gebhart/patrepeval huggingface dataset:
Evaluation of Anisotropic Biaxial Stress in Si1-X Ge x /Ge Mesa-Structure by Oil-Immersion Raman Spectroscopy (2015)

Si 1- x Ge x is one of the prospective materials for the next-generation transistors due to its high carrier mobility, especially for high Ge concentration Si 1- x Ge x . Inducing strain in the Si 1- x Ge x leads to transistor performance improvement, however it is difficult to evaluate strain induced in the channel region because the strained Si 1- x Ge x channel may be scaled down to nanosize and relaxed complicatedly. We adopted oil-immersion Raman spectroscopy to evaluate the stress in the Si 1- x Ge x nanostructure. In this technique, the anisotropic biaxial stress state in the Si 1- x Ge x nanostructure can be evaluated. As a result, the nanostructure size dependence of the biaxial stress states in the Si 1- x Ge x mesa structure on the Ge substrates was obtained, which was confirmed for the Si 1- x Ge x with 76, 85, 92% Ge concentrations.
A comparative analysis of recombinant Fab and full‐length antibody production in Chinese hamster ovary cells (2021)

Monoclonal antibodies are the leading class of biopharmaceuticals in terms of numbers approved for therapeutic purposes. Antigen-binding fragments (Fab) are also used as biotherapeutics and used widely in research applications. The dominant expression systems for full-length antibodies are mammalian cell-based, whereas for Fab molecules the preference has been an expression in bacterial systems. However, advances in CHO and downstream technologies make mammalian systems an equally viable option for small- and large-scale Fab production. Using a panel of full-length IgG antibodies and their corresponding Fab pair with different antigen specificities, we investigated the impact of the IgG and Fab molecule format on production from Chinese hamster ovary (CHO) cells and assessed the cellular capability to process and produce these formats. The full-length antibody format resulted in the recovery of fewer mini-pools posttransfection when compared to the corresponding Fab fragment format that could be interpreted as indicative of a greater overall burden on cells. Antibody-producing cell pools that did recover were subsequently able to achieve higher volumetric protein yields (mg/L) and specific productivity than the corresponding Fab pools. Importantly, when the actual molecules produced per cell of a given format was considered (as opposed to mass), CHO cells produced a greater number of Fab molecules per cell than obtained with the corresponding IgG, suggesting that cells were more efficient at making the smaller Fab molecule. Analysis of cell pools showed that gene copy number was not correlated to the subsequent protein production. The amount of mRNA correlated with secreted Fab production but not IgG, whereby posttranscriptional processes act to limit antibody production. In summary, we provide the first comparative description of how full-length IgG and Fab antibody formats impact on the outcomes of a cell line construction process and identify potential limitations in their production that could be targeted for engineering increases in the efficiency in the manufacture of these recombinant antibody formats.
Antimicrobial Blue Light Inactivation of Gram-Negative Pathogens in Biofilms: In Vitro and In Vivo Studies (2016)

aBL has antimicrobial activity in biofilms ofA. baumannii and P. aeruginosa and is a potential therapeutic approach for biofilm-related infections.
ΔNp63 transcriptionally regulates ATM to control p53 Serine-15 phosphorylation (2010)

Germline p63 point mutations are associated with a range of ectodermal developmental disorders, and targeted p63 deletion in the skin causes premature ageing. The DeltaNp63alpha-ATM-p53 damage-response pathway may therefore function in epithelial development, carcinogenesis and the ageing processes.
A lower bound on the probability of decoding error over a BSC channel (2002)

For a code C of length n and size |C, we estimate the error probability of the maximum likelihood decoding. In this paper we address this problem for the binary symmetric channel (BSC) defined by its transition probability p. We discuss the case when we know the distance distribution of the code. We also assume that the code is regular in the sense that the distribution of the distances from a codeword to other codewords does not depend on the choice of the initial codeword.
Doping a TiO2 Photoanode with Nb5+ to Enhance Transparency and Charge Collection Efficiency in Dye-Sensitized Solar Cells (2010)

The optoelectronic properties of our benchmark nanocrystalline anatase TiO2 photoanode were modified by means of aliovalent doping with Nb5+. Even for a low doping level, the charge collection efficiency can be noticeably improved as a result of a higher electron lifetime when using the heteroleptic Ru(+II) C101 dye. Particularly of interest, while this was only possible by adding additives in the electrolyte, the doping concentration allows tuning of the energetic of the trap state distribution; parameter particularly crucial for the injection rate and charge collection efficiency. This improvement brings the power conversion efficiency of a 7 μm thick transparent photoanode to 8.7% while intensifying the electrode’s transparency.
Making a Correct Diagnosis of Glaucoma: Data From the EMGT (2019)

A diagnosis made applying strict criteria to 2 initial visual field tests, supported by optic disc findings if visual field findings were borderline, was almost always correct.
Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system (2017)

Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to <i>in vitro</i> protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 <i>E. coli</i> HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3<sup>rd</sup> of that measured using the RTS 100 <i>E. coli</i> HY S30 system. Both of the 2 batch systems suffer from low ribosome recycling efficiency when translating proteins from 82 k<sub>D</sub> to 224 k<sub>D</sub>. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ∼1.5 to ∼2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.
<title>Engineering and physical concepts of the wave permittivity</title> (1994)

The physical concept and the mathematical formalism of the wave permittivity are introduced and analyzed through the Maxwell stress tensor theory. The concept of the wave permittivity may be proved extremely useful in order to characterize propagation parameters, in terms of stored energy associated with delayed wave formation phenomena such as partial standing waves, which in turn give rise to rapid precursors observable in the time domain. Such phenomena has been observed in air, in the radiating zone, or indispersive media such as waveguides. Engineering applications related to the concept of the wave permittivity are outlined.
Performance and leakage optimization in carbon and fluorine co-implanted pMOSFETs (2008)

In this work we demonstrate that effective tailoring of the extension junction in MOS devices with C co-implantation must be accompanied by re-optimization of the deep HDD (HDD+) profile and spacer dimensions. In this way junction and doping profile optimization can successfully improve short channel effect (SCE) control, without penalty in performance or junction leakage.
Differential involvement of N‐type calcium channels in transmitter release from vasoconstrictor and vasodilator neurons (2004)

1. The effects of calcium channel blockers on co-transmission from different populations of autonomic vasomotor neurons were studied on isolated segments of uterine artery and vena cava from guinea-pigs. 2. Sympathetic, noradrenergic contractions of the uterine artery (produced by 200 pulses at 1 or 10 Hz; 600 pulses at 20 Hz) were abolished by the N-type calcium channel blocker omega-conotoxin (CTX) GVIA at 1-10 nm. 3. Biphasic sympathetic contractions of the vena cava (600 pulses at 20 Hz) mediated by noradrenaline and neuropeptide Y were abolished by 10 nm CTX GVIA. 4. Neurogenic relaxations of the uterine artery (200 pulses at 10 Hz) mediated by neuronal nitric oxide and neuropeptides were reduced <50% by CTX GVIA 10-100 nm. 5. Capsaicin (3 microm) did not affect the CTX GVIA-sensitive or CTX GVIA-resistant neurogenic relaxations of the uterine artery. 6. The novel N-type blocker CTX CVID (100-300 nm), P/Q-type blockers agatoxin IVA (10-100 nm) or CTX CVIB (100 nm), the L-type blocker nifedipine (10 microm) or the 'R-type' blocker SNX-482 (100 nm), all failed to reduce CTX GVIA-resistant relaxations. The T-type channel blocker NiCl(2) (100-300 microm) reduced but did not abolish the remaining neurogenic dilations. 7. Release of different neurotransmitters from the same autonomic vasomotor axon depends on similar subtypes of calcium channels. N-type channels are responsible for transmitter release from vasoconstrictor neurons innervating a muscular artery and capacitance vein, but only partly mediate release of nitric oxide and neuropeptides from pelvic vasodilator neurons.
Preventing Fragmentation for Client Initiated Connections in the Session Initiation Protocol (SIP) (2007)

There is cases when a Session Initiation Protocol (SIP) client can
initiate a bidirectional UDP stream or a TCP connection to a SIP
server but the SIP server cannot do the same in the other direction.
The server can reuse the existing bidirectional UDP stream or TCP
connection but cannot use a TCP connection if the client chose to use
a bidirectional UDP stream. This document described a method to force
the client to initiate a TCP connection to the server.
Effects of an Agricultural Drainwater Bypass on Fishes Inhabiting the Grassland Water District and the Lower San Joaquin River, California (2001)

The Grassland Bypass Project, which began operation in September 1996, was conceived as a means of diverting brackish selenium-contaminated agricultural drainwater away from canals and sloughs needed for transporting irrigation water to wetlands within the Grassland Water District (the Grasslands), Merced County, California. The seleniferous drainwater is now routed into the San Luis Drain for conveyance to North Mud Slough and eventual disposal in the San Joaquin River. The purpose of this study was to determine the extent to which the Grassland Bypass Project has affected fishes in sloughs and other surface waters within and downstream from the Grasslands. During September–October 1997, 9,795 fish representing 25 species were captured at 13 sampling sites. Although several species exhibited restricted spatial distributions, association analysis and cluster analysis failed to identify more than one fish species assemblage inhabiting the various sites. However, seleniferous drainwater from the San Luis Drain has influenced selenium concentrations in whole fish within North Mud Slough and the San Joaquin River. The highest concentrations of selenium (12–23 μg/g, dry weight basis) were measured in green sunfish Lepomis cyanellus from the San Luis Drain where seleniferous drainwater is most concentrated, whereas the second highest concentrations occurred in green sunfish (7.6–17 μg/g) and bluegills Lepomis macrochirus (14–18 μg/g) from North Mud Slough immediately downstream from the drain. Although there was some variation, fish in the San Joaquin River generally contained higher body burdens of selenium when captured immediately below the mouth of North Mud Slough (3.1–4.8 μg/g for green sunfish, 3.7–5.0 μg/g for bluegills) than when captured upstream from the mouth (0.67–3.3 μg/g for green sunfish, 0.59–3.7 μg/g for bluegills). Waterborne selenium was the single most important predictor of selenium concentrations in green sunfish and bluegills, as judged by results from multiple-regression analyses. Among bluegills, water temperature also contributed to the prediction of selenium body burdens.
(Invited) Development of Single-Walled Carbon Nanotube-Based Optical Sensors Via Data Analytics (2020)

The photoluminescence of single-walled carbon nanotubes (SWCNTs) offers unique advantages for the development of biological sensors, including the potential to sensitize emission to many classes of analytes. Methods to selectively transduce the local concentration of an analyte via an optical signal often involves the attachment of existing molecular recognition elements to the nanotube surface, or the development of selectivities by high-throughput screening or selection techniques. Due to the existence of several mechanisms of optical modulation of SWCNTs, as well as multiple carbon nanotube species with differing bandgaps, and the increasing number of excipients and polymers that can be used for colloidal suspension and non-covalent functionalization, new methods in data analytics, sometimes dubbed ‘molecular perceptron’, can be used to facilitate selective recognition of bioanalytes to detect and process multi-parametric spectroscopic fingerprints. These methods will be discussed for the detection of single and multiplexed analytes.
Development of EUV resists in homogenous CO 2 solutions using CO 2 compatible salts (CCS): a kinetic view of dissolution of conventional resists in supercritical CO 2 (2006)

A novel method for the development of standard EUV photoresists in CO<sub>2</sub> using CO<sub>2</sub> compatible salts (CCS) is described and examined using a quartz crystal microbalance (QCM) technique in CO<sub>2</sub>. The fundamental steps of this development process are proposed to be 1) photoresist modification via CCS interaction with Bronsted acid groups in the resist; and 2) dissolution of the modified resist into CO<sub>2</sub>. Removal rates of non-exposed photoresist from the quartz crystal can be studied in real time under a variety of conditions to help elucidate the kinetics and mechanism of the CCS development process. A series of runs from 35 to 50 C at the same CO<sub>2</sub> density showed a strong effect of temperature on the development rate. In the presence of a large excess of CCS, the kinetics of dissolution appear to be zero order. An Arrhenius plot generated by this data gave an activation energy of 79.0 kJ/mol. The zero order kinetics of dissolution was confirmed with a series of runs at various CCS concentration that showed insignificant rate effects. Dynamic flow of the CCS solution in the QCM cell gave ~50% increase in rate of resist removal relative to the standard conditions using static CCS solution. The indication from the three sets of QCM experiments described here is that dissolution of the CCS modified polymer is the slow step in CCS development.
Attosecond physics at the nanoscale (2016)

Recently two emerging areas of research, attosecond and nanoscale physics, have started to come together. Attosecond physics deals with phenomena occurring when ultrashort laser pulses, with duration on the femto- and sub-femtosecond time scales, interact with atoms, molecules or solids. The laser-induced electron dynamics occurs natively on a timescale down to a few hundred or even tens of attoseconds, which is comparable with the optical field. On the other hand, the second branch involves the manipulation and engineering of mesoscopic systems, such as solids, metals and dielectrics, with nanometric precision. Although nano-engineering is a vast and well-established research field on its own, the merger with intense laser physics is relatively recent. In this article we present a comprehensive experimental and theoretical overview of physics that takes place when short and intense laser pulses interact with nanosystems, such as metallic and dielectric nanostructures. In particular we elucidate how the spatially inhomogeneous laser induced fields at a nanometer scale modify the laser-driven electron dynamics. Consequently, this has important impact on pivotal processes such as ATI and HHG. The deep understanding of the coupled dynamics between these spatially inhomogeneous fields and matter configures a promising way to new avenues of research and applications. Thanks to the maturity that attosecond physics has reached, together with the tremendous advance in material engineering and manipulation techniques, the age of atto-nano physics has begun, but it is in the initial stage. We present thus some of the open questions, challenges and prospects for experimental confirmation of theoretical predictions, as well as experiments aimed at characterizing the induced fields and the unique electron dynamics initiated by them with high temporal and spatial resolution.
Safety of Bedside Portable Low-Field Brain MRI in ECMO Patients Supported on Intra-Aortic Balloon Pump (2022)

(1) Background: Fifty percent of patients supported on veno-arterial extracorporeal membrane oxygenation (VA-ECMO) are concurrently supported with an intra-aortic balloon pump (IABP). Acute brain injury (ABI) is a devastating complication related to ECMO and IABP use. The standard of care for ABI diagnosis requires transport to a head CT (HCT) scanner. Recent data suggest that point-of-care (POC) magnetic resonance imaging (MRI) is safe and may be effective in diagnosing ABI in ECMO patients; however, no data exist in patients supported on ECMO with an IABP. We report pre-clinical safety data and a case series to evaluate the safety and feasibility of POC brain MRI in ECMO patients supported with IABP. (2) Methods: Prior to patient use, ex vivo testing with an IABP catheter within the Swoop<sup>®</sup> Portable MRI (0.064 T) System™ was conducted. After IRB approval, clinical testing was performed for the safety and feasibility of early ABI detection. (3) Results: No deflection force was measured with a 7.5 French Maquet Linear IABP within the 0.064 T field. Three adult ECMO patients (average age: 40 years; 67% female) supported with IABP completed four POC brain MRI exams (median exam time: 30 min). Multiple signal abnormalities were detected on the POC brain MRI, corresponding to HCT results. (4) Conclusions: Our preliminary results suggest that adult VA-ECMO patients with IABP support can be safely imaged with low-field POC brain MRI in the intensive care unit, allowing for the early and bedside imaging of patients.
Different classes of genomic inserts contribute to human antibody diversity (2022)

Recombination of antibody genes in B cells can involve distant genomic loci and contribute a foreign antigen-binding element to form hybrid antibodies with broad reactivity for <i>Plasmodium falciparum</i>. So far, antibodies containing the extracellular domain of the LAIR1 and LILRB1 receptors represent unique examples of cross-chromosomal antibody diversification. Here, we devise a technique to profile non-VDJ elements from distant genes in antibody transcripts. Independent of the preexposure of donors to malaria parasites, non-VDJ inserts were detected in 80% of individuals at frequencies of 1 in 10<sup>4</sup> to 10<sup>5</sup> B cells. We detected insertions in heavy, but not in light chain or T cell receptor transcripts. We classify the insertions into four types depending on the insert origin and destination: 1) mitochondrial and 2) nuclear DNA inserts integrated at VDJ junctions; 3) inserts originating from telomere proximal genes; and 4) fragile sites incorporated between J-to-constant junctions. The latter class of inserts was exclusively found in memory and in in vitro activated B cells, while all other classes were already detected in naïve B cells. More than 10% of inserts preserved the reading frame, including transcripts with signs of antigen-driven affinity maturation. Collectively, our study unravels a mechanism of antibody diversification that is layered on the classical V(D)J and switch recombination.
Production of the novel C-C chemokine MCP-4 by airway cells and comparison of its biological activity to other C-C chemokines. (1997)

Monocyte chemotactic protein-4 (MCP-4) is a newly identified C-C chemokine with potent eosinophil chemoattractant properties. We describe studies of its biological activity in vitro to induce chemotaxis of peripheral blood eosinophils and to induce histamine release from IL-3-primed peripheral blood basophils. MCP-4 and eotaxin caused a similar rise in eosinophil intracytoplasmic Ca2+ and complete cross-desensitization. MCP-4 also abolished the eosinophil Ca2+ response to MCP-3 and partially desensitized the response to macrophage inflammatory protein-1alpha. MCP-4 activated cell migration via either CCR2b or CCR3 in mouse lymphoma cells transfected with these chemokine receptors. MCP-4 inhibited binding of 125I-eotaxin to eosinophils and CCR3-transfected cells and inhibited 125I-MCP-1 binding to CCR2b-transfectants. MCP-4 mRNA was found in cells collected in bronchoalveolar lavage of asthmatic and nonasthmatic subjects and was prominently expressed in human lung and heart. MCP-4 mRNA was expressed in several human bronchial epithelial cell lines after cytokine stimulation. Pretreatment of BEAS-2B epithelial cells with the glucocorticoid budesonide inhibited MCP-4 mRNA expression. These features make MCP-4 a candidate for playing a role in eosinophil recruitment during allergic respiratory diseases.
Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin (2019)

MHC-I peptides are intracellular-cleaved peptides, usually 8-11 amino acids in length, which are presented on the cell surface and facilitate CD8<sup>+</sup> T cell responses. Despite the appreciation of CD8<sup>+</sup> T-cell antitumor immune responses toward improvement in patient outcomes, the MHC-I peptide ligands that facilitate the response are poorly described. Along these same lines, although many therapies have been recognized for their ability to reinvigorate antitumor CD8<sup>+</sup> T-cell responses, whether these therapies alter the MHC-I peptide repertoire has not been fully assessed due to the lack of quantitative strategies. We develop a multiplexing platform for screening therapy-induced MHC-I ligands by employing tandem mass tags (TMTs). We applied this approach to measuring responses to doxorubicin, which is known to promote antitumor CD8<sup>+</sup> T-cell responses during its therapeutic administration in cancer patients. Using both in vitro and in vivo systems, we show successful relative quantitation of MHC-I ligands using TMT-based multiplexing and demonstrate that doxorubicin induces MHC-I peptide ligands that are largely derived from mitotic progression and cell-cycle proteins. This high-throughput MHC-I ligand discovery approach may enable further explorations to understand how small molecules and other therapies alter MHC-I ligand presentation that may be harnessed for CD8<sup>+</sup> T-cell-based immunotherapies.