gebhart/patrepeval huggingface dataset:
Alterations in Dendritic Spine Maturation and Neurite Development Mediated by FAM19A1 (2021)

Neurogenesis and functional brain activity require complex associations of inherently programmed secretory elements that are regulated precisely and temporally. Family with sequence similarity 19 A1 (FAM19A1) is a secreted protein primarily expressed in subsets of terminally differentiated neuronal precursor cells and fully mature neurons in specific brain substructures. Several recent studies have demonstrated the importance of FAM19A1 in brain physiology; however, additional information is needed to support its role in neuronal maturation and function. In this study, dendritic spine morphology in <i>Fam19a1</i>-ablated mice and neurite development during in vitro neurogenesis were examined to understand the putative role of FAM19A1 in neural integrity. Adult <i>Fam19a1</i>-deficient mice showed low dendritic spine density and maturity with reduced dendrite complexity compared to wild-type (WT) littermates. To further explore the effect of FAM19A1 on neuronal maturation, the neurite outgrowth pattern in primary neurons was analyzed in vitro with and without FAM19A1. In response to FAM19A1, WT primary neurons showed reduced neurite complexity, whereas <i>Fam19a1</i>-decifient primary neurons exhibited increased neurite arborization, which was reversed by supplementation with recombinant FAM19A1. Together, these findings suggest that FAM19A1 participates in dendritic spine development and neurite arborization.
Imaging radiation dose in breast radiotherapy by X-ray CT calibration of Cherenkov light (2020)

Imaging Cherenkov emission during radiation therapy cancer treatments can provide a real-time, non-contact sampling of the entire dose field. The emitted Cherenkov signal generated is proportional to deposited dose, however, it is affected by attenuation from the intrinsic tissue optical properties of the patient, which in breast, ranges from primarily adipose to fibroglandular tissue. Patients being treated with whole-breast X-ray radiotherapy (n = 13) were imaged for 108 total fractions, to establish correction factors from the linear relationships between Cherenkov light and CT number (HU). This study elucidates this relationship in vivo, and a correction factor approach is used to scale each image to improve the linear correlation between Cherenkov emission intensity and dose ([Formula: see text]). This study provides a major step towards direct quantitative radiation dose imaging in humans by utilizing non-contact camera sensing of Cherenkov emission during the radiation therapy treatment.
Highly-twisted states of light from a high quality factor photonic crystal ring (2023)

Twisted light with orbital angular momentum (OAM) has been extensively studied for applications in quantum and classical communications, microscopy, and optical micromanipulation. Ejecting high angular momentum states of a whispering gallery mode (WGM) microresonator through a grating-assisted mechanism provides a scalable, chip-integrated solution for OAM generation. However, demonstrated OAM microresonators have exhibited a much lower quality factor (Q) than conventional WGM resonators (by >100×), and an understanding of the limits on Q has been lacking. This is crucial given the importance of Q in enhancing light-matter interactions. Moreover, though high-OAM states are often desirable, the limits on what is achievable in a microresonator are not well understood. Here, we provide insight on these two questions, through understanding OAM from the perspective of mode coupling in a photonic crystal ring and linking it to coherent backscattering between counter-propagating WGMs. In addition to demonstrating high-Q (10<sup>5</sup> to 10<sup>6</sup>), a high estimated upper bound on OAM ejection efficiency (up to 90%), and high-OAM number (up to l = 60), our empirical model is supported by experiments and provides a quantitative explanation for the behavior of Q and the upper bound of OAM ejection efficiency with l. The state-of-the-art performance and understanding of microresonator OAM generation opens opportunities for OAM applications using chip-integrated technologies.
On the Hardness of Decoding the Gale-Berlekamp Code (2007)

The Gale-Berlekamp (in short, GB) code is the dual code of the binary product code in which the horizontal and vertical constituent codes are both the parity code. It is shown that the problem of deciding whether there is a codeword of the GB code within a prescribed distance from a given received word, is NP-complete. The problem remains hard (in a well-defined sense) even if the decoder is allowed unlimited preprocessing that depends only on the code length. While the intractability of maximum-likelihood decoding for specific codes has already been shown by Bruck and Naor and Lobstein, the result herein seems to be the first that shows hardness for familiar (or "natural") codes. In contrast, it is also shown that, with respect to any memoryless binary symmetric channel with crossover probability less than 1/2, maximum-likelihood decoding can be implemented in linear time for all error events except for a portion that occurs with vanishing probability.
COHERENT PROTEIN DYNAMICS EXPLORED AT FELIX (2004)

We have used extremely narrow (1-2 cm −1 ), high energy pump-probe time domain spectroscopy to probe the heterogenously broadened amide I band in several proteins. We find that the short wavelength side of the amide I band can give rise to very large (50%) bleaching signals, indicating a very long dephasing time of at least 20 ps to the internal amino acid amide I stretch band.
Thermal fatigue reliability analysis of redistributed flip chip assemblies (2002)

The thermo-mechanical reliability of redistributed flip chip assemblies is in particular determined by the plastic deformations of the solder joints and by the stresses in the photo-BCB redistribution layers. Finite element simulations and Coffin Manson based reliability models are used to compare the thermal cycling reliability of redistributed and standard flip chip assemblies. The existence of a photosensitive BCB redistribution layer on the chip influences the thermal fatigue of the flip chip assembly. The largest reliability improvement using redistributed chips is achieved by moving the solder joints from the perimeter to the interior of the die resulting in an area array flip chip.
160-Gb/s tunable dispersion slope compensator using a chirped fiber Bragg grating and a quadratic heater (2005)

We demonstrate a tunable dispersion slope compensator using a linearly chirped fiber Bragg grating and a thin-film heater that provides a variable quadratic temperature gradient along the grating. We achieved 2-10-ps/nm/sup 2/ compensation over 3 nm suitable for 160-Gb/s return-to-zero signals.
Micellar Rod (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
INTRANASAL ADMINISTRATION OF HUMAN PANCREATIC TUMOR GH-RELEASING FACTOR-40 STIMULATES GH RELEASE IN NORMAL MEN (1983)

Human pancreatic tumor GH releasing factor-40 (hpGRF-40) selectively stimulates GH secretion in normal men and in some adult patients with GH deficiency. As the latter finding suggests that some children with GH deficiency may benefit from therapy with hpGRF-40 or an analogue, we investigated the effect of hpGRF-40 administered intranasally on GH release. Six normal men were given hpGRF-40 (30 ug/kg; test day) or an equivalent volume of vehicle alone (control day) at 0900 h. Immunoreactive GH was measured in serum obtained at intervals between 0800-1200 h. Mean (+/- SEM) integrated serum levels of GH (ng/ml/h) prior to and following administration of vehicle were not different (1.27 +/- 0.57 vs 0.87 +/- 0.28; p = 0.54). However, following hpGRF-40 administration, GH levels increased significantly (0.53 +/- 0.03 vs 2.88 +/- 0.75; p = 0.022). Peak levels of serum GH were detected within 30 min following hpGRF-40. Except for mild burning of the nasal mucosa reported by one subject, no side effects were noted. We conclude that, if hpGRF-40 or an analogue is shown to be useful in the treatment of some children with GH deficiency, the intranasal route of administration may be utilized and will be more acceptable for chronic therapy than intravenous, intramuscular, or subcutaneous injection.
Graphitic‐Shell Encapsulation of Metal Electrocatalysts for Oxygen Evolution, Oxygen Reduction, and Hydrogen Evolution in Alkaline Solution (2019)

Abstract Developing highly efficient, cost effective, and environmentally friendly electrocatalysts for the oxygen evolution reaction (OER), oxygen reduction reaction (ORR), and hydrogen evolution reaction (HER) is of interest for sustainable and clean energy technologies, including metal–air batteries and fuel cells. In this work, the screening of electrocatalytic activities of a series of single metallic iron, cobalt, and nickel nanoparticles and their binary and ternary alloys encapsulated in a graphitic carbon shell toward the OER, ORR, and HER in alkaline media is reported. Synthesis of these compounds proceeds by a two‐step sol–gel and carbothermal reduction procedure. Various ex situ characterizations show that with harsh electrochemical activation, the graphitic shell undergoes an electrochemical exfoliation. The modified electronic properties of the remaining graphene layers prevent their exfoliation, protect the bulk of the metallic cores, and participate in the electrocatalysis. The amount of near‐surface, higher‐oxidation‐state metals in the as‐prepared samples increases with electrochemical cycling, indicating that some metallic nanoparticles are not adequately encased within the graphite shell. Such surface oxide species provide secondary active sites for the electrocatalytic activities. The Ni–Fe binary system gives the most promising results for the OER, and the Co–Fe binary system shows the most promise for the ORR and HER.
Treatment of severe sepsis with nanoparticulate cell-free DNA scavengers (2020)

Severe sepsis represents a common, expensive, and deadly health care issue with limited therapeutic options. Gaining insights into the inflammatory dysregulation that causes sepsis would help develop new therapeutic strategies against severe sepsis. In this study, we identified the crucial role of cell-free DNA (cfDNA) in the regulation of the Toll-like receptor 9-mediated proinflammatory pathway in severe sepsis progression. Hypothesizing that removing cfDNA would be beneficial for sepsis treatment, we used polyethylenimine (PEI) and synthesized PEI-functionalized, biodegradable mesoporous silica nanoparticles with different charge densities as cfDNA scavengers. These nucleic acid-binding nanoparticles (NABNs) showed superior performance compared with their nucleic acid-binding polymer counterparts on inhibition of cfDNA-induced inflammation and subsequent multiple organ injury caused by severe sepsis. Furthermore, NABNs exhibited enhanced accumulation and retention in the inflamed cecum, along with a more desirable in vivo safety profile. Together, our results revealed a key contribution of cfDNA in severe sepsis and shed a light on the development of NABN-based therapeutics for sepsis therapy, which currently remains intractable.
Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score (2000)

Two methods were proposed recently to derive energy parameters from known native protein conformations and corresponding sets of decoys. One is based on finding, by means of a perceptron learning scheme, energy parameters such that the native conformations have lower energies than the decoys. The second method maximizes the difference between the native energy and the average energy of the decoys, measured in terms of the width of the decoys' energy distribution (Z-score). Whereas the perceptron method is sensitive mainly to “outlier” (i.e., extremal) decoys, the Z-score optimization is governed by the high density regions in decoy-space. We compare the two methods by deriving contact energies for two very different sets of decoys: the first obtained for model lattice proteins and the second by threading. We find that the potentials derived by the two methods are of similar quality and fairly closely related. This finding indicates that standard, naturally occurring sets of decoys are distributed in a way that yields robust energy parameters (that are quite insensitive to the particular method used to derive them). The main practical implication of this finding is that it is not necessary to fine-tune the potential search method to the particular set of decoys used. Proteins 2000;41:192–201. © 2000 Wiley-Liss, Inc.
ChemInform Abstract: Click‐Chemistry Approaches to π‐Conjugated Polymers for Organic Electronics Applications (2016)

Abstract Review: [46 refs.
Cellular Response of Polyvalent Oligonucleotide−Gold Nanoparticle Conjugates (2010)

Nanoparticles are finding utility in myriad biotechnological applications, including gene regulation, intracellular imaging, and medical diagnostics. Thus, evaluating the biocompatibility of these nanomaterials is imperative. Here we use genome-wide expression profiling to study the biological response of HeLa cells to gold nanoparticles functionalized with nucleic acids. Our study finds that the biological response to gold nanoparticles stabilized by weakly bound surface ligands is significant (cells recognize and react to the presence of the particles), yet when these same nanoparticles are stably functionalized with covalently attached nucleic acids, the cell shows no measurable response. This finding is important for researchers studying and using nanomaterials in biological settings, as it demonstrates how slight changes in surface chemistry and particle stability can lead to significant differences in cellular responses.
Use of literature mining for early identification of emerging contaminants in freshwater resources (2019)

Abstract Chemical and microbial contaminants in the aquatic environment pose a potential threat to humans and to ecosystems. Humans may be exposed to contaminants in water resources when used for drinking water production, agriculture, aquaculture or recreation. Climatological, social and demographic changes, as well as the increasing sensitivity of analytical techniques, may result in the augmented detection of contaminants. Recent research has shown that it takes about 15 years from the time of the first scientific study mentioning the presence of a contaminant in the environment for the issue to peak in scientific attention and regulatory action. One possible factor influencing this lengthy period is that the first article becomes lost in the vast number of publications. In this study, we therefore developed a methodology using literature mining to identify the first scientific study which reports the presence of a contaminant in the aquatic environment. The developed semi-automated methodology enables health and environment agencies to inform policy makers about contaminants in the aquatic environment that could be significant for public and environmental health in national, international and river basin settings. The methodology thereby assists the proactive governance of emerging contaminants in the aquatic environment. This was illustrated by a retrospective analysis of the period of emergence in the Netherlands of: (1) perfluorooctanoic acid in surface water, and (2) biological industrial wastewater treatment systems as potential infection sources for Legionnaires´ disease.
Composite Anodes for Secondary Magnesium Ion Batteries Prepared via Electrodeposition of Nanostructured Bismuth on Carbon Nanotube Substrates (2014)

Magnesium-ion batteries are attractive in part due to the high environmental abundance and low cost of magnesium metal. Anode materials other than Mg metal can provide access to new electrochemistries in non-corrosive Mg2+ electrolytes. A cyclic voltammetric method for the preparation of bismuth (Bi) based anodes was developed by systematically exploring electrodeposition using a quartz crystal microbalance. Controlled deposition of Bi on carbon nanotubes substrates could be achieved, enabling the first electrochemical investigation of bismuth-carbon nanotube (Bi-CNT) composite electrodes. Quasi-reversible Mg electrochemistry of Bi-CNT composite electrodes in non-corrosive magnesium-based electrolyte was demonstrated, with an initial delivered capacity exceeding 180 mAh/g. While the initial capacities were high, significant capacity decreases were observed with repeated cycling, indicating that additional development is warranted to further optimize this system.
IL-2 ANITSENSE OLIGONUCLEOTIDES BLOCK IL-2 GENE EXPRESSION AND HEART ALLOGRAFT REJECTION (1999)

109 Purpose: Although cyclosporine and tacrolimus each block allograft rejection by inhibition of interleukin-2 (IL-2) gene expression, the agents are nephrotoxic. Gene therapy with antisense oligonucleotides (oligo) may proffer a more selective, non-nephrotoxic strategy to prevent rejection. We examined whether IL-2 antisense oligo designed to inhibit IL-2 gene expression in vitro prolongs the survival of heart allografts in vivo.Methods: Twenty phosphorothioate (PS) IL-2 antisense oligos were designed based on the random selection of sequences from the IL-2 cDNA. Mouse T cell lymphoma cells (TIB 155) stimulated with concanavalin A (ConA) were electroporated with individual IL-2 antisense oligos or with scrambled control oligos. The supernatants were collected after 24-hour culture and analyzed by ELISA spot assay for IL-2 protein production. After the cell pellets were harvested for total RNA isolation, a semi-quantitative RT-PCR method, utilizing a pair of IL-2-specific primers, was used to measure IL-2 mRNA expression. The most effective IL-2 PS oligos, modified by attachment of 2′-methoxyethyl (2′-ME) groups at the first five and last five nucleotides, were also tested in vitro. C3H (H-2k) mice transplanted with BALB/c (H-2d) heart grafts were injected i.v. by a 7-day osmotic pump with 5, 10, or 20 mg/kg IL-2 antisense or control oligo. Results: One of the twenty tested PS oligos, IP-17328 (2 μM), inhibited IL-2 protein production by 44.6% in comparison to untreated positive controls. The same sequence 2′-ME-modified oligo, IP-17359 (2 μM), inhibited IL-2 production by 89% (both p<0.001); scrambled oligos were ineffective. Similarly, in comparison to non-treated controls, both PS IP-17328 and PS/2′-ME-modified IP-17359 oligos significantly decreased the expression of IL-2 mRNA in TIB 155 cells. Untreated C3H mice rejected BALB/c heart allografts at a mean survival time (MST) of 8.2 ± 0.8 days. The 2′-ME-modified scrambled control (IP-11483) at doses of 5 mg/kg (8.7 ± 1.2 days), 10 mg/kg (9.3 ± 0.58 days), or 20 mg/kg (10.0 ± 0.8 days) did not affect allograft survivals (all NS). In contrast, 5, 10, or 20 mg/kg 2′-ME-modified IP-17359 IL-2 antisense oligo prolonged survivals to 11.8 ± 1.3 days (p<0.05), 14.4 ± 1.8 days (p<0.01), and 17.3 ± 3.6 days (p<0.001), respectively. Conclusion: The 2′-ME-modofied IL-2 antisense oligo blocks IL-2 gene expression and prolongs the survival of heart allografts.
A survey of non-manuka New Zealand honeys for antibacterial and antifungal activities (2004)

SUMMARYTo assess the variation in antibacterial and antifungal activity of non-manuka honeys, a study was undertaken using 179 unifloral, unpasteurized honey samples obtained from commercial beekeepers throughout New Zealand. The honeys were tested against Staphylococcus aureus and Candida albicans, Escherichia coli and the dermatophyte Trichophyton mentagrophytes using agar well diffusion, measurement of minimum inhibitory concentration and modified agar well diffusion methods, respectively. Of the 179 non-manuka honey samples assessed, none showed non-peroxide or anti-yeast antimicrobial activities. By contrast, 50% of the samples tested showed antibacterial activity against S. aureus, with activity ranging from 5.0–27.9% phenol equivalent. Approximately 30% of the samples tested showed antibacterial activity against E. coli; however honey concentrations required for inhibition were, with one exception, in excess of 19%. Similarly, 35% of samples showed antifungal activity although the levels of activity measured were low.
Effect of GTx-758, an ERα agonist, on serum-free testosterone and serum PSA in men with advanced prostate cancer. (2013)

104 Background: Androgen deprivation therapy (ADT) improves disease-free survival in men with advanced prostate cancer, but patients develop castrate resistant prostate cancer (CRPC); one of the causes of which is ineffective castration. Total serum testosterone (T) does not accurately predict prostatic levels of T. Further reduction of androgens in men with CRPC can result in improvement of survival. Herein we compare the effects GTx-758 an oral, selective estrogen receptor alpha (ERα) agonist versus leuprolide on total and free (unbound) serum T levels in men with advanced prostate cancer. Methods: In Phase II studies, men with advanced prostate cancer (n=164) received 1000 mg or 2000 mg GTx-758 daily or Lupron Depot (4 month), while men with CRPC (n=9) received 2000 mg GTx-758 daily. Serum concentrations of total T, free T, SHBG and PSA were determined at baseline and during treatment. Results: In ADT naïve advanced prostate cancer patients, 28 days of 1000 mg or 2000 mg daily GTx-758 or Lupron therapy castrated (T&lt;50ng/dL) 50, 31 and 100% of patients, reducing mean serum total T in castrated patients to 23±14, 19±9 and 14±7 ng/dL, respectively. However, treatment with 1000 mg or 2000 mg GTx-758 daily reduced mean free T levels to a greater extent (0.9±0.7 and 0.7±0.7 pg/mL, respectively) than Lupron (1.7±1.1 pg/mL). Changes in PSA at 28 days were more closely associated with the observed changes in free T, with reductions of 74, 72 and 56% for 1000 mg, 2000 mg doses of GTx-758 and Lupron, respectively. In CRPC patients, 2000 mg GTx-758 daily did not further reduce serum total T levels, but did result in free T reductions and PSA decreases from baseline following 15 days of therapy in all of the men maintained on ADT with LHRH agonists alone. Conclusions: Although GTx-758 and LHRH based ADT both reduce total serum T and PSA levels in ADT naïve advanced prostate cancer patients, free T was rapidly reduced to a greater degree in the GTx-758 treated patients. In men with CRPC, GTx-758 therapy resulted in significant reductions in free T and resultant PSA declines. The ability of GTx-758 to reduce free T provides a unique mechanism to treat men with advanced prostate cancer and CRPC. Clinical trial information: NCT01326312.
Transparent conducting oxides (2018)

We find that layered materials composed of various oxides of cations with s 2 electronic configuration, XY2O4, X = In or Sc, Y = Ga, Zn, Al, Cd and/or Mg, exhibit isotropic electron effective mass which can be obtained via averaging over those of the corresponding single-cation oxide constituents.This effect is due to a hybrid nature of the conduction band formed from the s-states of all cations and the oxygen p-states.Moreover, the observed insensitivity of the electron effective mass to the oxygen coordination and to the distortions in the cation-oxygen chains suggests that a similar behavior can be expected in the technologically important amorphous state.These findings significantly broaden the range of materials as efficient transparent conductor hosts.