gebhart/patrepeval huggingface dataset:
Principles of proteome allocation are revealed using proteomic data and genome-scale models (2016)

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and "hedging" against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σ<sup>S</sup>. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models.
Serum leptin concentrations, leptin mRNA expression, and food intake during the estrous cycle in rats (2013)

The aim of this study was to investigate food intake, serum leptin levels, and leptin mRNA expression during the sexual cycle in rats. Female Wistar-Imamichi rats aged 8-10 weeks were used in this experiment. Food intake was measured during the light and dark phases (light on at 07:00 and off at 19:00) of the 4-day estrous cycle in female rats. Serum leptin levels were measured by ELISA, and leptin mRNA expression levels were analyzed using real-time PCR on diestrous- and proestrous-stage rats. Our results revealed that during the sexual cycle, food intake was significantly higher in the dark phase compared with the light phase. Food intake in proestrous females was significantly lower in the light and dark phases compared with the other groups. Serum leptin concentrations were significantly higher in both phases in proestrous rats compared with diestrous rats. There was a significant increase in leptin mRNA expression in adipose tissue during the proestrous period compared with the diestrous period. These findings suggest that increased leptin mRNA expression and serum leptin levels, which are induced by estrogen during the proestrous stage, may play a role in regulating appetitive behavior.
Did Hans Memling Employ Optical Projections When Painting Flower Still-Life? (2005)

David Hockney has recently hypothesized that some early Renaissance painters employed optical devices such as concave mirrors to project images of a scene or part of a scene onto their supports, which they then traced or painted over. As one of many examples, he has claimed that Hans Memling (ca. 1440–1494) built an optical projector to create his Flower Still Life, specifically when rendering its carpet. The author's perspective analysis on the image of this carpet shows that, while there is a “break” in perspective consistent with refocusing or tipping of an optical projector, there are also other larger, more significant perspective deviations that are inconsistent with the use of a projector. After presenting a simple sensitivity analysis of these results and rebutting anticipated objections, the author concludes by rejecting the claim that optical projections were used in the creation of this still life.
L-Carnosin verhindert die Akkumulation von extrazellulärer Matrix unter HochGlucose über Modifikation des TGF-β Systems (2008)

Fragestellung: Die Vulnerabilität von Diabetikern eine diabetische Nephropathie (DN) zu entwickeln ist u.a. genetisch festgelegt. Wir konnten das Gen CNDP-1 (Serum Carnosinase) identifizieren, dessen Polymorphismus im Signalpeptid mit der Empfänglichkeit für DN assoziiert ist. Patienten, die homozygot für die kürzeste allelische Form (Mannheim Allel) des Gens sind, entwickeln seltener eine diabetische Nephropathie. Diese allelische Form geht mit niedriger Aktivität des Enzyms einher und führt somit zu höheren Carnosin (L-Carn) Spiegeln. Durch welchen Mechanismus L-Carn protektiv wirkt ist bisher nur unzureichend geklärt. Das Signalmolekül TGF-β spielt bei der Entwicklung der DN eine Schlüsselrolle. Es verursacht u.a die Akkumulation von extrazellulärer Matrix (EZM), einem der Merkmale der DN. In der gegenwärtigen Studie untersuchen wir, ob L-Carn in humanen Mesangialzellen (MC) Einfluss auf TGF-β und seine Signalwege hat.
Efficient synthesis and biological properties of the 2′-trifluoromethyl analogues of acyclic nucleosides and acyclic nucleoside phosphonates (2011)

Efficient and optimized procedure for the preparation of several acyclic nucleosides and acyclic nucleoside phosphonates substituted at the C-2′ position of the aliphatic part by the trifluoromethyl group is described. Trifluoromethyloxirane was found to be an excellent reagent for the introduction of the 1,1,1-trifluoropropan-2-ol moiety. Surprisingly, the next reaction of these 1,1,1-trifluoropropan-2-ols with the reagent for the introduction of the methylphosphonic residue afforded the desired phosphonates in very high yields and finally a novel simple and scalable procedure for the isolation of free phosphonic acids, after the reaction of dialkyl phosphonates with bromotrimethylsilane, was developed. Prepared compounds were evaluated for their biological properties, but none of the prepared phosphonic acids or acyclic nucleosides exhibits any antiviral, antiproliferative or anti-toxin activities.
Video compression and enhancement sensors using column-parallel architecture (2002)

We propose two novel image sensors, compression sensor and motion adaptive sensor, which have computational elements on the sensor plane. They make use of column-parallel architecture. The compression sensor can significantly reduce the amount of pixel data in order to overcome the communication bottle neck for high pixel rate imaging by making use of very fast analog processing on the sensor plane. We also propose motion adaptive sensor for enhancing images and wider dynamic range. The proposed sensor is able to control the suitable storage time in each pixel which results in no motion-blur and no saturation. It is expected to have a wide dynamic range, high temporal resolution in the moving area and high SNR in the static area.
Exploiting vulnerability to secure user privacy on a social networking site (2011)

As (one's) social network expands, a user's privacy protection goes beyond his privacy settings and becomes a social networking problem. In this research, we aim to address some critical issues related to privacy protection: Would the highest privacy settings guarantee a secure protection? Given the open nature of social networking sites, is it possible to manage one's privacy protection? With the diversity of one's social media friends, how can one figure out an effective approach to balance between vulnerability and privacy? We present a novel way to define a vulnerable friend from an individual user's perspective is dependent on whether or not the user's friends' privacy settings protect the friend and the individual's network of friends (which includes the user). As a single vulnerable friend in a user's social network might place all friends at risk, we resort to experiments and observe how much security an individual user can improve by unfriending a vulnerable friend. We also show how privacy weakens if newly accepted friends are unguarded or unprotected. This work provides a large-scale evaluation of new security and privacy indexes using a Facebook dataset. We present and discuss a new perspective for reasoning about social networking security. When a user accepts a new friend, the user should ensure that the new friend is not an increased security risk with the potential of negatively impacting the entire friend network. Additionally, by leveraging the indexes proposed and employing new strategies for unfriending vulnerable friends, it is possible to further improve security and privacy without changing the social networking site's existing architecture.
Arylamidrazones as Novel Corticotropin Releasing Factor Receptor Antagonists (2002)

The arylamidrazones have been found to be potent corticotropin releasing factor (CRF) receptor antagonists structurally distinct from previously reported CRF1 antagonists. Attempts to modify the arylamidrazone core suggested an important role for the anilino NH moiety. The right-hand-side 2-nitro feature in lead 1 could be replaced with substituents methyl, chloro, cyano, or trifluoromethyl with a 4- to 10-fold reduction in receptor binding. With appropriate left-hand-side modifications, this potency loss could be recovered.
S-DFP: shifted dynamic fixed point for quantized deep neural network training (2021)

Abstract Recent advances in deep neural networks have achieved higher accuracy with more complex models. Nevertheless, they require much longer training time. To reduce the training time, training methods using quantized weight, activation, and gradient have been proposed. Neural network calculation by integer format improves the energy efficiency of hardware for deep learning models. Therefore, training methods for deep neural networks with fixed point format have been proposed. However, the narrow data representation range of the fixed point format degrades neural network accuracy. In this work, we propose a new fixed point format named shifted dynamic fixed point (S-DFP) to prevent accuracy degradation in quantized neural networks training. S-DFP can change the data representation range of dynamic fixed point format by adding bias to the exponent. We evaluated the effectiveness of S-DFP for quantized neural network training on the ImageNet task using ResNet-34, ResNet-50, ResNet-101 and ResNet-152. For example, the accuracy of quantized ResNet-152 is improved from 76.6% with conventional 8-bit DFP to 77.6% with 8-bit S-DFP.
Changes in nasal, pharyngeal and salivary secretory IgA levels in patients with COVID-19 and the possibility of correction of their secretion using combined intranasal and oral administration of a pharmaceutical containing antigens of opportunistic microorganisms (2023)

As part of combination therapy, the bacteria-based immunostimulant agent Immunovac VP4 increases SIgA levels in the nasal and pharyngeal compartments and induces clinical improvement. Induced mucosal immunity is central to the prevention of respiratory infections, particularly in patients with post-COVID-19 syndrome.
Spatial sampling requirements for Received Signal Level measurements in cellular networks (2017)

A method for determination of a required spatial resolution in the collection of the Received Signal Level (RSL) is discussed. The method treats RSL measurements as a three dimensional surface that is sampled through the data collection process. Using 2-D Fourier analysis the cutoff frequency for the Fourier transform of the RSL surface is determined. The cutoff frequency and the spatial sampling resolution are related through Nyquist sampling criterion. The approach was experimentally verified in a typical suburban environment. The results show that spatial resolution requirement is between 50 and 100m.
In-vivo measurement of radio frequency electric fields in mice brain (2023)

With the development of novel technologies, radio frequency (RF) energy exposure is expanding at various wavelengths and power levels. These developments necessitate updated approaches of RF measurements in complex environments, particularly in live biological tissue. Accurate dosimetry of the absorbed RF electric fields (E-Fields) by the live tissue is the keystone of environmental health considerations for this type of ever-growing non-ionizing radiation energy. In this study, we introduce a technique for direct in-vivo measurement of electric fields in living tissue. Proof of principle in-vivo electric field measurements were conducted in rodent brains using Bismuth Silicon Oxide (BSO) crystals exposed to varying levels of RF energy. Electric field measurements were calibrated and verified using in-vivo temperature measurements using optical temperature fibers alongside electromagnetic field simulations of a transverse electromagnetic (TEM) cell.
Viscosity and Glass Transition Temperature of Aqueous Mixtures of Trehalose with Borax and Sodium Chloride (1999)

The glass transition temperature (Tg) and viscosity of aqueous trehalose and its mixtures with either NaCl or Na2B4O7 (borax) have been measured over a wide range of concentration. Borax and sodium chloride increase the viscosity and Tg‘ of aqueous trehalose. Although the presence of ionic charges may partly explain some of the observed effects, it is clear that ionic solutes that form complexes with trehalose lead to a greater increase in Tg. The viscosity of supercooled aqueous mixtures was measured at several temperatures, most of them above the so-called crossover temperature, Tg‘, where a change in the dynamics of relaxation processes is expected. The viscosities of all the binary and ternary mixtures exhibit the same temperature dependence when the temperature is scaled according to the Tg values; a change in the slope of the linearized WLF representation is observed at a temperature close to 1.2Tg. Above this temperature, a power law expression provides a similar description of the temperature dependence of viscosity as the WLF equation, the former having a physical justification in the mode coupling theory.
A fully integrated Hall sensor microsystem for contactless current measurement (2012)

Contactless current measurement based on Hall-effect sensors can be performed in either closed- or open- loop configuration. In this paper an open-loop sensor system with a current-mode output is described. The system measures the magnetic field induced around the current path targeting high linearity, accuracy and speed. As the accuracy of the Hall sensor microsystem is affected by temperature-dependent offset and sensitivity of the sensing element, system-level solutions are developed to minimize these effects. The full system integration represents a design challenge as both voltage and current references are directly involved in the sensitivity calibration and both contribute to the system sensitivity drift. The measurements show a sensitivity drift lower than 80ppm/°C, the offset drifts less than 300nT/°C and the non-linearity is less than ±0.08%. The effects of the varying external field on the calibration loop are analyzed and the theoretical prediction is validated by measurement.
T215. THE ANTIPSYCHOTIC ACTION OF HALOPERIDOL IN PSYCHOTIC-LIKE RATS REQUIRES PRESYNAPTIC VESICULAR ACCUMULATION (2020)

Abstract Background The therapeutic effects of antipsychotic drugs (APDs) are mainly attributed to their post synaptic inhibitory functions on the dopamine D2 receptor, which however, cannot explain the delayed onset of full therapeutic efficacy. It was previously shown that APDs accumulate in presynaptic vesicles during chronic treatment and are released like neurotransmitters in an activity-dependent manner triggering an auto-inhibitory feedback mechanism. Although closely mirroring therapeutic action onset, the functional consequence of the APD accumulation remained unclear. Here we show that the accumulation of the APD haloperidol (HAL) is required for full therapeutic action in psychotic-like rats. Methods We designed a haloperidol (HAL) analogue compound (HAL-F), which lacks the accumulation property of HAL, but retains its antagonist action at dopamine D2 receptors. Results By perfusing lysotracker fluorophore-stained cultured hippocampal neurons, we confirmed the accumulation of HAL and the non-accumulation of HAL-F. In an AMPH-hypersensitization psychosis-like model in rats, we found that subchronic i.c.v. delivered HAL, but not HAL-F attenuates psychotic-like behavior in rats in an amphetamine-induced hyperlocomotion test and the a pre-puls inhibition of an acustic startle response. Discussion These findings suggest the presynaptic accumulation of HAL as an essential prerequisite for its full antipsychotic action and may better explain the time course of APD action. Targeting accumulation properties of APDs may, thus, become a new strategy to improve APD action.
An epitaxially-grown charge modulation device (1997)

A charge modulation device (CMD) has been fabricated in a p-type epitaxial layer grown from the buried-channel silicon region of a charge-coupled device (CCD). Construction of the CMD directly above the CCD buried-channel and over the oxidized CCD transfer gates lowers the effective sense capacitance while providing isolation of the CMD source/drain regions. Responsivity values of 28 and 66 /spl mu/V/e for feedback and no feedback conditions, respectively, were measured dynamically on test devices. Input-referred noise values of approximately four electrons r.m.s. were calculated from noise spectral density measurements assuming a low-pass filter 3 dB cutoff frequency of 5 MHz and correlated double sampling.
Multisite Study of a Second Generation Whole Blood Rapid Assay for Cardiac Troponin T (1999)

We evaluated a second generation, qualitative, whole blood rapid assay for cardiac troponin T (cTnT), which employs a more cardio-specific troponin T mouse monoclonal capture antibody. Using quantitative cTnT enzyme-linked immunosorbent assay (ELISA) results as the benchmark for accuracy, we compared the performance of the second generation and the original whole blood rapid assays in 445 samples from patients with the following diagnoses, determined by medical record review: myocardial infarction, coronary bypass surgery, ischaemic heart disease, musculoskeletal disease, renal failure or other noncardiac conditions. Overall, concordance between the second generation cTnT Rapid Assay™ and the quantitative cTnT ELISA, compared using the McNemar test and a cut-off concentration of 0·1 μg/L, was in the range 76–94% for each patient group. Using a receiver operating characteristic plot, the cut-off for the second generation cTnT Rapid Assay was in the range 0·06–0·08 μg/L. We conclude that the second generation cTnT whole blood assay has a 2·5-fold lower analytical cut-off than the original rapid assay (0·2 μg/L) and may represent a more sensitive clinical tool for the rapid triage and risk stratification of cardiac patients.
Preparation of Macrocyclic Z-Enoates and (E,Z)- or (Z,E)-Dienoates through Catalytic Stereoselective Ring-Closing Metathesis (2014)

The first examples of catalyst-controlled stereoselective macrocyclic ring-closing metathesis reactions that generate Z-enoates as well as (E,Z)- or (Z,E)-dienoates are disclosed. Reactions promoted by 3.0-10 mol % of a Mo-based monoaryloxide pyrrolide complex proceed to completion within 2-6 h at room temperature. The desired macrocycles are formed in 79:21 to >98:2 Z/E selectivity; stereoisomerically pure products can be obtained in 43-75% yield after chromatography. Utility is demonstrated by application to a concise formal synthesis of the natural product (+)-aspicilin.
Think Locally, Act Globally: Federated Learning with Local and Global\n Representations (2020)

Federated learning is a method of training models on private data distributed\nover multiple devices. To keep device data private, the global model is trained\nby only communicating parameters and updates which poses scalability challenges\nfor large models. To this end, we propose a new federated learning algorithm\nthat jointly learns compact local representations on each device and a global\nmodel across all devices. As a result, the global model can be smaller since it\nonly operates on local representations, reducing the number of communicated\nparameters. Theoretically, we provide a generalization analysis which shows\nthat a combination of local and global models reduces both variance in the data\nas well as variance across device distributions. Empirically, we demonstrate\nthat local models enable communication-efficient training while retaining\nperformance. We also evaluate on the task of personalized mood prediction from\nreal-world mobile data where privacy is key. Finally, local models handle\nheterogeneous data from new devices, and learn fair representations that\nobfuscate protected attributes such as race, age, and gender.\n
Using advanced mass spectrometry techniques to fully characterize atmospheric organic carbon: current capabilities and remaining gaps (2017)

Organic compounds in the atmosphere vary widely in their molecular composition and chemical properties, so no single instrument can reasonably measure the entire range of ambient compounds. Over the past decade, a new generation of in situ, field-deployable mass spectrometers has dramatically improved our ability to detect, identify, and quantify these organic compounds, but no systematic approach has been developed to assess the extent to which currently available tools capture the entire space of chemical identity and properties that is expected in the atmosphere. Reduced-parameter frameworks that have been developed to describe atmospheric mixtures are exploited here to characterize the range of chemical properties accessed by a suite of instruments. Multiple chemical spaces (e.g. oxidation state of carbon vs. volatility, and oxygen number vs. carbon number) were populated with ions measured by several mass spectrometers, with gas- and particle-phase α-pinene oxidation products serving as the test mixture of organic compounds. Few gaps are observed in the coverage of the parameter spaces by the instruments employed in this work, though the full extent to which comprehensive measurement was achieved is difficult to assess due to uncertainty in the composition of the mixture. Overlaps between individual ions and regions in parameter space were identified, both between gas- and particle-phase measurements, and within each phase. These overlaps were conservatively found to account for little (<10%) of the measured mass. However, challenges in identifying overlaps and in accurately converting molecular formulas into chemical properties (such as volatility or reactivity) highlight a continued need to incorporate structural information into atmospheric measurements.
ChemInform Abstract: Protein Design: Template‐Assembled Synthetic Proteins (1991)

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.