gebhart/patrepeval huggingface dataset:
Surface-oxide-controlled InGaAs/InAlAs inverted-type metal-oxide-semiconductor high electron mobility transistors for sub-THz high-power amplifiers (2022)

Abstract Herein, we successfully improved the maximum oscillation frequency and maximum stable gain (MSG) across a wide bias range of surface-oxide-controlled (SOC) InGaAs/InAlAs inverted-type metal-oxide-semiconductor high-electron-mobility transistors (inverted MOS-HEMTs) by reducing the gate leakage current and drain conductance ( g d ). H 2 O vapor treatment selectively decreased the narrow band gap indium oxide at the surface of the In-based epitaxial layer via the SOC process before the gate oxide deposition. Furthermore, the calculation of band profiles indicated that the g d reduction was possibly attributed to the suppression of impact ionization in the InGaAs channel by inverted MOS-HEMTs. Consequently, SOC-inverted MOS-HEMTs demonstrated a high MSG of &gt;12 dB at 100 GHz across a wide bias range.
A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma (2018)

Pre-mRNA splicing can contribute to the switch of cell identity that occurs in carcinogenesis. Here, we analyze a large collection of RNA-seq data sets and report that splicing changes in hepatocyte-specific enzymes, such as <i>AFMID</i> and <i>KHK</i>, are associated with HCC patients' survival and relapse. The switch of <i>AFMID</i> isoforms is an early event in HCC development and is associated with driver mutations in <i>TP53</i> and <i>ARID1A</i> The switch of <i>AFMID</i> isoforms is human-specific and not detectable in other species, including primates. Finally, we show that overexpression of the full-length <i>AFMID</i> isoform leads to a higher NAD<sup>+</sup> level, lower DNA-damage response, and slower cell growth in HepG2 cells. The integrative analysis uncovered a mechanistic link between splicing switches, de novo NAD<sup>+</sup> biosynthesis, driver mutations, and HCC recurrence.
Cuttlefish bone (cuttlebone), by near-ambient pressure XPS (2021)

Near ambient pressure-x-ray photoelectron spectroscopy (NAP-XPS) is a less traditional form of XPS that allows samples to be analyzed at relatively high pressures, i.e., at greater than 2500 Pa. NAP-XPS can probe moderately volatile liquids, biological samples, porous materials, and/or polymeric materials that outgas significantly. In this submission, we show the survey, Ca 2p, C 1s, O 1s, and N 1s NAP-XPS spectra of two biological samples (cuttlefish bones in their native state and implanted with nitrogen ions), which are materials that would be difficult to analyze by conventional XPS. The measurements were performed at 100 Pa in ambient air to compensate for surface charging. Peak fits of the Ca 2p, C 1s, and N 1s narrow scans are presented.
Marine scavenging: The relative importance of mass transfer and reaction rates (1996)

We present an analysis of factors regulating the scavenging rate of trace elements and nutrients by settling particles in the ocean. The overall process limiting marine scavenging rates is determined by comparing the relative kinetics of dissolved phase mass transfer and particle‐associated sorption rates. Measured scavenging and uptake rates of a variety of marine particle types are then compared to theoretically calculated mass transfer rate constants. Our calculations show that for most marine environments, sorption rates arc much slower than external mass transfer of dissolved species. External mass transfer is therefore not the limiting process. Particle‐associated processes such as adsorption, intraparticle reactions, and particle repackaging must control the overall scavenging rates observed in the ocean.
The transfer and amplification of cyanostilbene molecular function to advanced flexible optical paints through self-crosslinkable side-chain liquid crystal polysiloxanes (2021)

A self-crosslinkable side-chain liquid crystal polysiloxane containing cyanostilbene (Si-CSM) was newly synthesized for the development of a new generation of flexible optical paints. The photoisomerization of the cyanostilbene moiety at the molecular level was transferred and amplified to the phase transition of Si-CSM, resulting in changes in the macroscopic optical properties of the Si-CSM thin film. The self-crosslinking reaction between Si-H groups in the Si-CSM polymer backbone caused the self-crosslinked Si-CSM thin film to be very elastic and both thermally and chemically stable. Therefore, the self-crosslinked Si-CSM thin film endured stretching and bending deformations under relatively harsh conditions. In addition, the uniaxially oriented and self-crosslinked Si-CSM thin film generated linearly polarized light emission. Polarization-dependent and photopatternable secret coatings were fabricated via a spontaneous self-crosslinking reaction after coating the Si-CSM paint and irradiating ultraviolet (UV) light through a photomask. This newly developed flexible optical Si-CSM paint can be applied in next-generation optical coatings.
Multiband and Small Coplanar Antenna System for Wireless Handheld Devices (2013)

Multiband and small antennas are strongly demanded in current wireless handheld or portable devices that require multiband operation. Nowadays, trends are focused on exciting ground plane radiation modes in order to reduce as much as possible the volume devoted to the antenna element. This paper studies different geometries for determining which one better excites a ground plane radiation mode at different frequency regions. The results demonstrate that a non-resonant pad element attains the best tradeoff between performance and geometry complexity. A multiband antenna system featuring small coplanar pad elements is proposed for providing operation at the communication standards LTE700 (698-787 MHz), GSM850 (824-894 MHz), GSM900 (880-960 MHz), GSM1800 (1710-1880 MHz), GSM1900 (1850-1990 MHz), UMTS (1920-2170 MHz), LTE2100 (1920-2170 MHz), LTE2300 (2300-2400 MHz), LTE2500 (2500-2690 MHz) as well as at the satellite positioning systems GPS (1575 MHz), Galileo L1 (1559-1591 MHz), Glonass (1592-1609 MHz). A radiofrequency system comprising broadband matching networks is included to provide the required impedance bandwidth. Numerical results give physical insight into the behavior of the proposed planar element. A prototype is built to demonstrate the feasibility of the proposal. The proposed radiating system is appealing for the new wireless handheld devices due to its small size (153 ), planar profile, and multiband performance.
Cine phase contrast magnetic resonance imaging of calf muscle contraction in pediatric patients with cerebral palsy and healthy children: comparison of voluntary motion and electrically evoked motion (2023)

Abstract The aim of this study is to investigate the feasibility of phase contrast imaging for assessment of muscle function in children with cerebral palsy. Time-resolved cine phase contrast MRI at 3T was synchronized with (a) electrical muscle stimulation (EMS) of the calf muscle and (b) voluntary plantarflexion following visual instructions. Fourteen ambulatory pediatric patients with equinus and 13 normally developing, healthy children were scanned. Ten patients were scanned pre and post botulinum toxin treatment. Four patients and four healthy children performed voluntary plantarflexion additionally to EMS. The achieved force was higher for the voluntary task for both patients and healthy controls, but its periodicity was worse compared to the stimulated contraction in patients. Therefore, it was possible to acquire contraction velocity time courses showing two distinct velocity peaks – the first for voluntary muscle contraction and the second for release – in four out of four healthy controls but in none of the patients. During EMS, two distinct velocity peaks could be resolved if the tolerated current was high enough to evoke sufficient contraction. That was achieved in 21% of the scans in patients (15 out of 72 scans during EMS in total) compared to 82% (14 out of 17) in healthy children. Then, the data quality was sufficient to generate strain maps. However, it was not possible to detect an effect of botulinum toxin in these patients since we did not succeed in acquiring data with sufficient quality both pre- and post-treatment. In conclusion, both EMS and voluntary motion worked well in healthy, normally developing children. Compliance was higher for the voluntary task for both patients and healthy controls. In conclusion, it was necessary to use EMS for a successful measurement of contraction/release velocity and strain in CP patients and although in this cohort the results were inconclusive, in the future optimization of the stimulation protocol could increase the acceptance and improve the output.
Microresonator frequency comb based high‐speed transmission of intensity modulated direct detection data (2022)

Globally, the long-haul transmission of ultra-high bandwidth data is enabled through coherent communications. Driven by the rapid pace of growth in interconnectivity over the last decade, long-haul data transmission has reached capacities on the order of tens to hundreds of terabits per second, over fiber reaches which may span thousands of kilometers. Data center communications operate in regimes featuring shorter reaches and higher cost sensitivity. While integrated microresonator frequency combs are poised to revolutionize light sources used for high-speed data transmission over fiber, recent progress has focused largely on coherent detection schemes. Furthermore, though state-of-the-art intensity modulators are advancing in speed, it has not been demonstrated in the literature if microresonator-based comb lines can accommodate higher intensity modulated direction data (IMDD) line rates in tandem with these advancements. In this manuscript, we demonstrate the use of microresonator frequency combs pumped with a single laser for the transmission of high-speed IMDD data. We demonstrate error-free transmission of 30 Gbs<sup>-1</sup> per comb non-return-to-zero data over fiber lengths of 6 km, as well as bit error rates under the forward error correction limit for propagation through 20 km of optical fiber. 60 Gbs<sup>-1</sup> and 42 Gbs<sup>-1</sup> pulse modulation amplitude 4 (PAM4) data modulated on each frequency comb line is further quantified to have a bit error rate under the forward error correction limit for fiber reaches of up to 6 km and 20 km respectively. The results showcase CMOS-compatible microresonator frequency comb modulated using IMDD formats as a promising technology for high-speed transmission in the data center transceiver industry.
Mitigating residual stress in Cu metallization (2012)

The application of a cryogenic thermal excursion to passivated copper films has been demonstrated to dramatically reduce the magnitude of residual stress and to induce compressive, in-plane stress at room temperature. In-situ x-ray diffraction measurements reveal the evolution of in-plane stress within SiCxNyHz and TaN capped Cu films, which undergo significant plastic behavior on cooling and as the film approaches room temperature during heating. The resulting compressive stress represents a more favorable condition to mitigate voiding within the metallization. In-situ and ex-situ measurements of SiCxNyHz capped Cu films reveal that the final stress state is independent of cooling rate.
Acidic Nanoparticles Are Trafficked to Lysosomes and Restore an Acidic Lysosomal pH and Degradative Function to Compromised ARPE-19 Cells (2012)

Lysosomal enzymes function optimally in acidic environments, and elevation of lysosomal pH can impede their ability to degrade material delivered to lysosomes through autophagy or phagocytosis. We hypothesize that abnormal lysosomal pH is a key aspect in diseases of accumulation and that restoring lysosomal pH will improve cell function. The propensity of nanoparticles to end up in the lysosome makes them an ideal method of delivering drugs to lysosomes. This study asked whether acidic nanoparticles could traffic to lysosomes, lower lysosomal pH and enhance lysosomal degradation by the cultured human retinal pigmented epithelial cell line ARPE-19. Acidic nanoparticles composed of poly (DL-lactide-co-glycolide) (PLGA) 502 H, PLGA 503 H and poly (DL-lactide) (PLA) colocalized to lysosomes of ARPE-19 cells within 60 min. PLGA 503 H and PLA lowered lysosomal pH in cells compromised by the alkalinizing agent chloroquine when measured 1 hr. after treatment, with acidification still observed 12 days later. PLA enhanced binding of Bodipy-pepstatin-A to the active site of cathepsin D in compromised cells. PLA also reduced the cellular levels of opsin and the lipofuscin-like autofluorescence associated with photoreceptor outer segments. These observations suggest the acidification produced by the nanoparticles was functionally effective. In summary, acid nanoparticles lead to a rapid and sustained lowering of lysosomal pH and improved degradative activity.
Macro- and Microscale Analysis of Bearing Surface Damage on Total Shoulder Replacements (2013)

Damage to bearing surfaces of total joint replacements (TJR) can have clinical consequences: wear debris generated from ultra-high molecular weight polyethylene (UHMWPE) surfaces can cause osteolysis and subsequent implant loosening [1]. Counterbearing metallic damage may significantly increase UHMWPE wear [2]. Documenting the morphology, frequency and location of bearing surface damage may provide insight into wear initiation and prevention. While scoring methodologies have been available and validated for total hip replacements (THR) and total knee replacements (TKR) [3–4], there is a paucity of validated scoring protocols for total shoulder replacements (TSR) [5]. Our previous work presented a damage scoring methodology to evaluate the severity and coverage of six damage modes on retrieved cobalt chrome (CoCr) humeral heads [6]. In this study, we adapt that protocol to include bearing surface damage on the counter-bearings (UHMWPE glenoid components). Additionally, we incorporate the results of 3D profilometry analysis of scratches in the Co-Cr humeral heads [6]. Ultimately, this macroscale and microscale analysis, combined with clinical data, for coupled TSR retrievals will provide insight on the origin, evolution and consequences of bearing damage in vivo.
Regulation of HER2 Oncogene Transcription by a Multifunctional Coactivator/Corepressor Complex (2014)

Transcription of the HER2 oncogene can be repressed by estrogen (E2). We now show that, a splice isoform of the nuclear receptor coactivator AIB1, AIB1-Δ4, is able to reverse E2 repression of HER2 gene expression in breast cancer cells. The first 224 amino acids of AIB1 that are absent in AIB1-Δ4, bind a co-repressor, ANCO1. Using chromatin immunoprecipitation assay approaches in MCF7 and BT474 cell lines, we demonstrate that AIB1 and AIB1-Δ4 can bind to the E2 regulatory site in the first intron of the HER2 gene, after E2 treatment, but only full-length AIB1 recruits ANCO1. Consistent with E2-induced chromatin repression, the AIB1-ANCO1 complex recruits HDAC3 and HDAC4 to the intronic estrogen response element and the proximal promoter acquires the repressive chromatin mark H3K9me3 and loses H3K4me1. In contrast, AIB1-Δ4 does not recruit ANCO 1, HDAC3, or HDAC4 and the proximal promoter retains activation marks of H3K4me1. In cell lines with low levels of ANCO1 (T47D), E2 does not repress HER2 gene transcription but the repressive response can be restored by overexpression of ANCO1. ANCO1 can also repress other E2-responsive genes, indicating that AIB1, AIB1-Δ4 and ANCO1 are important determinants of endocrine and growth factor responsiveness in breast cancer.
An Incremental Prefix Filtering Approach for the All Pairs Similarity Search Problem (2010)

Given a set of records, a threshold value t and a similarity function, we investigate the problem of finding all pairs of records such that similarity between each pair is above t. We propose several optimizations on the existing approaches to solve the problem. Our algorithm outperforms the state-of-the-art algorithms in the case with large and high-dimensional datasets. The speedup we achieved varied from 30% to 4-x depending on the similarity threshold and the dataset properties.
Structure-assisted discovery of an aminothiazole derivative as a lead molecule for inhibition of bacterial fatty-acid synthesis (2007)

Fatty-acid synthesis in bacteria is of great interest as a target for the discovery of antibacterial compounds. The addition of a new acetyl moiety to the growing fatty-acid chain, an essential step in this process, is catalyzed by beta-ketoacyl-ACP synthase (KAS). It is inhibited by natural antibiotics such as cerulenin and thiolactomycin; however, these lack the requirements for optimal drug development. Structure-based biophysical screening revealed a novel synthetic small molecule, 2-phenylamino-4-methyl-5-acetylthiazole, that binds to Escherichia coli KAS I with a binding constant of 25 microM as determined by fluorescence titration. A 1.35 A crystal structure of its complex with its target reveals noncovalent interactions with the active-site Cys163 and hydrophobic residues of the fatty-acid binding pocket. The active site is accessible through an open conformation of the Phe392 side chain and no conformational changes are induced at the active site upon ligand binding. This represents a novel binding mode that differs from thiolactomycin or cerulenin interaction. The structural information on the protein-ligand interaction offers strategies for further optimization of this low-molecular-weight compound.
Reticle defect printability for sub-0.3k 1 chromeless phase lithography (CPL) technology (2002)

Chromeless Phase Lithography (CPL) with a high NA exposure tool is shown to be an attractive technology solution for the 65nm node. Under strong image enhancement conditions, the traditional definition of minimum defect printability specifications is no longer adequate. This paper investigates defect printability issues for CPL technology. Based on optimized scattering bar OPC treatments through pitch, a set of defect printability quantification (DPQ) patterns was designed. In the DPQ design, a number of defect types have been programmed with progressively increasing defect size from 0.05(l/NA) to 0.3(l/NA). Each defect type and size on the actual CPL reticle were then fully characterized using an advanced CD SEM metrology system, the KLA8450RT with both wafer and reticle capabilities. This is a very critical step for quantifying defect printability, since in order to accurately assess the printability, the defect dimension must be well correlated to the original DPQ design on the reticle. The DPQ reticle was then printed using a high numerical aperture (NA) scanner (ASML /850T) so that it is possible to characterize the defect printability for each of the programmed defects and the impact on CD through pitch. Minimum printable defect (MPD), maximum non-printable defect (MNPD), and critical dimension (CD) variation percentage were used as metrics to characterize the critical defect size and the sensitivity of each defect type. The purpose of this study is to understand the tolerance of the CLM technology to printable defects and establish a realistic and sensible defect specification.
In the shadow of misperception (2011)

Few research studies focus on how the use of assistive technologies is affected by social interaction among people. We present an interview study of 20 individuals to determine how assistive technology use is affected by social and professional contexts and interactions. We found that specific assistive devices sometimes marked their users as having disabilities; that functional access took priority over feeling self-conscious when using assistive technologies; and that two misperceptions pervaded assistive technology use: (1) that assistive devices could functionally eliminate a disability, and (2) that people with disabilities would be helpless without their devices. Our findings provide further evidence that accessibility should be built into mainstream technologies. When this is not feasible, assistive devices should incorporate cutting edge technologies and strive to be designed for social acceptability, a new design approach we propose here.
The Crystal Structure of Human Δ4-3-Ketosteroid 5β-Reductase Defines the Functional Role of the Residues of the Catalytic Tetrad in the Steroid Double Bond Reduction Mechanism (2008)

The 5beta-reductases (AKR1D1-3) are unique enzymes able to catalyze efficiently and in a stereospecific manner the 5beta-reduction of the C4-C5 double bond found into Delta4-3-ketosteroids, including steroid hormones and bile acids. Multiple-sequence alignments and mutagenic studies have already identified one of the residues presumably located at their active site, Glu 120, as the major molecular determinant for the unique activity displayed by 5beta-reductases. To define the exact role played by this glutamate in the catalytic activity of these enzymes, biochemical and structural studies on human 5beta-reductase (h5beta-red) have been undertaken. The crystal structure of h5beta-red in a ternary complex with NADP (+) and 5beta-dihydroprogesterone (5beta-DHP), the product of the 5beta-reduction of progesterone (Prog), revealed that Glu 120 does not interact directly with the other catalytic residues, as previously hypothesized, thus suggesting that this residue is not directly involved in catalysis but could instead be important for the proper positioning of the steroid substrate in the catalytic site. On the basis of our structural results, we thus propose a realistic scheme for the catalytic mechanism of the C4-C5 double bond reduction. We also propose that bile acid precursors such as 7alpha-hydroxy-4-cholesten-3-one and 7alpha,12alpha-dihydroxy-4-cholesten-3-one, when bound to the active site of h5beta-red, can establish supplementary contacts with Tyr 26 and Tyr 132, two residues delineating the steroid-binding cavity. These additional contacts very likely account for the higher activity of h5beta-red toward the bile acid intermediates versus steroid hormones. Finally, in light of the structural data now available, we attempt to interpret the likely consequences of mutations already identified in the gene encoding the h5beta-red enzyme which lead to a reduction of its enzymatic activity and which can progress to severe liver function failure.