gebhart/patrepeval huggingface dataset:
1,3,2-Oxathiaphospholane approach to the synthesis of P-chiral stereodefined analogs of oligonucleotides and biologically relevant nucleoside polyphosphates (2008)

Abstract Among the various classes of modified nucleotides and oligonucleotides, phosphorothioate analogs, in which the sugar-phosphate backbone is modified by the substitution of a sulfur atom for one of the nonbridging oxygen atoms, have been most extensively studied in both in vitro and in vivo experiments. However, this substitution induces P-chirality of the dinucleoside phosphorothioate moiety. Consequently, even short phosphorothioate oligonucleotides synthesized using standard chemical methods exist as mixtures of many diastereoisomers. In our laboratory, the oxathiaphospholane (OTP) method has been developed for a stereocontrolled synthesis of oligo(deoxyribonucleoside phosphorothioate)s. Recently, this approach has been extended to ribonucleoside derivatives, and stereodefined phosphorothioate diribonucleotides were incorporated into oligomers suitable for mechanistic studies on deoxyribozymes. Next, it was found that the OTP ring can be opened with nucleophiles as weak as the phosphate or pyrophosphate anion, giving rise to nucleoside α-thiopolyphosphates. Surprisingly, the reaction between nucleoside OTP and O , O -dialkyl H-phosphonate or O , O -dialkyl H-phosphonothioate led to nucleoside 5'- O -(α-thio-β- O , O -dialkyl-hypophosphate) or 5'- O -(α,β-dithio-β- O , O -dialkyl-hypophosphate), respectively, i.e., derivatives containing a direct P-P bond.
TEMPERATURE-SENSITIVE MUTANTS BLOCKED IN THE FOLDING OR SUBUNIT ASSMBLY OF THE BACTERIOPHAGE P22 TAILSPIKE PROTEIN. I. FINE-STRUCTURE MAPPING (1980)

As part of a study of protein folding, we have constructed a fine-structure map of 9 existing and 29 newly isolated UV- and hydroxylamine-induced temperature-sensitive (ts) mutations in gene 9 of Salmonella bacteriophage P22. Gene 9 specifies the polypeptide chain of the multimeric tail spikes, six of which form the cell attachment organelle of the phage. The 38 ts mutants were mapped against deletion lysogens with endpoints in gene 9. They mapped in 10 of the 15 deletion intervals. Two- and three-factor crosses between mutants within each interval indicated that at least 31 ts sites are represented among the 38 mutants. To determine the distribution of ts sites within the physical map, we identified the protein fragments from infection of su- hosts with 10 gene 9 amber mutants. Their molecular weights, ranging from 13,900 to 55,000 daltons, were combined with the genetic data to yield a composite map of gene 9. The 31 ts sites were distributed through most of the gene, but were most densely clustered in the central third.--None of the ts mutant pairs tested exhibited intragenic complementation. Studies of the defective phenotypes of the ts mutants (Goldenberg and King 1981; Smith and King 1981) revealed that most do not affect the thermostability of the mature protein, but instead prevent the folding or subunit assembly of the mutant chains synthesized at restrictive temperature. Thus, many of these ts mutations identify sites in the polypeptide chain that are critical for the folding or maturation of the tail-spike protein.
Through-package wireless powering via piezoelectric micromachined ultrasonic transducers (2018)

The paper reports on a chip-scale wireless power transfer method using elastic waves traveling though plastic packaging media with arbitrary thicknesses. Piezoelectric micromachined ultrasonic transducers (pMUTs) are utilized for harnessing the longitudinal bulk acoustic waves generated by an external acoustic probe. Aluminum nitride pMUTs are developed through a simple and CMOS compatible process. In order to emulate the effect of the package, PLA plastic pieces with various thicknesses are 3D printed and used in the experiments. PMUTs as small as 200×200 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> resulted in -30 dB power transfer efficiency in the case of a 1 mm thick PLA package.
Alpha-1 Antitrypsin Mitigates the Inhibition of Airway Epithelial Cell Repair by Neutrophil Elastase (2015)

Neutrophil elastase (NE) activity is associated with many destructive lung diseases and is a predictor for structural lung damage in early cystic fibrosis (CF), which suggests normal maintenance of airway epithelium is prevented by uninhibited NE. However, limited data exist on how the NE activity in airways of very young children with CF affects function of the epithelia. The aim of this study was to determine if NE activity could inhibit epithelial homeostasis and repair and whether any functional effect was reversible by antiprotease alpha-1 antitrypsin (α1AT) treatment. Viability, inflammation, apoptosis, and proliferation were assessed in healthy non-CF and CF pediatric primary airway epithelial cells (pAECnon-CF and pAECCF, respectively) during exposure to physiologically relevant NE. The effect of NE activity on pAECCF wound repair was also assessed. We report that viability after 48 hours was significantly decreased by 100 nM NE in pAECnon-CF and pAECCF owing to rapid cellular detachment that was accompanied by inflammatory cytokine release. Furthermore, both phenotypes initiated an apoptotic response to 100 nM NE, whereas ≥ 50 nM NE activity significantly inhibited the proliferative capacity of cultures. Similar concentrations of NE also significantly inhibited wound repair of pAECCF, but this effect was reversed by the addition of α1AT. Collectively, our results demonstrate free NE activity is deleterious for epithelial homeostasis and support the hypothesis that proteases in the airway contribute directly to CF structural lung disease. Our results also highlight the need to investigate antiprotease therapies in early CF disease in more detail.
Effect of electric field on laser induced damage threshold of multilayer dielectric gratings (2007)

This paper studies gratings engraved in multilayer dielectric stacks for ultra high intensity laser compressors application. We design various grating profiles with high reflected efficiencies for 1780 l/mm multilayer dielectric gratings (MLD). Each grating is defined to exhibit a different electric field maximum value in the pillars of the grating. A damage testing facility operating at 1.053 mum, 500 fs pulse duration is used to damage test the parts manufactured from these designs. It is evidenced that for fixed incident angle and materials the damage of the grating is directly related to the electric field intensity maximum in the material, which depends on the groove profile. Laser induced damage thresholds of 5 J/ cm(2) are experimentally reached with very high and uniform efficiencies.
High-Speed Si/Ge Avalanche Photodiodes with Enhanced Responsivity (2021)

Reflectors have been integrated at the end of the Si/Ge waveguide avalanche photodiodes (APDs) to enhance the responsivity without compromising the bandwidth. The responsivity is improved from ∼ 0.75 A/W to ∼ 1 A/W assisted with a distributed Bragg reflector (DBR) or a loop reflector (LR) while maintaining a high bandwidth of 25 GHz. The enhanced responsivity improves the sensitivity by 1-2 dB with 32 Gbit/s NRZ modulation.
Large format arrays of kinetic inductance detectors for the TolTEC millimeter-wave imaging polarimeter (Conference Presentation) (2018)

Microwave Kinetic Inductance Detectors (MKIDs) provide a technological path towards the high-yield, large-format detector arrays needed for the next generation of experiments. The intrinsically integrated readout components of MKIDs generally give rise to high multiplexing factors, simplified assembly, and streamlined experimental integration. We describe the first MKID arrays fabricated and tested on monolithic 150 mm diameter silicon substrates – a crucial scaling in fabrication capacity that is necessary for future large-scale experiments aiming to incorporate hundreds of thousands of detectors in the coming years. The arrays described here are being developed for the TolTEC millimeter-wave imaging polarimeter being constructed for the 50-meter Large Millimeter Telescope (LMT), with observations planned to begin in early 2019. TolTEC uses dichroic filters to define three physically independent focal planes for operation in observational bands centered at 1.1, 1.4, and 2.0 mm. Each focal plane observes in just one wavelength band, allowing the use of simple to produce, direct-absorption pixel designs with each pixel comprising two detectors that are sensitive to orthogonal states of linear polarization. TolTEC comprises approximately 7,000 polarization sensitive MKIDs designed to operate at a base temperature of 100 mK. The primary working material used for these devices are TiN/Ti/TiN multilayer films, which have several advantageous qualities including: low two-level system noise at the TiN-silicon interface; linear responsivity; uniformity in deposition; and tunable transition temperature, sheet resistance and sheet inductance. We describe the detailed pixel and array layout designs, including focal plane integration and optical coupling via spline-profiled, silicon-platelet, feedhorn-coupled waveguide. We present measurements of full arrays and/or prototype small arrays of devices operating in each of the three observation bands and compare the observed noise and optical performance to that predicted from models and simulations. We also describe the fabrication methods used to produce these large-format arrays with high yield and uniformity.
A UWB antenna combined with the CRLH metamaterial UWB bandpass filter having the bandstop at the 5 GHz-band WLAN (2009)

This paper investigates how a ultrawide band (UWB) antenna can get the stopband created by the UWB filter which has a notch at the 5 GHz-band WLAN(wireless local area network) service. Particularly, we proposed the design of the composite right- and left-handedness (CRLH) metamaterial UWB notched-bandpass filter to have the smallest component possible connected to the feedline of the UWB antenna. We will see the lambda/9-long UWB filter with and without the notch, and the acceptable VSWRs of the UWB antenna before and after being combined with the notched metamaterial UWB filter.
p300-Mediated Acetylation of Histone Demethylase JMJD1A Prevents Its Degradation by Ubiquitin Ligase STUB1 and Enhances Its Activity in Prostate Cancer (2020)

The androgen receptor (AR) pathway plays a central role in the development of castration-resistant prostate cancer (CRPC). The histone demethylase JMJD1A has been shown to regulate activities of AR and c-Myc transcription factors and promote prostate cancer progression. Here, we report that JMJD1A protein stability is controlled by the ubiquitin ligase STUB1. High levels of JMJD1A were strongly correlated with low STUB1 levels in human CRPC specimens. STUB1 inhibited AR activity, AR-V7 levels, and prostate cancer cell growth partly through degradation of JMJD1A. Furthermore, the acetyltransferase p300 acetylated JMJD1A at lysine (K) 421, a modification that recruits the BET family member BRD4 to block JMJD1A degradation and promote JMJD1A recruitment to AR targets. Increased levels of both total and K421-acetylated JMJD1A were observed in prostate cancer cells as they developed resistance to the AR antagonist enzalutamide. Treatment of prostate cancer cells with either p300 or BET inhibitors destabilized JMJD1A, and enzalutamide-resistant prostate cancer cells were more sensitive than parental cells to these inhibitors. Together, our findings identify a critical role for acetylation of JMJD1A in regulating JMJD1A stability and AR activity in CRPC. These newly identified mechanisms controlling JMJD1A protein stability provide potential druggable targets to encourage the development of additional therapies for advanced prostate cancer. SIGNIFICANCE: Identification of mechanisms regulating JMJD1A protein stability reveals new strategies to destabilize JMJD1A and concomitantly inhibit AR activities as potential prostate cancer therapy.
The Glyco-enzyme adaptor GOLPH3 Links Intra-Golgi Transport Dynamics to Glycosylation Patterns and Cell Proliferation (2019)

Abstract Glycans are ubiquitous sugar polymers with major biological functions that are assembled by glyco-enzymes onto cargo molecules during their transport through the Golgi complex. How the Golgi determines glycan assembly is poorly understood. By relying on the Golgi cisternal maturation model and using the glyco-enzyme adaptor and oncoprotein GOLPH3 as a molecular tool, we define the first example of how the Golgi controls glycosylation and associated cell functions. GOLPH3, acting as a component of the cisternal maturation mechanism, selectively binds and recycles a subset of glyco-enzymes of the glycosphingolipid synthetic pathway, hinders their escape to the lysosomes and hence increases their levels through a novel lysosomal degradation-regulated mechanism. This enhances the production of specific growth-inducing glycosphingolipids and reprograms the glycosphingolipid pathway to potentiate mitogenic signaling and cell proliferation. These findings unravel unforeseen organizing principles of Golgi-dependent glycosylation and delineate a paradigm for glycan assembly by the Golgi transport mechanisms. Moreover, they indicate a new role of cisternal maturation as a regulator of glycosylation, and outline a novel mechanism of action for GOLPH3-induced proliferation.
Influence of counterions on the structure of bis(oxazoline)copper(ii) complexes; an EPR and ENDOR investigation (2012)

X- and Q-band EPR and ENDOR spectroscopy was used to study the structure of a series of heteroleptic and homoleptic copper bis(oxazoline) complexes, based on the (-)-2,2'-isopropylidenebis[(4S)-4-phenyl-2-oxazoline] ligand and bearing different counterions (chloride versus triflate); labelled [Cu(II)(1a-c)]. The geometry of the two heteroleptic complexes, [Cu(II)(1a)] and [Cu(II)(1c)], depended on the choice of counterion. Formation of the homoleptic complex was only evident when the Cu(II)(OTf)(2) salt was used (Cu(II)(Cl)(2) inhibited the transformation from heteroleptic to homoleptic complexes). The hyperfine and quadrupole parameters for the surrounding ligand nuclei were determined by ENDOR. Well resolved (19)F and (1)H couplings confirmed the presence of both coordinated water and TfO(-) counterions in [Cu(1a)].
Asymptotic enumeration of binary matrices with bounded row and column weights (2011)

Consider the set A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> of all n×n binary matrices in which the number of 1's in each row and column is at most n/2. We show that the redundancy, n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> - log <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> |An|, of this set equals ρn + o(n), for a constant ρ ≈ 1.42515.
Critical dimension error analysis for 0.13 μm photolithography and beyond (2001)

This article reports on a comprehensive study of critical dimension (CD) error analysis for the 0.13 μm generation and beyond. Systematic CD distribution is extracted by averaging nine wafers. The remaining noise signals are treated as random CD errors. Systematic CD error is further broken down into intra- and interfield CD errors by Fourier analysis. Interfield CD error is brought in comparison with the temperature distribution of postexposure bake hot plate, and they are found in good match. A polynomial expansion method further decomposes the interfield distribution into tilt and spiral parts, which are supposedly contributed by hot-plate and spin modules. The random CD error is also analyzed in this article.
Chronic rejection of a lung transplant is characterized by a profile of specific autoantibodies (2010)

Obliterative bronchiolitis (OB) continues to be the major limitation to long-term survival after lung transplantation. The specific aetiology and pathogenesis of OB are not well understood. To explore the role of autoreactivity in OB, we spotted 751 different self molecules onto glass slides, and used these antigen microarrays to profile 48 human serum samples for immunoglobulin G (IgG) and IgM autoantibodies; 27 patients showed no or mild bronchiolitis obliterans syndrome (BOS; a clinical correlate of OB) and 15 patients showed medium to severe BOS. We now report that these BOS grades could be differentiated by a profile of autoantibodies binding to 28 proteins or their peptides. The informative autoantibody profile included down-regulation as well as up-regulation of both IgM and IgG specific reactivities. This profile was evaluated for robustness using a panel of six independent test patients. Analysis of the functions of the 28 informative self antigens showed that eight of them are connected in an interaction network involved in apoptosis and protein metabolism. Thus, a profile of autoantibodies may reflect pathological processes in the lung allograft, suggesting a role for autoimmunity in chronic rejection leading to OB.
Data Discovery Use Cases (1999)

There needs to be a solution for locating and capturing data in a
standardized way. Data may be cached, copied and/or stored at multiple
locations in the network on route to its final destination. With an
increasingly high volume of devices connecting to the Internet,
support for network caching and replication is critical for continuous
data availability. There are data repositories throughout a modern
network and there needs to be a standardized way to locating the
repositories and discovering the desired data within. There are
several use cases which illustrate a need for a data discovery
solution. An application might need to query the network to discover
resources (program, service, resource) that can help the local
application perform a particular task. Additionally, there could be
volumes of data which needs to be searched and discovered in order to
provide a result to be acted upon by the application. These are a
couple of the use cases being addressed in this document.
The Borderline Dysplastic Hip: Arthroscopy or PAO? (2018)

Objectives: The borderline dysplastic hip (characterized by a lateral centre-edge angle (LCEA): 20 - 25° and an acetabular index (AI): 10 - 15°) can pose a significant challenge as symptoms may be due to insufficient acetabular coverage, the presence of femoro-acetabular impingement (FAI) or both. Accordingly, different treatment options have been described, including peri-acetabular osteotomy (PAO), hip arthroscopy, open arthrotomy or a combination of procedures. This study aims to determine patient and deformity-specific characteristics that direct treatment decision-making in the borderline dysplastic hip. Furthermore, we describe the early-term results of both the PAO and hip arthroscopy in treating this challenging patient population. Methods: A prospective, multicenter, longitudinal surgical cohort of young adult hips was searched. From 2060 hips, 291 hips satisfied the inclusion criteria of idiopathic borderline dysplasia, adequate follow-up (&gt; 1-year) and functional outcome. Demographic and radiographic features are included in Table 1. Fifty-five hips (19%) had a previous hip operation (most commonly a hip arthroscopy). A number of different procedure types were performed which were broadly divided into 3 groups; PAO-only (n=42), hip arthroscopy-only (n=127) or PAO and intra-articular treatment (either arthroscopically or open, addressing the cam morphology and/or labral pathology) (n=122). Outcome measures included complications-, re-operations- rates and clinical outcomes using the Harris Hip (HHS) and HOOS scores; pre-operatively and at follow-up; the difference was defined as Δ. Patient characteristics, radiographic morphology and clinical outcome measures were compared between the 3 groups. Results: Patients that underwent a PAO were younger and more likely to be female. The PAO groups had a greater number of previous hip procedures (26%, 24%), most of which were hip arthroscopies. The patients that underwent hip arthroscopy had greater incidence of high alpha angles (66%) compared to the PAO groups (35%, 38%) (p&lt;0.001). The PAO groups having slightly more dysplastic features (LCEA, AI, ACEA) (Table 1). At a mean follow-up of 2.5 years, there were no differences in the complication (7-10%, p=0.8) or re-operation rates (13%). Pre-operatively, the PAO groups had inferior HOOS and WOMAC scores compared to the arthroscopy group (p=0.02-7). No differences in the post-op scores were seen (Table 1). The groups that addressed the intra-articular pathology (arthroscopy and PAO-articular treatment) had significantly greater ΔHHS (23) compared to PAO-only (13) (p=0.02). Conclusion: Younger patients, those with a failed previous arthroscopy, without evidence of intra-articular wear and with worse pre-operative function were more likely to receive a PAO (with or without articular adjunct treatment). Addressing the intra-articular and impingement-related pathology (in addition to a when a PAO is considered necessary) was associated with better improvement in PROMs and should be strongly considered in the borderline hip. [Table: see text]
FPGA implementation of a multi-view stereo approach for depth estimation and image reconstruction for plenoptic cameras (2017)

In this paper a concept for an algorithm for depth estimation and image reconstruction for a plenoptic camera is presented. The algorithm follows a multi-view stereo approach and is intended for an FPGA-based Xilinx Zynq Ultrascale+ SoC platform to allow for real-time processing in an embedded environment. The micro-lens array separates a complete image in many micro-images. The micro-images are considered as individual cameras and the processing is calculated in a multi-view stereo approach. To accomplish an adequate frame rate and a reasonable resolution efficient processing steps and fixed-point integer calculation are chosen.&#13;\nThe conceptual algorithm will be implemented and tried out in an experimental setting in 2019.
Extracellular vesicles as trans‐genomic agents: Emerging roles in disease and evolution (2017)

The composition of genetic material in extracellular vesicles (EV) has sparked interest particularly in the potential for horizontal gene transfer by EV. Although the RNA content of EV has been studied extensively, few reports have examined the DNA content of EV. It is still unclear how DNA is packaged inside EV, and whether they are functional in recipient cells. In this review, we describe the biological significance of genetic material in EV and their possible impacts in recipient cells, with focus on DNA from cancer cell-derived EV and the potential roles they may play in the cancer microenvironment. Another important feature of the genetic content of EV is the presence of retrotransposon elements. In this review, we discuss the possibility of an EV-mediated mechanism for the dispersal of retrotransposon elements, and their potential involvement in the development of genetically influenced diseases. In addition to this, we discuss the potential involvement of EV in the transfer of genetic material across species, and their possible impacts in modulating genome evolution.