (2014)

Access to real-time aggregated BG data reports through the use of a data management software program improved the efficacy of our TGC program.
Single-frequency operation of a Cr:YAG laser from 1332 nm to 1554 nm (2000)

Summary form only given. We describe the first demonstration, to our knowledge, of single-frequency operation from a Cr:YAG laser. The wavelength range of operation, from 1332 nm to 1554 nm, with output powers as high as 680 mW, provides a unique narrow linewidth source, potential applications include, but are not limited to, injection seeding of optical parametric oscillators for remote sensing applications such as DIAL, near-infrared spectroscopy, and optical telecommunications instrumentation.
High-Resolution Silicon Photomultiplier Time-of-Flight Dedicated Head PET System for Clinical Brain Studies (2022)

We acquired brain <sup>18</sup>F-FDG and <sup>18</sup>F-flutemetamol PET images using a time-of-flight system dedicated to the head (dhPET) and a conventional whole-body PET/CT (wbPET) system and evaluated the clinical superiority of dhPET over wbPET. <b>Methods:</b> There were 18 subjects for the <sup>18</sup>F-FDG PET study and 17 subjects for the <sup>18</sup>F-flutemetamol PET study. <sup>18</sup>F-FDG PET images were first obtained using wbPET, followed by dhPET. <sup>18</sup>F-flutemetamol PET images were first obtained using wbPET, followed by dhPET. Images acquired using dhPET and wbPET were compared by visual inspection, voxelwise analysis, and SUV ratio (SUVR). <b>Results:</b> All <sup>18</sup>F-FDG and <sup>18</sup>F-flutemetamol images acquired using dhPET were judged as visually better than those acquired using wbPET. The voxelwise analysis demonstrated that accumulations in the cerebellum, in the lateral occipital cortices, and around the central sulcus area in dhPET <sup>18</sup>F-FDG images were lower than those in wbPET <sup>18</sup>F-FDG images, whereas accumulations around the ventricle systems were higher in dhPET <sup>18</sup>F-FDG images than those in wbPET <sup>18</sup>F-FDG images. Accumulations in the cerebellar dentate nucleus, in the midbrain, in the lateral occipital cortices, and around the central sulcus area in dhPET images were lower than those in wbPET images, whereas accumulations around the ventricle systems were higher in dhPET <sup>18</sup>F-flutemetamol images than those in wbPET <sup>18</sup>F-flutemetamol images. The mean cortical SUVRs of <sup>18</sup>F-FDG and <sup>18</sup>F-flutemetamol dhPET images were significantly higher than those of <sup>18</sup>F-FDG and <sup>18</sup>F-flutemetamol wbPET images, respectively. <b>Conclusion:</b> The dhPET images had better image quality by visual inspection and higher SUVRs than wbPET images. Although there were several regional accumulation differences between dhPET and wbPET images, understanding this phenomenon will enable full use of the features of this dhPET system in clinical practice.
Upper bound on mutual quantum information between two partially mixed qubits (2020)

Polarization entangled photons become partially mixed when transmitted through channels with polarization mode dispersion. We experimentally build a channel that maximizes the amount of mutual quantum information shared between two qubits for a given amount of entanglement left in the two photon system.
TPQA: Three point quadrature approximation MPPT algorithm (2013)

Growing concerns about environmental issues and the world energy crisis have attracted a great deal of interests for the development and application of the photovoltaic (PV) power system that uses the nonpolluting and the most abundant solar energy. This paper introduces a novel maximum power point tracking (MPPT) algorithm that is based on the fact that the PV power curve is similar to a parabolic curve in nature. The algorithm is implemented and validated on Simulink/MATLAB. The simulation results show enhancement in tracking time and accuracy in comparison to the Perturb and Observe (P&O) algorithm.
Three proteins involved in Caenorhabditis elegans vulval invagination are similar to components of a glycosylation pathway (1999)

We have molecularly analyzed three genes, sqv-3, sqv-7, and sqv-8, that are required for wild-type vulval invagination in Caenorhabditis elegans. The predicted SQV-8 protein is similar in sequence to two mammalian beta(1,3)-glucuronyltransferases, one of which adds glucuronic acid to protein-linked galactose-beta(1, 4)-N-acetylglucosamine. SQV-3 is similar to a family of glycosyltransferases that includes vertebrate beta(1, 4)-galactosyltransferases, which create galactose-beta(1, 4)-N-acetylglucosamine linkages. One model is therefore that SQV-8 uses a SQV-3 product as a substrate. SQV-7 is similar to members of a family of nucleotide-sugar transporters. The sqv genes therefore are likely to encode components of a conserved glycosylation pathway that assembles a C. elegans carbohydrate moiety, the absence of which perturbs vulval invagination.
Inorganic and organometallic polymers (2015)

AccessScience is an authoritative and dynamic online resource that contains incisively written, high-quality educational material covering all major scientific disciplines. An acclaimed gateway to scientific knowledge, AccessScience is continually expanding the ways it can demonstrate and explain core, trustworthy scientific information that inspires and guides users to deeper knowledge.
Derivative surface photovoltage spectroscopy; a new approach to the study of absorption in semiconductors: GaAs (1979)

Derivative surface photovoltage spectroscopy was achieved with wavelength modulation; it was applied to GaAs and permitted, in a single experiment, the determination of changes in the absorption coefficient over an energy range of 0.5 to 4.3 eV. Photoionization characteristics of deep levels were determined. All known critical-point transitions up to 4.3 eV were clearly obtained from second-derivative spectra. In addition, previously unresolved transitions were observed at about 2.6 eV. Oscillatory photovoltage in high magnetic fields was observed, and it was used to identify the transitions in the vicinity of the energy gap.
Heterogeneously Integrated Photodiodes on Silicon (2015)

This paper reviews progress in the field of heterogeneously integrated photodiodes with a focus on InP-based high-speed high-power modified uni-traveling carrier photodiodes on silicon-on-insulator waveguides. Discrete, balanced, and photodiode arrays are described.
Large scale microfluidic systems for sequential trapping, labeling and content extraction of single cells (2009)

Parallel and sequential manipulation of trapping, labeling and content extraction of single cell was realized using a 2-D simple flow channels. The proposed system consists of main channels, cell trapping pockets, drain channels and single cell content collection channels. We fabricated prototypes having 16 cell trapping pockets and 512 cell trapping pockets. Sequential all single cell handling for COS-1 cell was confirmed in 16 pockets type [1]. The sequential trapping and labeling were achieved in 512 pockets type. Capture rate for COS-1 cell was 83.2% and that for BAT cell was 70.3%. These devices are useful for high throughput single cell analysis.
Psychophysical quantification of individual differences in timbre perception (2000)

cote interne IRCAM: McAdams00a
Elastic Light Single-Scattering Spectroscopy for the Detection of Cervical Precancerous Ex vivo (2012)

Potential application of elastic light single-scattering spectroscopy (ELSSS) for differentiating high-grade squamous intraepithelial lesions (HSIL) from non-HSIL tissues was investigated. An ELSSS system was used to acquire spectra from cervix tissues. A single-fiber optical probe with a diameter of 100 μm was used for both delivery and detection of white light to and from the cervix tissue. Spectroscopic measurements were acquired from 95 ex vivo biopsy samples of 60 pap smear positive patients and normal cervix tissue from 10 patients after hysterectomy were used as a negative control group. Spectroscopic results of 95 cervix biopsy were compared to the histopathology of the biopsy samples. Sensitivity and specificity of the ELSSS system in the differentiation of HSIL and non-HSIL tissues are 87.5% and 45.6%, respectively, for the pap smear and colposcopy positive biopsy samples. The ELSSS system has the potential for use in real-time diagnosis of HSIL tissues as an adjunct to Papanicolaou test (pap smear) and colposcopy.
Infrared Radiation Induced Spin Photocurrents in GaN Low-Dimensional Structures (2006)

Infrared radiation spin photocurrents have been observed in GaN quantum well structures. Observed currents change sign upon reversing of radiation helicity demonstrating an existence of Rashba/Dresselhaus spin splitting of the conduction band in this new type of materials. Approvement of spin degeneracy removal in GaN structures allows to consider this material as a candidate for semiconductor spintronic.
Ten new microsatellite markers in cutlassfishTrichiurus lepturusderived from an enriched genomic library (2010)

Abstract Cutlassfish (Trichiurus lepturus Linnaeus 1758) is a commercially important fish in Korea. In recent years, the catch of cutlassfish in the coastal waters of Korea has significantly declined. Its genetic characterization has been little studied. To assist conservation and management efforts, we isolated and characterized 10 microsatellite loci using an enrichment method based on magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. To characterize each locus, 30 individuals from a natural T. lepturus population in the coastal waters of Jeju Island, Korea, were genotyped. All loci except two, KTh9B and KTh22A, were polymorphic, with an average of 14.3 alleles per locus (range, 10–22). The mean observed and expected heterozygosities were 0.80 (range, 0.50–0.97) and 0.82 (range, 0.68–0.95), respectively. A significant deviation from Hardy-Weinberg equilibrium was observed at three loci (KTh6B, KTh10, and KTh16). This high variability indicates that these microsatellites may be useful for high-resolution studies of population genetics.
Leptin regulation of aromatase activity in adipose stromal cells from regularly cycling women. (1999)

These data demonstrate that in approximately 30 percent of our subject population leptin was able to stimulate aromatase activity in adipose stromal cells at high concentrations. The elevated levels of aromatase activity may contribute to increase circulating estrogen levels in certain obese women and suggest that elevated leptin concentrations in obese women may cause locally elevated estrogen concentrations in the breast and thereby promote tumor formation.
Digital Implementation of Active Vibration Control of a Structure (2007)

An adaptive feedback algorithm is designed and implemented on a digital signal processor (DSP) system for the active vibration control (AVC) of a small structure. Real time experimental results show that the convergence speed and stability of the system are related to the exciting frequency, filter order, and the sampling frequency. The theoretical upper bound of the sampling frequency for a particular exciting frequency and filter order is compared with experiment, which is very important for designing practical digital AVC applications that control low-frequency vibration using low-cost data converters such as coder-decoder chips that only support high sampling frequencies.
Double Patterning Layout Decomposition for Simultaneous Conflict and Stitch Minimization (2010)

Double patterning lithography (DPL) is considered as a most likely solution for 32 nm/22 nm technology. In DPL, the layout patterns are decomposed into two masks (colors), and manufactured through two exposures and etch steps. If the spacing between two features (polygons) is less than certain minimum coloring distance, they have to be assigned opposite colors. However, a proper coloring is not always feasible because two neighboring patterns within the minimum distance may be in the same mask due to complex pattern configurations. In that case, a feature may need to be split into two parts to resolve the conflict, resulting in stitch insertion which causes yield loss due to overlay and line-end effect. While previous layout decomposition approaches perform coloring and splitting separately, in this paper, we propose a simultaneous conflict and stitch minimization algorithm with an integer linear programming (ILP) formulation. Since ILP is in class NP-hard, the algorithm includes three speed-up techniques: (1) grid merging; (2) independent component computation; and (3) layout partition. In addition, our algorithm can be extended to handle design rules such as overlap margin and minimum width for practical use as well as off-grid layout. Our approach can reduce 33% of stitches and remove conflicts by 87.6% compared with two phase greedy decomposition.
Issues related to gluten-free diet in coeliac disease (2008)

Gluten-free diet remains the cornerstone of therapy of coeliac disease. More studies addressing the need of gluten-free diet for cases of 'potential' coeliac disease are necessary, as well as studies linking the best available analytical detection of gluten to the clinical threshold of tolerance.
ChemInform Abstract: Studies on Glycosides. Part 10. An alternate Method for Highly Stereoselective Synthesis of Alkyl β‐D‐Glucopyranosides. (1993)

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.
Genetic Ancestry–dependent Differences in Breast Cancer–induced Field Defects in the Tumor-adjacent Normal Breast (2019)

Purpose: Genetic ancestry influences evolutionary pathways of cancers. However, whether ancestry influences cancer-induced field defects is unknown. The goal of this study was to utilize ancestry-mapped true normal breast tissues as controls to identify cancer-induced field defects in normal tissue adjacent to breast tumors (NATs) in women of African American (AA) and European (EA) ancestry. Experimental Design: A tissue microarray comprising breast tissues of ancestry-mapped 100 age-matched healthy women from the Komen Tissue Bank (KTB) at Indiana University (Indianapolis, IN) and tumor-NAT pairs from 100 women (300 samples total) was analyzed for the levels of ZEB1, an oncogenic transcription factor that is central to cell fate, mature luminal cell–enriched estrogen receptor alpha (ERα), GATA3, FOXA1, and for immune cell composition. Results: ZEB1+ cells, which were localized surrounding the ductal structures of the normal breast, were enriched in the KTB-normal of AA compared with KTB-normal of EA women. In contrast, in EA women, both NATs and tumors compared with KTB-normal contained higher levels of ZEB1+ cells. FOXA1 levels were lower in NATs compared with KTB-normal in AA but not in EA women. We also noted variations in the levels of GATA3, CD8+ T cells, PD1+ immune cells, and PDL1+ cell but not CD68+ macrophages in NATs of AA and EA women. ERα levels did not change in any of our analyses, pointing to the specificity of ancestry-dependent variations. Conclusions: Genetic ancestry–mapped tissues from healthy individuals are required for proper assessment and development of cancer-induced field defects as early cancer detection markers. This finding is significant in light of recent discoveries of influence of genetic ancestry on both normal biology and tumor evolution.
Movie and video scale-time equalization application to flicker reduction (2005)

Image flicker is a general film effect, which can be observed in videos as well as in old films, and consists of fast variations of the frame contrast and brightness. Reducing flicker of a sequence improves its visual quality and can be an essential first treatment before ulterior manipulations. This paper presents an axiomatic analysis of the problem, which leads to a global and fast method of "de-flicker," based on the scale-space theory. The stability of this process, called scale-time equalization, is ensured by the scale-time framework. Results on different sequences are given and show great visual improvement.
Problems and pitfalls in evaluating studies for pacing in heart failure. (1997)

Pacing therapy has been recently proposed as a new non-pharmacological approach to patients suffering from congestive heart failure refractory to medical therapy (refractory CHF), but the extention and the real benefit of this method remains to be defined. Although pacing therapy for refractory CHF has been restricted to patients in sinus rhythm presenting atrial, atrioventricular or interventricular conduction disturbances, considerable conflicting results have been published. The contradictory data is most likely due to large heterogeneity of the investigated study population (ie etiology of CHF, NYHA class, duration of follow-up, end-points of the study, etc.), to difference in study methology as well as in the site and modality of acute and chronic pacing. Although several empirical data indicates, at least in some individuals, major improvement in CHF symptoms by properly coordinating the atria and the ventricles thus reducing pre-systolic mitral and/or tricuspidal regurgitation or finally, prolonging the diastolic filling time, a lack of understanding of the mechanisms responsible for acute and chronic benefit persists. In evaluating pacemaker therapy as a new supportive treatment for CHF, the clinical investigator must consider that each study protocol embodies assumptions and methodological limitations and thus provides an incomplete analysis of potential benefit. Relying solely on noninvasive measures is risky due to problems of sensitivity and repeatability.