gebhart/patrepeval huggingface dataset:
Biosensors Show the Pharmacokinetics of S-Ketamine in the Endoplasmic Reticulum (2019)

The target for the "rapid" (<24 h) antidepressant effects of S-ketamine is unknown, vitiating programs to rationally develop more effective rapid antidepressants. To describe a drug's target, one must first understand the compartments entered by the drug, at all levels-the organ, the cell, and the organelle. We have, therefore, developed molecular tools to measure the subcellular, organellar pharmacokinetics of S-ketamine. The tools are genetically encoded intensity-based S-ketamine-sensing fluorescent reporters, iSKetSnFR1 and iSKetSnFR2. In solution, these biosensors respond to S-ketamine with a sensitivity, S-slope = delta(F/F<sub>0</sub>)/(delta[S-ketamine]) of 0.23 and 1.9/μM, respectively. The iSKetSnFR2 construct allows measurements at <0.3 μM S-ketamine. The iSKetSnFR1 and iSKetSnFR2 biosensors display >100-fold selectivity over other ligands tested, including R-ketamine. We targeted each of the sensors to either the plasma membrane (PM) or the endoplasmic reticulum (ER). Measurements on these biosensors expressed in Neuro2a cells and in human dopaminergic neurons differentiated from induced pluripotent stem cells (iPSCs) show that S-ketamine enters the ER within a few seconds after appearing in the external solution near the PM, then leaves as rapidly after S-ketamine is removed from the extracellular solution. In cells, S-slopes for the ER and PM-targeted sensors differ by <2-fold, indicating that the ER [S-ketamine] is less than 2-fold different from the extracellular [S-ketamine]. Organelles represent potential compartments for the engagement of S-ketamine with its antidepressant target, and potential S-ketamine targets include organellar ion channels, receptors, and transporters.
Shape evolution of multiple interacting droplets in inkjet deposition (2015)

Purpose – The aim of this paper is to advance the understanding of the droplet deposition process to better predict and control the manufacturing results for ink-jet deposition. Design/methodology/approach – As material interface has both geometric and physical significance to manufacturing, the approach the authors take is to study the interface evolution during the material joining process in ink-jet deposition using a novel shape metric and a previously developed powerful simulation tool. This tool is an experimentally validated numerical solver based on the combination of the lattice Boltzmann method and the phase-field model that enabled efficient simulation of multiple-droplet interactions in three dimensions. Findings – The underlying physics of two-droplet interaction is carefully examined, which provides deep insights into the effects of the printing conditions on the interface evolution of multiple-droplet interaction. By studying line printing, it is found that increasing impact velocity or decreasing fluid viscosity can reduce manufacturing time. For array printing, the authors have found the issue of air bubble entrapment that can lead to voids in the manufactured parts. Research limitations/implications – The array of droplets impinges simultaneously, in contrast to most ink-jet printers. Sequential impingement of lines of droplet needs to be studied. Also, impingement on non-planar surfaces has not been investigated yet, but is important for additive manufacturing. Finally, it is recognized that the droplet hardening mechanisms need to be incorporated in the simulation tool to predict and control the final shape and size of the arbitrary features and manufacturing time for ink-jet deposition. Practical implications – The research findings in this paper imply opportunities for optimization of printing conditions and print head design. Furthermore, if precise droplet control can be achieved, it may be possible to eliminate the need for leveling roller in the current commercial printers to save machine and manufacturing cost. Originality/value – This work represents one of the first attempts for a systematic study of the interface dynamics of multiple-droplet interaction in ink-jet deposition enabled by the novel shape metric proposed in the paper and a previously developed numerical solver. The findings in this paper advanced the understanding of the droplet deposition process. The physics-based approach of analyzing the simulation results of the interface dynamics provides deep insights into how to predict and control the manufacturing relevant outcomes, and optimization of the deposition parameters is made possible under the same framework.
LiNi0.8Fe0.1Al0.1O2 as a Cobalt-Free Cathode Material with High Capacity and High Capability for Lithium-Ion Batteries (2022)

Obtaining cathode materials with high capacity and cycle stability is one of the main challenges regarding the success of electric vehicle technologies. However, most of the widely used materials with these properties involve the use of toxic and expensive cobalt as the active material. To overcome this challenge, this work proposes a novel cobalt-free cathode material, synthesized for the first time using a solid-state reaction, whose general formula is LiNi0.8Fe0.1Al0.1O2 (NFA). This class of materials offers high capacity and reduces the battery costs by removing cobalt, without jeopardizing the structural stability and safety of the NFAs. The morphology and the structural properties of the obtained NFA cathode material were characterized using different techniques, e.g., scanning electronic microscopy, X-ray diffraction, X-ray fluorescence, and infrared and Raman spectroscopies. The electrochemical activity and diffusivity of the Li-ion during lithium removal and its insertion into the bulk of the NFA cathode demonstrated high-yield specific capacities of ≈180 mAh g−1 at 0.1C, along with a reasonable rate capability and cycling stability, with a capacity retention of ≈99.6% after 100 charge/discharge cycles at a rate of C/2, and whose operando X-ray diffraction experiments have been used to study the crystallographic transitions during the lithiation–delithiation reaction.
Tumor-infiltrating nerves create an electro-physiologically active microenvironment and contribute to treatment resistance (2020)

ABSTRACT Patients with densely innervated tumors do poorly as compared to those with sparsely innervated disease. Why some tumors heavily recruit nerves while others do not, remains unknown as does the functional contribution of tumor-infiltrating nerves to cancer. Moreover, while patients receive chemotherapeutic treatment, whether these drugs affect nerve recruitment has not been tested. Using a murine model of ovarian cancer, we show that tumor-infiltrating sensory nerves potentiate tumor growth, decrease survival, and contribute to treatment resistance. Furthermore, matched patient samples show significantly increased tumor innervation following chemotherapy. In vitro analysis of tumor-released extracellular vesicles (sEVs) shows they harbor neurite outgrowth activity. These data suggest that chemotherapy may alter sEV cargo, endowing it with robust nerve recruiting capacity.
OFDM mobile packet transmission system with multiuser detection and metric combining ARQ (2005)

This paper proposes an OFDM mobile packet transmission scheme that employs both non-linear multiuser detection (MUD) and automatic repeat request (ARQ) with metric combining for improving throughput performance. The scheme identifies users by detecting user identification (ID) symbols located at the head of a packet, and can separate the packets by MUD when the packets collide. Furthermore, it forces the respective transmitters to retransmit the same packets so as to reproduce the collision if the cyclic redundancy check (CRC) detects some errors, and employs metric combining for decreasing the number of retransmissions. In order to verify the throughput performance, computer simulations are conducted. The simulation results show that the proposed scheme can achieve much greater throughput than the conventional ones.
Chip to Wafer Hybrid Bonding with Cu Interconnect: High Volume Manufacturing Process Compatibility Study (2019)

Solder reflow technology is volume manufacturing ready to an interconnect pitch of about 60um for two main reasons. Solder has the ability to compensate for height differences among the interconnects on a die or package through the melting and re-solidification process. The second reason is that pick-and-place tools combined with mass reflow process offer an extremely high throughput and low cost process. Unfortunately, this technology appears to be limited to a minimum pitch of 40 μm. Therefore, the industry is searching for a solid state bonding technology to enable further pitch scaling. The candidate technology should have the following key attributes: 1) a mechanism to precisely control the metal height variation to prevent open joints, 2) high assembly throughput; 3) low temperature for certain applications; and 4) a pathway to future generations of pitch scaling. DBI <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Ultra is a die to wafer (D2W) Direct Bond Interconnect (DBI <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> ) technology that utilizes D2W low temperature hybrid bonding to achieve all of the attributes listed above. It offers precise Cu height variation control through the chemical mechanical polishing (CMP) process. With an extremely efficient pick and place process for assembly, it has a throughput comparable to the solder flip chip reflow process. A spontaneous dielectric-to-dielectric bond at room temperature with a metal-to-metal connection (usually Cu-to-Cu bond) by a low temperature batch annealing process (150-300°C) is attractive for heterogeneous integration. Ultimately, it can scale to a sub-micron pitch. In the past two years, significant progress has been made in the DBI Ultra technology. A bonding process with high volume production throughput has been demonstrated with electrical test yield above 90% with a daisy chain structure that covers 50 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of bonding area. The bonded parts also showed superior reliability performance in temperature cycling, high temperature storage and autoclave testing. This paper demonstrates the low temperature anneal capability of the technology and presents the detailed comparative analysis of the technology against the competing solid Cu-to-Cu thermal compression bonding (Cu-Cu TCB) process.
7-ENOB resolution photonic analog-to-digital conversion of narrowband microwave signals at 40 GHz (2008)

An optical sub-sampling downconversion receiver for analog-to-digital conversion of narrowband high-frequency microwave signals is demonstrated. The measured SNDR in 2-MHz bandwidth at 40-GHz carrier frequency is 44 dB corresponding to 7-ENOB resolution.
Remote sensing of blood oxygenation using red-eye pupil reflection (2019)

We describe a new method to remotely and non-invasively sense the oxygen saturation of choroidal blood. The methodology provides a proxy for remote sensing of cerebral and systemic blood oxygenation. We demonstrate the technique at short range but it has potential for systemic oximetry at large standoff ranges.
Enhanced Photoresponse in Few-Layer SnS<sub>2</sub> Field-Effect Transistors Modified with Methylammonium Lead Iodide Perovskite (2023)

We demonstrate that decoration with methylammonium lead iodide perovskite (MAPbI3) nanoparticles is an efficient approach to engineer strong visible light photoresponse in electronic devices based on two-dimensional (2D) materials with limited optical absorptivity. This approach was demonstrated using 2D SnS2, a promising electronic material with a band gap of about 2.3 eV and poor absorption in the visible range of spectrum. Field-effect transistors based on pristine 2D SnS2 show an n-type transport with high on–off ratios. Decoration with isolated MAPbI3 nanoparticles qualitatively retains the transfer characteristics of the devices but dramatically increases their photoresponse in the entire visible range of the spectrum. In particular, the photoresponse of the MAPbI3-decorated devices to the red light is entirely engineered by the perovskite modification of SnS2, which by itself does not absorb in the red region of the spectrum. The MAPbI3-decorated SnS2 devices exhibit stable, reproducible photoswitching over numerous cycles with response times of no longer than 12 ms. An analysis of a MAPbI3–SnS2 heterostructure by Kelvin probe force microscopy resulted in an energy level diagram suggesting a transfer of the photoexcited electrons in MAPbI3 to the conduction band of the n-type SnS2 channel. The photoresponse characteristics of the perovskite-modified SnS2 devices were shown to be consistent with the intrinsic optical properties of MAPbI3. The described perovskite decoration approach should be applicable to engineering photoresponse in a variety of other devices based on 2D electronic materials with low optical absorptivity.
Nuclear Dynamics and Electronic Eﬀects of Hydrogen on Solid Surfaces (2016)

Hydrogen is involved in a variety of chemical processes on surfaces. While hydrogen exhibits vibrational and rotational dynamics in its adsorption state, it in some cases undergoes diffusion into the substrate as well as on the surface, and participates in chemical reactions. Furthermore, hydrogen exchanges an electron with surfaces having a significant effect on the surface electronic structure. In this personal account, we review our recent studies on surface nuclear dynamics of hydrogen, hydrogen transport across surfaces, catalytic hydrogenation/isotope exchange reactions, and charge transfer between the surface and hydrogen by using a depth-resolved technique of nuclear reaction analysis and a quantum-state-selective detection of resonance enhanced multiphoton ionization in combination with surface science techniques. As a future prospect, we refer to ultraslow μ spin rotation spectroscopy for a direct probe of the hydrogen charge state at surfaces.
Neonatal and Pediatric Candidemia: Results From Population-Based Active Laboratory Surveillance in Four US Locations, 2009–2015 (2018)

The incidence of candidemia among neonates and infants declined after 2009 but remained stable from 2012 to 2015. Antifungal drug resistance is uncommon. Reasons for the lack of recent declines in neonatal and infant candidemia deserve further exploration. In this article, we describe the epidemiology of candidemia in children in the United States and on the basis of data collected as part of US Centers for Disease Control and Prevention active population-based surveillance. Trends in incidence, clinical characteristics, species distribution, and resistance rates are presented.
Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer (2010)

On the basis of integrated transcriptome analysis, we show that not all transcriptional start site clusters (TSCs) in the intergenic regions (iTSCs) have the same properties; thus, it is possible to discriminate the iTSCs that are likely to have biological relevance from the other noise-level iTSCs. We used a total of 251,933,381 short-read sequence tags generated from various types of transcriptome analyses in order to characterize 6039 iTSCs, which have significant expression levels. We analyzed and found that 23% of these iTSCs were located in the proximal regions of the RefSeq genes. These RefSeq-linked iTSCs showed similar expression patterns with the neighboring RefSeq genes, had widely fluctuating transcription start sites and lacked ordered nucleosome positioning. These iTSCs seemed not to form independent transcriptional units, simply representing the by-products of the neighboring RefSeq genes, in spite of their significant expression levels. Similar features were also observed for the TSCs located in the antisense regions of the RefSeq genes. Furthermore, for the remaining iTSCs that were not associated with any RefSeq genes, we demonstrate that integrative interpretation of the transcriptome data provides essential information to specify their biological functions in the hypoxic responses of the cells.
Predictive Pathogen Biology: Genome-Based Prediction of Pathogenic Potential and Countermeasures Targets (2018)

Bacterial pathogens have numerous processes by which their genomic DNA is acquired or rearranged as part of their normal physiology (e.g., exchange of plasmids through conjugation) or by bacteriophage that parasitize bacteria and often insert into the bacterial genome as prophages. These processes occur with relatively high probability/frequency, and may lead to sudden changes in virulence, as new genetic material is added to the chromosome, or structural changes in the chromosome affect gene expression. We set out to devise methods to measure the rates of these processes in bacteria using next generation DNA sequencing. Using very deep sequencing on genomes we had assembled, using library preparation methods and bioinformatics tools designed to help find mobile elements and signs of their insertion, we were able to find numerous examples of attempted novel genome arrangements, revealing data that can be used to calculate rates of different mechanisms of genome change.
A randomized trial of megestrol acetate with or without premarin in the treatment of potentially responsive metastatic breast cancer: A study of the Eastern Cooperative Oncology Group (E2185) (1996)

Sequential treatment with premarin and megestrol acetate is not superior to treatment with megace alone in potentially hormone responsive patients with advanced breast cancer.
Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron (2007)

There was an error published in Development134, 801-811.On p. 802, Engleka et al.(2005) was mistakenly cited. The text should have read `We crossed Pax3-cretg/+;N2f/+ (floxed Notch2)/+males (Li et al., 2000) to N2f/f females to obtain Pax3-cretg/+;N2f/f embryos or pups'.The authors apologise to readers for this mistake.
Telomerase activity, MIB‐1, PCNA, HPV 16 and p53 as diagnostic markers for cervical intraepithelial neoplasia<sup>Note</sup> (2001)

The present investigation evaluated the relationship between dysplasia of the uterine cervix and telomerase activity, expression of p53, MIB-1 and PCNA. Telomerase activity was measured on cervical cytobrush material from 126 women suspected of having dysplasia and 61 controls using the telomeric repeat amplification protocol. Immunohistochemistry was used to detect the tumor suppressor protein p53 and cell proliferation, the latter by MIB-1 and PCNA expression. Infection with human papillomavirus 16 was detected by PCR amplification and Southern blot hybridization of DNA extracted from the same brush material. Positive telomerase activity was found in 5 of 43 (11.6%) normal samples, 12 of 57 (21.1%) samples with inflammation or koilocytosis, 7 of 17 (41.2%) CIN 1 (cervical intraepithelial neoplasia, grade 1), 8 of 20 (40.0%) CIN 2, and 25 of 42 (59.5%) CIN 3/ CIS. Telomerase activity was significantly related to the level of dysplasia (p<0.001) and proliferation measured by MIB-1 (p=0.019), but not to the level of PCNA (p=0.445), HPV 16 status (p=0.098) or staining for p53 (p=0.271). Dysplasia was also related to PCNA, MIB1, p53, and presence of HPV 16. A sequential increase in the examined parameters, paralleling the progression of abnormality, was observed. PCNA and telomerase showed an increase in CIN 1, MIB-1 and HPV16 in CIN 2, and finally p53 in CIN 3/CIS.
Long-term outcomes of osilodrostat in Cushing's disease: LINC 3 study extension (2022)

Abstract Objective To investigate the long-term efficacy and tolerability of osilodrostat, a potent oral 11β-hydroxylase inhibitor, for treating Cushing's disease (CD). Design/methods A total of 137 adults with CD and mean 24-h urinary free cortisol (mUFC) &amp;gt; 1.5 × upper limit of normal (ULN) received osilodrostat (starting dose 2 mg bid; maximum 30 mg bid) during the prospective, Phase III, 48-week LINC 3 (NCT02180217) core study. Patients benefiting from osilodrostat at week 48 could enter the optional extension (ending when all patients had received ≥ 72 weeks of treatment or discontinued). Efficacy and safety were assessed for all enrolled patients from the core study baseline. Results Median osilodrostat exposure from the core study baseline to study end was 130 weeks (range 1–245) and median average dose was 7.4 mg/day (range 0.8–46.6). The reduction in mean mUFC achieved during the core was maintained during the extension and remained ≤ ULN. Of 106 patients, 86 (81%) patients who entered the extension had mUFC ≤ ULN at week 72. Improvements in cardiovascular/metabolic-related parameters, physical manifestations of hypercortisolism (fat pads, central obesity, rubor, striae, and hirsutism in females), and quality of life in the core study were also maintained or improved further during the extension. No new safety signals were reported; 15/137 (10.9%) and 12/106 (11.3%) patients discontinued for adverse events during the core and extension, respectively. Mean testosterone in females decreased towards baseline levels during the extension. Conclusions Data from this large, multicentre trial show that long-term treatment with osilodrostat sustains cortisol normalisation alongside clinical benefits in most patients with CD and is well tolerated.
Physicochemical Characterization of Two Protic Hydroxyethylammonium Carboxylate Ionic Liquids in Water and Their Mixture (2022)

A systematic study on the physicochemical properties of two protic ionic liquids (ILs) {2-hydroxyethylammonium acetate ([Mea][Ac]) and 2-hydroxyethylammonium hexanoate ([Mea][Hex])} and their mixtures with water was performed. The density and viscosity were assessed across the entire range of aqueous dilutions between 278 and 393 K. The conductivities, water activities, and surface tension of the binary systems in water were also assessed, and the influence of anions was evaluated. Differential scanning calorimetry (DSC), Fourier transform infrared (FTIR), and 1H and 13C nuclear magnetic resonance (NMR) techniques were used to study the systems at different IL compositions. The excess molar volumes (VE) and thermal expansion coefficients were calculated, with negative values for VE across the entire concentration range. Density data were fitted to a polynomial for density prediction, function of temperature, and concentration, with the average deviation percentage not exceeding 0.63%. The viscosities of the binary systems were studied considering six different models and were better predicted by the model of Herráez et al. at IL concentrations higher than 0.25 mole fraction. The systems containing [Hex]− exhibited higher water activities and lower conductivity and surface tension. All studied systems exhibited a glass transition event, which varied according to the IL composition. The FTIR and NMR analysis confirmed the distinct molecular arrangement of [Mea][Ac] and [Mea][Hex] systems.
Anterior temporal lobectomy with amygdalohippocampectomy for mesial temporal sclerosis: predictors of long-term seizure control (2013)

Seizure freedom of nearly 90% can be achieved with ATL-AH in properly selected patients with MTS and concordant preoperative studies. The low number of poor outcomes and exclusion of multistage patients limit the statistical power to determine preoperative variables that predict failure. Strong Wada memory lateralization was associated with excellent long-term outcome and adds important localization information to structural and neurophysiological data in predicting outcome after ATL-AH for MTS.