gebhart/patrepeval huggingface dataset:
Sono-optogenetics facilitated by a circulation-delivered rechargeable light source for minimally invasive optogenetics (2019)

Optogenetics, which uses visible light to control the cells genetically modified with light-gated ion channels, is a powerful tool for precise deconstruction of neural circuitry with neuron-subtype specificity. However, due to limited tissue penetration of visible light, invasive craniotomy and intracranial implantation of tethered optical fibers are usually required for in vivo optogenetic modulation. Here we report mechanoluminescent nanoparticles that can act as local light sources in the brain when triggered by brain-penetrant focused ultrasound (FUS) through intact scalp and skull. Mechanoluminescent nanoparticles can be delivered into the blood circulation via i.v. injection, recharged by 400-nm photoexcitation light in superficial blood vessels during circulation, and turned on by FUS to emit 470-nm light repetitively in the intact brain for optogenetic stimulation. Unlike the conventional "outside-in" approaches of optogenetics with fiber implantation, our method provides an "inside-out" approach to deliver nanoscopic light emitters via the intrinsic circulatory system and switch them on and off at any time and location of interest in the brain without extravasation through a minimally invasive ultrasound interface.
The Art of Filling Protein Pockets Efficiently with Octahedral Metal Complexes (2012)

Better fit, less effort: An easy-to-synthesize ruthenium phthalimide complex (tan-colored carbon atoms in the picture) was designed to bind within the active site of the p21-activated kinase 1 in a novel fashion that differs from that of the previously established staurosporine-inspired metallopyridocarbazoles (gray-colored carbon atoms).
The amino acid sequence of adenylate kinase from Paracoccus denitrificans and its relationship to mitochondrial and microbial adenylate kinases (1989)

The complete amino acid sequence of adenylate kinase (MgATP + AMP in equilibrium MgADP + ADP) from Paracoccus denitrificans has been determined. 1. The S-[14C]carboxymethylated protein was cleaved with clostripain, cyanogen bromide and endoproteinase Lys-C; 18, 9 and 6 fragments, respectively, were analyzed. Some of these peptides were further degraded by trypsin, Staphylococcus aureus V8 protease and carboxypeptidases A and B. The fragments were separated by HPLC and sequenced with a gas-phase sequencer. 2. Sequencing the whole unblocked protein yielded the N-terminal region. The C-terminal residues were obtained by carboxypeptidase-Y digestion in agreement with the sequence of tryptic and cyanogen bromide peptides. 3. The final sequence shows 217 amino acids with Mr = 23,609 and contains one free cysteine and a disulfide bond. 4. The comparison of the P. denitrificans sequence with other known adenylate kinases shows highest similarity with the structurally known Escherichia coli enzyme (47%). The only and catalytically relevant His in the paracoccal enzyme is close to the site of binding of adenosine(5')pentaphospho(5')adenosine to E. coli adenylate kinase. The disulfide bridge is located in the 30-residue segment, which is indicative of the large variants and is absent in cytosolic adenylate kinase. The similarity to the mitochondrial intermembrane-space and matrix adenylate kinase isoenzymes is only 40% and 30%, respectively, while 39% of redidues are identical to those of yeast cytosolic adenylate kinase. Therefore, adenylate kinases do not support the hypothesis of a close relationship between Paracoccus and mitochondria.
Reduced-Order Modeling of Thermal Dynamics in District Energy Networks using Spectral Clustering (2022)

Simulation of thermal dynamics in city-scale district energy grids often becomes computationally prohibitive for long simulation runs. Current model order reduction methods offer limited interpretability with regards to the non-reduced system, and are not in general applicable for e.g., varying flow rates, multiple producers, or changing flow directions. This article presents a novel method based on graph theory that approximates the solution of an optimization problem that minimizes the local truncation error for heat transport in the grid. It is shown that the method can be used to reduce the thermal dynamic model of a city-scale energy grid, resulting in a coarser temporal and spatial resolution. The relative root mean square error was 2.3\% for the temperature in the evaluation scenario, comparing the reduced-order system with the non-reduced system at the instances of the coarser time-step.
Hydrogen sulfide (H2S) stimulates capsaicin‐sensitive primary afferent neurons in the rat urinary bladder (2004)

In the rat isolated urinary bladder, NaHS (30 microm-3 mm) and capsaicin (10 nm-3 microm) produced concentration-dependent contractile responses (pEC(50)=3.5+/-0.02 and 7.1+/-0.02, respectively) undergoing dramatic tachyphylaxis. In preparations in which sensory nerves were rendered desensitized (defunctionalized) by high-capsaicin (10 microm for 15 min) pretreatment, neither capsaicin itself nor NaHS produced any motor effect. NaHS-induced contractile effects were totally prevented by the simultaneous incubation with tachykinin NK(1) (GR 82334; 10 microm) and NK(2) (nepadutant; 0.3 microm) receptor-selective antagonists. Tetrodotoxin (1 microm) only partially reduced the response to NaHS. These results provide pharmacological evidence that H(2)S stimulates capsaicin-sensitive primary afferent nerve terminals, from which tachykinins are released to produce the observed contraction by activating NK(1) and NK(2) receptors. While the molecular site of action of H(2)S remains to be investigated, our discovery may have important physiological significance since H(2)S concentrations capable of stimulating sensory nerves overlap those occurring in mammalian tissues under normal conditions.
A role for NT-3 in the hyperinnervation of neonatally wounded skin (2012)

Neurotrophin-3 (NT-3) is a target-derived neurotrophic factor that regulates sensory neuronal survival and growth. Here we report that NT-3 plays a critical permissive role in cutaneous sensory nerve sprouting that contributes to pain and sensitivity following skin wounding in young animals. Sensory terminal sprouting in neonatally wounded dermis and epidermis is accompanied by increased NT-3 transcription, NT-3 protein levels, and NT-3 protein release 3-7 days post skin injury in newborn rats and mice. Functional blockade of NT-3 activity with specific antibodies greatly reduces sensory neurite outgrowth induced by wounded skin, but not by naïve skin, in dorsal root ganglion/skin co-cultures. The requirement for NT-3 for sensory terminal sprouting in vivo is confirmed by the absence of wound-induced hyperinnervation in heterozygous transgenic mice (NT-3(+/-)lacZ). We conclude that upregulation of NT-3 in neonatally wounded skin is a critical factor mediating the sensory nerve sprouting that underlies hypersensitivity and pain following skin injury.
Figure S4 from LAMC2 Regulates Key Transcriptional and Targetable Effectors to Support Pancreatic Cancer Growth (2023)

&lt;p&gt;Suppl. Figure 4. A. Correlation plot of mRNA expression levels of LAMC2 and AXL in the PDAC human data set from ICGC. B. Correlation plot of mRNA expression levels of LAMC2 and AXL in the PDAC human data set from TCGA.&lt;/p&gt;
Mixed Conductive Soft Solids by Electrostatically Driven Network Formation of a Conjugated Polyelectrolyte (2018)

A conjugated polyelectrolyte (poly[2,6-(4,4-bis-potassium butanylsulfonate-4H-cyclopenta-[2,1-b;3,4-b’]-dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)], PCPDTBT-SO3K) assembles into a novel, hierarchical hydrogel structure with all structural evidence indicating dominant electrostatic rather than aromatic or mesogen interactions. PCPDTBT-SO3K forms an entangled polymer mesh, where polymer chains are tied together by ionic cross-links, comprising microgel clusters that percolate to form a macroscopic three-dimensional network. With increasing temperature, ions gain mobility to move toward the exterior of the microgel clusters, dissolving the ionic cross-links and inhibiting network percolation through electrostatic repulsion. While π–π stacking interactions may be present in a disorganized fashion, no long-range π–π stacking is evident in X-ray scattering. Soft materials based on PCPDTBT-SO3K remain semiconducting and exhibit elevated ionic conductivity at the structural reorganization temperature.
Sensory neurons from N-syndecan-deficient mice are defective in survival (2008)

Extracellular matrix is a crucial regulator of development, plasticity and regeneration in the nervous system. We have now found that N-syndecan, the receptor for the extracellular matrix component heparin-binding growth-associated molecule, is required for survival of primary sensory neurons. We demonstrate massive cell death of cultured dorsal root ganglion (DRG) neurons from mice deficient in the N-syndecan gene as compared with wild-type controls. Importantly, this cell death could not be prevented by nerve growth factor - the neurotrophin, which activates multiple antiapoptotic cascades in DRG neurons. The survival deficiency was observed during first postnatal week. In contrast, DRG neurons from young adult N-syndecan knockout mice exhibited normal survival. This study identifies a completely new syndecan-dependent type of signaling that regulates cell death in neurons.
Heterogeneity of tibial plateau cartilage in response to a physiological compressive strain rate (2012)

Knowledge of the extent to which tibial plateau cartilage displays non-uniform mechanical topography under physiologically relevant loading conditions is critical to evaluating the role of biomechanics in knee osteoarthritis. Cartilage explants from 21 tibial plateau sites of eight non-osteoarthritic female cadaveric knees (age: 41-54; BMI: 14-20) were tested in unconfined compression at 100% strain/s. The elastic tangent modulus at 10% strain (E(10%) ) was calculated for each site and averaged over four geographic regions: not covered by meniscus (I); covered by meniscus-anterior (II); covered by meniscus-exterior (III); and covered by meniscus-posterior (IV). A repeated-measures mixed model analysis of variance was used to test for effects of plateau, region, and their interaction on E(10%) . Effect sizes were calculated for each region pair. E(10%) was significantly different (p<0.05) for all regional comparisons, except I-II and III-IV. The regional pattern of variation was consistent across individuals. Moderate to strong effect sizes were evident for regional comparisons other than I-II on the lateral side and III-IV on both sides. Healthy tibial cartilage exhibits significant mechanical heterogeneity that manifests in a common regional pattern across individuals. These findings provide a foundation for evaluating the biomechanical mechanisms of knee osteoarthritis.
Synthesis of [18F]phencyclidines for glutamate receptor mapping (1989)

Peer Reviewed
TRA-1-60-positive/CD45low cells found in the peripheral blood of prostate cancer patients with metastatic disease – A proof-of-concept study (2020)

The data suggest that metastatic prostate cancer patient have significant numbers of TRA+/CD45<sup>low</sup> cells which might represent a potential tool for diagnostic assessment in the future.
MMSE estimation of arrival time with application to ultrasonic signals (1993)

This paper deals with arrival time estimation of a narrow-band signal disturbed by white gaussian noise. In order to estimate the distance between a transmitting source and a reflecting target an estimator, based on the criterion of minimum mean square error (MMSE), is investigated. The MMSE-estimator is implemented in an experimental ultrasound pulse-echo system, and results of comparative simulations between the MAP-estimator and the MMSE-estimator are given. The results are compared to the theoretical Weiss-Weinstein lower bound. As expected, the MMSE-estimator has smaller mean square error than the MAP-estimator. For high SNRs, however, the mean square error obtained by the MAP-estimator manages to approach that of the MMSE-estimator. Other di#erences between the two estimators are revealed in additional experiments in which the range estimates are used to generate 3-dimensional surface pictures.
Random encounters and amoeba locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii (2022)

International audience
Patience is a virtue (2014)

The vast quantities of log-based data appearing in data centers has generated an interest in sorting almost-sorted datasets. We revisit the problem of sorting and merging data in main memory, and show that a long-forgotten technique called Patience Sort can, with some key modifications, be made competitive with today's best comparison-based sorting techniques for both random and almost sorted data. Patience sort consists of two phases: the creation of sorted runs, and the merging of these runs. Through a combination of algorithmic and architectural innovations, we dramatically improve Patience sort for both random and almost-ordered data. Of particular interest is a new technique called ping-pong merge for merging sorted runs in main memory. Together, these innovations produce an extremely fast sorting technique that we call P3 Sort (for Ping-Pong Patience+ Sort), which is competitive with or better than the popular implementations of the fastest comparison-based sort techniques of today. For example, our implementation of P3 sort is around 20% faster than GNU Quicksort on random data, and 20% to 4x faster than Timsort for almost sorted data. Finally, we investigate replacement selection sort in the context of single-pass sorting of logs with bounded disorder, and leverage P3 sort to improve replacement selection. Experiments show that our proposal, P3 replacement selection, significantly improves performance, with speedups of 3x to 20x over classical replacement selection.
Design, synthesis, and pr eliminary characterization of tyrosine-containing polyarylates: New biomaterials for medical applications (1994)

Five structurally related, aliphatic polyarylates were synthesized from tyrosine-derived diphenols and diacids. The diphenols were a homologous series of three desaminotyrosyl-tyrosine alkyl esters (ethyl, hexyl, octyl) which had previously been used in the synthesis of mechanically strong and tissue-compatible polycarbonates. The diacids (succinic acid, adipic acid, sebacic acid) were selected among compounds that were known to be of low systemic toxicity. By using different diacids as comonomers, the flexibility of the polymer backbone could be varied while the desaminotyrosyl-tyrosine alkyl esters provided pendent chains of various length. Some of the thermal and mechanical properties of the five polymers could be correlated to their chemical structure: the glass transition temperature decreased from 53 to 13 degrees C, and the tensile modulus (measured at room temperature) decreased from 1500 to about 3 MPa when the length of the aliphatic diacid in the polymer backbone and/or the length of the alkyl ester pendent chain was increased. The presence of an arylate bond in the polymer backbone introduced a hydrolytically labile linkage into the polymer structure. Under physiological conditions in vitro all polymers degraded: thin films retained only about 30-40% of their initial molecular weight (Mw) after 26 weeks of storage in phosphate buffer solutions (pH 7.4) at 37 degrees C. Release studies with p-nitroaniline as a model drug indicated that a diffusion controlled release process occurred. The rate of p-nitroaniline release could be correlated with the glass transition temperature of the polymer.
Environmental Availability of Uranium in an Acidic Plume at the Savannah River Site (2007)

Uranium partitioning in soils collected from an acid and U impacted sandy Coastal Plain aquifer at the Savannah River Site (SRS) was investigated. The influences of hydrologic regime (vadose zone or saturated zone), proximity to the source input (impacted or unimpacted soils), and soil weathering (field or laboratory‐spiked soils) on the environmental availability U were examined. Environmental availability (availability for groundwater transport) was operationally defined using a sequential extraction technique and was applied to vadose zone, saturated zone, and background soils. For saturated zone locations, matched porewater–soil sets of field samples were collected, and data generated from these samples were used to examine U partitioning under field conditions. Laboratory batch sorption studies of uranyl ion to background soils were conducted as a function of pH. Subsequently, the soil used in the sorption study was subjected to sequential extraction to investigate the environmental availability in laboratory spiked samples. Based on sequential extraction behavior of U‐impacted soils and background soils and the acidic plume chemistry, U concentrations in the first three sequential extraction steps [deionized water, CaCl 2 , and acetic acid/Ca(NO 3 ) 2 ] were operationally defined as available, and the final two extraction steps (crystalline iron oxide and residual extraction steps) were operationally defined as unavailable. Based on this operational definition, soils impacted by the acidic U plume exhibited a greater fraction of available and total U. Vadose‐zone soils had a smaller fraction of available U than corresponding saturated zone samples. Sequential extractions of U sorbed to background soils in a short‐term laboratory experiment showed greater U availability compared with field soils collected within the contaminant plume. Field‐derived K d values ranged from 0.1 to 300 L kg −1 and were highly correlated with porewater pH.
"Grip-that-there": An Investigation of Explicit and Implicit Task\n Allocation Techniques for Human-Robot Collaboration (2021)

In ad-hoc human-robot collaboration (HRC), humans and robots work on a task\nwithout pre-planning the robot's actions prior to execution; instead, task\nallocation occurs in real-time. However, prior research has largely focused on\ntask allocations that are pre-planned - there has not been a comprehensive\nexploration or evaluation of techniques where task allocation is adjusted in\nreal-time. Inspired by HCI research on territoriality and proxemics, we propose\na design space of novel task allocation techniques including both explicit\ntechniques, where the user maintains agency, and implicit techniques, where the\nefficiency of automation can be leveraged. The techniques were implemented and\nevaluated using a tabletop HRC simulation in VR. A 16-participant study, which\npresented variations of a collaborative block stacking task, showed that\nimplicit techniques enable efficient task completion and task parallelization,\nand should be augmented with explicit mechanisms to provide users with\nfine-grained control.\n
Absorption by water increases fluorescence image contrast of biological tissue in the shortwave infrared (2018)

Recent technology developments have expanded the wavelength window for biological fluorescence imaging into the shortwave infrared. We show here a mechanistic understanding of how drastic changes in fluorescence imaging contrast can arise from slight changes of imaging wavelength in the shortwave infrared. We demonstrate, in 3D tissue phantoms and in vivo in mice, that light absorption by water within biological tissue increases image contrast due to attenuation of background and highly scattered light. Wavelengths of strong tissue absorption have conventionally been avoided in fluorescence imaging to maximize photon penetration depth and photon collection, yet we demonstrate that imaging at the peak absorbance of water (near 1,450 nm) results in the highest image contrast in the shortwave infrared. Furthermore, we show, through microscopy of highly labeled ex vivo biological tissue, that the contrast improvement from water absorption enables resolution of deeper structures, resulting in a higher imaging penetration depth. We then illustrate these findings in a theoretical model. Our results suggest that the wavelength-dependent absorptivity of water is the dominant optical property contributing to image contrast, and is therefore crucial for determining the optimal imaging window in the infrared.
Educating future chip designers (1987)

The evolution of analog and digital integrated circuits from small elements to complex systems is clearly documented in the past issues of the DIGEST. Improvements in technology and CAD, raise some vital questions about the areas that future chip designers need to understand and the venue for this training. The answers depend strongly on the techniques and tools available for the chip designer: whether CAD will provide powerful compilers, freeing the designer to focus on system issues, or whether the demands of performance tuning debugging and normal design will force the designer to understand circuits. To discuss these issues, panelists will review opinions on the relative importance of the spectrum from device physics to system architecture.
Statement of World Aquatic Scientific Societies on the Need to Take Urgent Action Against Human-caused Climate Change, Based on Scientific Evidence [Dear Colleague Letter] (2020)

Dear Colleague Letter from the American Fisheries Society to fellow scientific societies, July 25, 2020, about the urgent need for responsive collective action to mitigate impending radical climate change. Includes the Statement of World Aquatic Scientific Societies on the Need to Take Urgent Action Against Human-Caused Climate Change, Based on Scientific Evidence, emphasizing the importance of aquatic ecosystems. Includes extensive citations and notes. "Water is the most important natural resource on Earth as it is vital for life. Aquatic ecosystems, freshwater or marine, provide multiple benefits to human society, such as provisioning of oxygen, food, drinking water, genetic resources; regulation of atmospheric composition and climate; water purification; storm buffering; mitigation of floods/droughts; recreation areas, and other purposes. Our existence and well-being depend on the health and well-functioning of aquatic ecosystems. People naturally distribute around water--approximately 40% of the world's population lives within 100 km (62 mi) of a coast. "The world’s aquatic resources are now under their greatest threat in human history. Human-caused climate change is accelerating the degradation of aquatic ecosystems and services they provide. Aquatic ecosystems are among the most affected worldwide, e.g. in case of freshwater ecosystems, a biodiversity decline of 83% was recorded only between 1970–2014, while up to 90% of coral reefs will disappear by mid-century, if the current trends continue."