gebhart/patrepeval huggingface dataset:
Negative regulatory element in the mammary specific whey acidic protein promoter (1994)

Expression of the whey acidic protein (WAP) gene is tightly regulated in a tissue and developmental stage specific manner, in that the WAP gene is exclusively expressed in the mammary gland during pregnancy and lactation. Using both deletion and competition analyses, evidence is provided for the existence of a negative regulatory element (NRE) in the WAP promoter located between -413 and -93 with respect to the WAP transcriptional initiation site. This NRE dramatically decreases transcription from linked heterologous promoter-reporter gene constructs. The activity of NRE requires WAP promoter sequences that are 230 bp apart since subfragments of the NRE fail to inhibit transcription of adjoining reporter genes. Nuclear extracts from different cell types, in which the WAP gene is not active, contain a protein or complex that specifically interacts with the entire NRE but not with subfragments of it. The contact points between this protein (NRE binding factor [NBF]) and the NRE element have been partially determined. Mutation of the implicated nucleotides severely reduces the ability of NBF to bind, and such mutated promoter fragments fail to alleviate transcriptional repression in competition experiments. This suggests that NBF binding to the NRE is at least in part responsible for the negative regulation of the WAP promoter. Since NBF is not detectable in the lactating mammary gland, where the WAP gene is expressed, we speculate that it may be a determinant of the expression spectrum of the WAP gene.
Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines (2020)

As the interface between the gut microbiota and the mucosal immune system, there has been great interest in the maintenance of colonic epithelial integrity through mitochondrial oxidation of butyrate, a short-chain fatty acid produced by the gut microbiota. Herein, we showed that the intestinal epithelium could also oxidize long-chain fatty acids, and that luminally delivered acylcarnitines in bile could be consumed via apical absorption by the intestinal epithelium, resulting in mitochondrial oxidation. Finally, intestinal inflammation led to mitochondrial dysfunction in the apical domain of the surface epithelium that may reduce the consumption of fatty acids, contributing to higher concentrations of fecal acylcarnitines in murine Citrobacter rodentium-induced colitis and human inflammatory bowel disease. These results emphasized the importance of both the gut microbiota and the liver in the delivery of energy substrates for mitochondrial metabolism by the intestinal epithelium.
Supplementary Table 6-7 from Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer (2023)

&lt;p&gt;Supplementary Table 6, 7&lt;/p&gt;
A psychophysical model for predicting footwear fit (2009)

In this study, two psychophysical models are proposed to predict perceived footwear fit with consideration of foot-shoe dimensional differences in the toe, metatarsophalangeal joint (MPJ) and mid-foot regions. A third-degree polynomial was constructed to predict the preference rating on a 7-point Likert scale from perceived footwear fit (5-point scale).
3D models coding and morphing for efficient video compression (2004)

This paper presents new results in the field of video coding and compression using 3D information. Contrary to prior art in 3D model-based coding where 3D models have to be known, the 3D models are here automatically computed from the original video sequence. The camera parameters and the scene content are supposed unknown and we only assume a static scene viewed by a moving monocular camera. The video sequence is then processed on the fly. A stream of 3D models is extracted and compressed, using adapted computer vision and compression techniques. The visualization of the reconstructed video sequence uses an adapted morphing method. We finally show results obtained with the proposed compression scheme, compared with the H26L compression standard. We demonstrate the efficiency of our approach, especially in the field of very low bitrate coding.
Mitochondrial complementation occurs in rat hippocampal axons and supports the synaptic vesicle cycle. (2022)

Mitochondria exert powerful control over cellular physiology, contributing to ion homeostasis, energy production, and metabolite biosynthesis. Mitochondrial trafficking and function are vital to neurons, with organelle impairment or altered morphology observed in every neurodegenerative disorder studied. While this organelle and its biosynthetic products are critical for cellular function, decreased output and/or byproducts (e.g., free radicals), can be harmful, and organelle quality control (QC) mechanisms are required to maintain function and prevent a cascade of damage. Owing to its length and general lack of biosynthetic machinery, the axon is particularly sensitive to damage and there is little consensus regarding the details of mitochondrial QC mechanisms in this compartment. Here we investigate the basal, unstressed behavior of axonal mitochondria, focusing on mitochondrial trafficking and fusion to better understand potential QC mechanisms. We observed size and redox asymmetry of mitochondrial traffic in the axon, suggestive of an active QC mechanism. Importantly, we demonstrate, in detail, biochemical complementation of axonal mitochondria. Upon disruption of mitochondrial fusion, we observed an altered synaptic proteome, presynaptic calcium dyshomeostasis, decreased levels of exocytosis, and a reduction in synaptic vesicle recruitment from the reserve pool during extended stimulation. These results support an active mitochondrial trafficking and fusion related QC process that supports presynaptic physiology.
A Microfabricated Gas–Liquid Segmented Flow Reactor for High‐Temperature Synthesis: The Case of CdSe Quantum Dots (2005)

Monodisperse CdSe-Quantenpunkte (QDs) mit ausgezeichneten optischen Eigenschaften sind mit einem Gas-flüssig-segmentierten Fluss-Mikroreaktor erhältlich, der mehrere Temperaturzonen aufweist (siehe Bild; rot=beheizte, blau=gekühlte Quenching-Zone). Das bessere Mischen und die engen Verweilzeitverteilungen des segmentierten Flusses liefern QDs, die denen aus Einphasenoperationen überlegen sind.
Quantum Hall effect in Bernal stacked and twisted bilayer graphene grown on Cu by chemical vapor deposition (2012)

We examine the quantum Hall effect in bilayer graphene grown on Cu substrates by chemical vapor deposition. Spatially resolved Raman spectroscopy suggests a mixture of Bernal (A-B) stacked and rotationally faulted (twisted) domains. Magnetotransport measurements performed on bilayer domains with a wide 2D band reveal quantum Hall states (QHSs) at filling factors $\ensuremath{\nu}=4$, 8, 12, consistent with a Bernal stacked bilayer, while magnetotransport measurements in bilayer domains defined by a narrow 2D band show a superposition of QHSs of two independent monolayers. The analysis of the Shubnikov--de Haas oscillations measured in twisted graphene bilayers provides the carrier density in each layer as a function of the gate bias and the interlayer capacitance.
Supercapacitive operational mode in microbial fuel cell (2020)

Supercapacitive microbial fuel cells (SC-MFCs) are an emerging and promising field that has captured the attention of scientists in the past few years. This hybridization consists in the integration of supercapacitive features in the MFC electrodes to boost the performance output. The MFC anaerobic and aerobic enviroments induce self-polarization of the electrodes. The electrodes can be discharged galvanostatically and then self-recharged by the biotic/abiotic environments. During the discharge, two main phenomena named electrostatic and faradaic take place but the separation and quantification of the two contributes seems to be challenging. Galvanostatic discharges of SC-MFC produce at least one order of magnitude higher current/power compared with continuous operations, making it promising for pulsed type applications.
Optochemical Control of Biological Processes in Cells and Animals (2017)

Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
Quantification strategies for MRI (2013)

Quantification strategies have been a long-standing challenge since the early days of magnetic resonance molecular and cellular imaging. Quantitative imaging is desirable in the framework of comparative or follow-up studies in order to establish objective evidences of a specific target expression pertaining to a specific disease. Numerous strategies of increasing complexity have been proposed to address this need. In this chapter, common strategies related to quantitative molecular imaging for MRI are briefly reviewed and their respective outcomes are discussed. The focus is on relaxation contrast agents (CAs) that generate magnetic resonance contrast by affecting the proton relaxation times, and which are the most common kind of CAs used in MRI. Particular attention is paid to cutting-edge applications that enable local CA quantification as well as distinction of the bound/activated subpopulation of the CA.
Anodal tDCS to V1 blocks visual perceptual learning consolidation (2013)

Purpose and background. The purpose of this study was to examine the effects of visual cortex Transcranial Direct Current Stimulation (tDCS) on contrast sensitivity and consolidation of learning. Previous studies have demonstrated improvements in visual contrast sensitivity as a result of anodal tDCS, and decrements in sensitivity due to cathodal tDCS. Further, other studies have demonstrated polarity-specific effects of tDCS to motor cortices on consolidation of learned motor tasks. However, no studies have examined effects of tDCS on overnight consolidation of visual perceptual learning. Methods. Over two consecutive days, twenty-four healthy participants performed a contrast detection task. Each day included two sessions: a baseline measurement followed by measurements made during tDCS stimulation (active or sham). Participants were separated into three groups of eight participants each. One group received anodal stimulation to primary visual cortex (V1) on the first day, while another received cathodal stimulation; stimulation polarity was reversed for these groups on the second day. The third group received sham stimulation on both days. Results. We observed no improvements or decrements in contrast sensitivity relative to the same-day baseline during real tDCS, nor were there any measurable within-session learning trends. However, participants in the groups that received either cathodal or sham tDCS on Day 1 demonstrated significantly improved task performance on Day 2, while no such improvement was found for the participants who received anodal stimulation on Day 1. Discussion and conclusions. These results indicate that anodal tDCS blocked overnight consolidation of visual learning; possible mechanisms for this blocking include engagement of inhibitory homeostatic plasticity mechanisms, or alteration of the signal-to-noise ratio within stimulated cortex. To our knowledge this is the first study to demonstrate the effects of tDCS on consolidation of learning within the visual cortex. Meeting abstract presented at VSS 2013
BLADE TIP OPTIMIZATION FOR ROTARY BLOOD PUMP VIA CFD (2002)

In rotary blood pumps the flow between the blade tips and the housing has significant effects on pump efficiency and blood damage. In addition to shear, cavitation may occur at the tip gap, which may cause damage of the red blood cells. A 2-Dimensional incompressible turbulent flow simulation is performed in this study for a simplified impeller tip flow model of a rotary blood pump. The turbulence is accounted for by the k-epislon turbulence model and further modeled by sophisticated LES (Large Eddy Simulation). A very refined mesh, which is nearly perpendicular to the wall, is generated with the elliptic method. Cavitation simulation is also conducted with the free-surface flow modelling by the VOF (Volume of Fluid) method to investigate the blood cell damage. Extensive numerical studies are investigated for various blade trailing edge shapes corresponding to different gaps. The detailed velocity field, pressure distribution and shear stress field are predicted, and the hydraulic losses are estimated for different cases. As a result, both the trailing edge shape and the gap are optimized to increase efficiency and reduce blood damage.
Biocatalysis of Deracemization in 1,2-Diols (1998)

The fungus Corynosporium cassiicola DSM 62475 is shown to induce deracemization in certain 1,2-diols, including the synthetically important indane-1,2-diol, by enantioconvergent stereoinversion processes in which the recovered enantiomer is not a substrate for the dehydrogenase enzymes involved.
Reprise (2016)

Everyday tools and objects often need to be customized for an unplanned use or adapted for specific user, such as adding a bigger pull to a zipper or a larger grip for a pen. The advent of low-cost 3D printing offers the possibility to rapidly construct a wide range of such adaptations. However, while 3D printers are now affordable enough for even home use, the tools needed to design custom adaptations normally require skills that are beyond users with limited 3D modeling experience.
Antireflection Coating Design for Triple-Junction III–V/Ge High-Efficiency Solar Cells Using Low Absorption PECVD Silicon Nitride (2012)

The design of antireflection coating (ARC) for multijunction solar cells is challenging due to the broadband absorption and the need for current matching of each subcell. Silicon nitride, which is deposited by plasma-enhanced chemical vapor deposition (PECVD) using standard conditions, is widely used in the silicon wafer solar cell industry but typically suffers from absorption in the short-wavelength range. We propose the use of silicon nitride deposited by low-frequency PECVD (LFSiN) optimized for high refractive index and low optical absorption as a part of the ARC design for III–V/Ge triple-junction solar cells. This material can also act as a passivation/encapsulation coating. Simulations show that the SiO <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{{\rm 2}}$</tex> </formula> /LFSiN double-layer ARC can be very effective in reducing the reflection losses over the wavelength range of the limiting subcell for top subcell-limited, as well as middle subcell-limited, triple-junction solar cells. We also demonstrate that the structure’s performance is stable over expected variations in the layer parameters (thickness and refractive index) in the vicinity of the optimal values.
Role of PI3K/Akt and mTOR complexes in Th17 cell differentiation (2013)

Interleukin (IL)-17-producing helper T (Th17) cells serve as a Th subset involved in epithelial cell- and neutrophil-mediated immune responses against extracellular microbes and in the development of various autoimmune diseases. The differentiation of Th17 cells is controlled by a number of intracellular signaling cascades and a complex network of transcription factors. Recently, it has been shown that PI3K, Akt, and mammalian target of rapamycin (mTOR) complexes, such as mTORC1 and mTORC2, also positively regulate Th17 differentiation both in vivo and in vitro via multiple mechanisms; here, we review the current knowledge regarding the mechanisms through which these molecules enhance Th17 differentiation.
X-ray magnetic circular dichroism on Co monodispersive cluster assemblies (2000)

X-ray absorption near edge structure (XANES) spectra and x-ray magnetic circular dichroism (XMCD) spectra at the Co K edge have been measured for Co clusters with the mean diameter d= 6-13 nm. The spectral analysis indicates that the fcc phase is predominant for d= 6 nm, while the hcp phase gradually increases with increasing din agreement with the results of transmission electron microscopy. The 4p orbital moments of clusters tend to decrease in the smaller cluster, but the reduction is small compared with the case of the multilayers, suggesting the importance of surface effects of the Co cluster system.
Detection of an 85,000-dalton phosphoprotein in ts110 murine sarcoma virus-infected cells with antiserum against a v-mos peptide (1983)

We have used an antiserum directed against a synthetic v-mos peptide (anti-C3 serum) to screen ts110 murine sarcoma virus (MuSV)-infected cells for the presence of v-mos-encoded proteins. Anti-C3 serum specifically recognized an 85,000-dalton protein doublet (P85) from [35S]methionine-labeled ts110 MuSV-infected producer cells grown at 32 degrees C, the permissive temperature for transformation. The P85 doublet was also recognized by an antiserum directed against the viral gag protein p15. P85 was present but at 2- to 10-fold-lower levels in ts110 MuSV-infected producer cells grown at 39 degrees C, the restrictive temperature for transformation. The P85gag-mos fusion product was the only v-mos protein reproducibly detected in this ts110 MuSV-transformed cell line. Immunoprecipitation of 32P-labeled cells with anti-C3 serum revealed that the upper band of the P85 doublet is phosphorylated, containing mostly phosphoserine and some phosphothreonine. Cells acutely infected with ts110 MuSV contained slightly higher levels of P85 than did the ts110 MuSV-infected producer cell line. Anti-C3 serum specifically recognized a 33,000-dalton protein (p33) in the acutely infected cells labeled with [35S]methionine. p33 was present in trace amounts and may represent a previously unidentified ts110 MuSV-encoded v-mos protein.
Improvements in Light Yield and Energy Resolution by Li+ Codoping (Lu0.75Y0.25)3Al5O12:Pr3+ Single Crystal Scintillators (2018)

In this study, we demonstrated a drastic improvement in energy resolution of (Lu 0.75 Y 0.25 ) 3 Al 5 O 12 :Pr (LuYAG) single crystal scintillators from 4.8% to 4.1% at 662 keV upon Li + codoping, which is the best value ever reported in the class of oxide single crystal scintillators. Li + codoping can also significantly enhance its scintillation yield from 16 000 to 25 000 photons MeV −1 , but slightly prolong the scintillation decay time. As Li + codoping was found to have a negligible effect on the light yield non‐proportionality, we attributed the significant improvement in energy resolution to the reduced statistical variance in the number of photoelectrons produced in the photomultiplier tube ( R stat ).
Figure Legends from Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC) (2023)

&lt;p&gt;Supplementary Figure Legends for Figures S1 to S13&lt;/p&gt;
Catalytic dysregulation of SHP2 leading to Noonan syndromes affects platelet signaling and functions (2019)

Src homology 2 domain-containing phosphatase 2 (SHP2), encoded by the PTPN11 gene, is a ubiquitous protein tyrosine phosphatase that is a critical regulator of signal transduction. Germ line mutations in the PTPN11 gene responsible for catalytic gain or loss of function of SHP2 cause 2 disorders with multiple organ defects: Noonan syndrome (NS) and NS with multiple lentigines (NSML), respectively. Bleeding anomalies have been frequently reported in NS, but causes remain unclear. This study investigates platelet activation in patients with NS and NSML and in 2 mouse models carrying PTPN11 mutations responsible for these 2 syndromes. Platelets from NS mice and patients displayed a significant reduction in aggregation induced by low concentrations of GPVI and CLEC-2 agonists and a decrease in thrombus growth on a collagen surface under arterial shear stress. This was associated with deficiencies in GPVI and αIIbβ3 integrin signaling, platelet secretion, and thromboxane A2 generation. Similarly, arterial thrombus formation was significantly reduced in response to a local carotid injury in NS mice, associated with a significant increase in tail bleeding time. In contrast, NSML mouse platelets exhibited increased platelet activation after GPVI and CLEC-2 stimulation and enhanced platelet thrombotic phenotype on collagen matrix under shear stress. Blood samples from NSML patients also showed a shear stress-dependent elevation of platelet responses on collagen matrix. This study brings new insights into the understanding of SHP2 function in platelets, points to new thrombopathies linked to platelet signaling defects, and provides important information for the medical care of patients with NS in situations involving risk of bleeding.
Direct Detection of Transcription Factors in Cotyledons during Seedling Development Using Sensitive Silicon-Substrate Photonic Crystal Protein Arrays (2015)

Transcription factors control important gene networks, altering the expression of a wide variety of genes, including those of agronomic importance, despite often being expressed at low levels. Detecting transcription factor proteins is difficult, because current high-throughput methods may not be sensitive enough. One-dimensional, silicon-substrate photonic crystal (PC) arrays provide an alternative substrate for printing multiplexed protein microarrays that have greater sensitivity through an increased signal-to-noise ratio of the fluorescent signal compared with performing the same assay upon a traditional aminosilanized glass surface. As a model system to test proof of concept of the silicon-substrate PC arrays to directly detect rare proteins in crude plant extracts, we selected representatives of four different transcription factor families (zinc finger GATA, basic helix-loop-helix, BTF3/NAC [for basic transcription factor of the NAC family], and YABBY) that have increasing transcript levels during the stages of seedling cotyledon development. Antibodies to synthetic peptides representing the transcription factors were printed on both glass slides and silicon-substrate PC slides along with antibodies to abundant cotyledon proteins, seed lectin, and Kunitz trypsin inhibitor. The silicon-substrate PC arrays proved more sensitive than those performed on glass slides, detecting rare proteins that were below background on the glass slides. The zinc finger transcription factor was detected on the PC arrays in crude extracts of all stages of the seedling cotyledons, whereas YABBY seemed to be at the lower limit of their sensitivity. Interestingly, the basic helix-loop-helix and NAC proteins showed developmental profiles consistent with their transcript patterns, indicating proof of concept for detecting these low-abundance proteins in crude extracts.