gebhart/patrepeval huggingface dataset:
Novel insights from 3D models: the pivotal role of physical symmetry in epithelial organization (2015)

3D tissue culture models are utilized to study breast cancer and other pathologies because they better capture the complexity of in vivo tissue architecture compared to 2D models. However, to mimic the in vivo environment, the mechanics and geometry of the ECM must also be considered. Here, we studied the mechanical environment created in two 3D models, the overlay protocol (OP) and embedded protocol (EP). Mammary epithelial acini features were compared using OP or EP under conditions known to alter acinus organization, i.e. collagen crosslinking and/or ErbB2 receptor activation. Finite element analysis and active microrheology demonstrated that OP creates a physically asymmetric environment with non-uniform mechanical stresses in radial and circumferential directions. Further contrasting with EP, acini in OP displayed cooperation between ErbB2 signalling and matrix crosslinking. These differences in acini phenotype observed between OP and EP highlight the functional impact of physical symmetry in 3D tissue culture models.
Comment on: Marquez et al. Low-Frequency Variants in HMGA1 Are Not Associated With Type 2 Diabetes Risk. Diabetes 2012;61:524–530 (2012)

We read with interest the article in Diabetes by Marquez et al. (1) that followed a recent abstract from this group (2) in which it reported that HMGA1 gene variants were associated with type 2 diabetes (T2D). It is surprising, therefore, that the same authors now conclude the opposite (1). We have described four functional HMGA1 variants that were associated with T2D in ∼10% of 3,278 Italian patients (3) and confirmed this finding in two other populations—U.S. and French (3).

We have no explanation as to why the Marquez group does not agree with itself. There are several explanations, however, for the discrepancies between our studies …
Metallothionein as a clonable tag for protein localization by electron microscopy of cells (2015)

A benign, clonable tag for the localization of proteins by electron microscopy of cells would be valuable, especially if it provided labelling with high signal-to-noise ratio and good spatial resolution. Here we explore the use of metallothionein as such a localization marker. We have achieved good success with desmin labelled in vitro and with a component of the yeast spindle pole body labelled in cells. Heavy metals added after fixation and embedding or during the process of freeze-substitution fixation provide readily visible signals with no concern that the heavy atoms are affecting the behaviour of the protein in its physiological environment. However, our methods did not work with protein components of the nuclear pore complex, suggesting that this approach is not yet universally applicable. We provide a full description of our optimal labelling conditions and other conditions tried, hoping that our work will allow others to label their own proteins of interest and/or improve on the methods we have defined.
Tcl1 protein functions as an inhibitor of de novo DNA methylation in B-cell chronic lymphocytic leukemia (CLL) (2012)

B-cell chronic lymphocytic leukemia (CLL) is the most common human leukemia. Deregulation of the T-cell leukemia/lymphoma 1 oncogene (TCL1) in mouse B cells causes a CD5(+) leukemia similar to aggressive human CLL. To examine the mechanisms by which Tcl1 protein exerts its oncogenic activity in B cells, we performed proteomics experiments to identify its interacting partners. We found that Tcl1 physically interacts with de novo DNA methylthansferases Dnmt3A and Dnmt3B. We further investigated the effects of Tcl1 up-regulation on the enzymatic activity of Dnmt3A and found that Tcl1 overexpression drastically inhibits Dnmt3A function. In addition, B cells from TCL1 transgenic mice showed a significant decrease in DNA methylation compared with WT controls. Similarly, CLL samples with high Tcl1 expression showed a decrease in DNA methylation compared with CLL samples with low Tcl1 expression. Given the previous reports of inactivating mutations of DNMT3A in acute myelogenous leukemia and myelodysplastic syndrome, our results suggest that inhibition of de novo DNA methylation may be a common oncogenic mechanism in leukemogenesis.
Fabrication of a $\hbox{TiN}_{x}/\hbox{Ni/Au}$ Contact on ZnO Films With High Thermal Stability and Low Resistance (2011)

A novel contact structure comprising of TiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1.22</sub> /Ni/Au has been deposited on Ga-doped and In-doped zinc oxide (ZnO) epilayer grown on a yttria-stabilized ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> substrate. It is found that the contact resistivity ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> is around 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> Ω cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for heavily doped ZnO, whereas a ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> value of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> Ω cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is achieved for ZnO with light doping concentration. Attributed to the barrier effect of TiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1.22</sub> intermediate layers, thermal annealing does not change the contact resistivity, but it is affected significantly by different surface treatments (atomic oxygen or nitrogen). For atomic oxygen-treated ZnO surface, the carrier density is increased, which leads to lower contact resistivity. It is shown that the contact structure of TiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1.22</sub> /Ni/Au with TiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1.22</sub> as the intermediate layer can provide a high-quality ohmic contact with low ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> and good thermal stability.
The effect of the crosslinking enzyme tyrosinase on gel formation and texture of acid-induced milk gels (2008)

Caseins were crosslinked by Trichoderma reesei tyrosinase in both raw and heat-treated skim milk. Tyrosinaseinduced crosslinking was beneficial in the preparation of acidified milk gels from raw milk, but it did not have an effect on acid gels made from heat-treated milk
Link Maintenance Protocol for Cognitive Radio System with OFDM PHY (2007)

For secondary usage of spectrum in a cognitive radio system, in order to maintain reliable continuous communication among secondary users, secondary radios need to make contact, communicate and switch to an open RF channel simultaneously when the current channel is reclaimed by a primary user. In this paper, we describe a link maintenance protocol aimed at solving this issue. The communication channel is monitored and dynamically updated based on spectrum availability. Spectral sensing is employed at the receivers to monitor the spectrum and assist in RF channel synchronization between transmitter and receiver. Simulation results characterizing the performance of this protocol are provided. A prototype system with a pair of cognitive radios featuring this protocol is also introduced.
Simpira v2: A Family of Efficient Permutations Using the AES Round Function. (2016)

This paper introduces Simpira, a family of cryptographic permutations that supports inputs of 128 × b bits, where b is a positive integer. Its design goal is to achieve high throughput on virtually all mod- ern 64-bit processors, that nowadays already have native instructions for AES. To achieve this goal, Simpira uses only one building block: the AES round function. For b = 1, Simpira corresponds to 12-round AES with fixed round keys, whereas for b ≥ 2, Simpira is a Generalized Feistel Structure (GFS) with an F -function that consists of two rounds of AES. We claim that there are no structural distinguishers for Simpira with a complexity below 2 128 , and analyze its security against a variety of at- tacks in this setting. The throughput of Simpira is close to the theoretical optimum, namely, the number of AES rounds in the construction. For example, on the Intel Skylake processor, Simpira has throughput below 1 cycle per byte for b ≤ 4 and b = 6. For larger permutations, where moving data in memory has a more pronounced effect, Simpira with b = 32 (512 byte inputs) evaluates 732 AES rounds, and performs at 824 cycles (1.61 cycles per byte), which is less than 13 % off the theoretical optimum. If the data is stored in interleaved buffers, this overhead is reduced to less than 1 %. The Simpira family offers an efficient solution when processing wide blocks, larger than 128 bits, is desired.
Controversies in acute kidney injury: the 2011 Brussels Roundtable (2011)

The recent advent of consensus definitions for acute kidney injury (AKI) has led to improvement in epidemiology of this complex disease and facilitated the development of new diagnostic makers and new therapies. However, important new challenges are also apparent. We still do not really understand why AKI occurs and urgently need to develop new therapies to treat it. Progress in this area will require new ideas and thinking outside the conventional box. By confronting some of the most significant controversies in the field of AKI we seek to develop new concepts that will ultimately yield new results.
Optimum real-time data transmission scheduling for channel searching in IEEE 802.11 wireless LANs (2005)

In transmitting real-time data over IEEE 802.11 wireless local area networks (WLANs), interference considerably degrades the quality of service (QoS). To minimize this damage, the radio channel should be switched to an unused new channel as soon as interference is detected on the current channel. For that purpose, the system has to know in advance,which channels are in use and which are not. The paper proposes an efficient method to search in advance for channels that are not in use by downlink real-time data transmission scheduling. The proposed method enables all stations (STAs) belonging to the basic service set (BSS) to perform fair and time-randomized other channel measurement. Therefore, the probability of detecting packets in other channel measurement becomes higher, and the BSS can select a channel that is not in use if interference is detected on the current channel. Adopting the proposed method, the BSS can successfully obtain stable throughput for real-time data transmission. The simulated throughput (video streaming) and packet detection probability in other channel measurements confirms the effectiveness of the proposed method.
[Immunohistochemical arguments in favor of co-localization of neuropeptides in hypothalamo-infundibular neuron systems]. (1984)

Light and electron microscope methods which can be used to examine the possibilities of co-occurrence of peptides are reviewed. The results obtained using some of them are exposed and discussed, concerning i/the light microscope demonstration of the CRF/vasopressin coexistence in rat and guinea-pig. ii/the electron microscope demonstration of the granular colocalization of LH-RH/C-terminal ACTH and somatostatin/enkephalin in the guinea-pig median eminence.
Exploring and Expanding the Structural Diversity of Self‐Assembling Dendrons through Combinations of AB, Constitutional Isomeric AB2, and AB3 Biphenyl‐4‐Methyl Ether Building Blocks (2006)

General, efficient and inexpensive methods for the synthesis of dendritic building blocks methyl 3',4'-dihydroxybiphenyl-4-carboxylate, 3',5'-dihydroxybiphenyl-4-carboxylate, and methyl 3',4',5'-trihydroxybiphenyl-4-carboxylate were elaborated. In all syntheses the major step involved an inexpensive Ni(II)-catalyzed Suzuki cross-coupling reaction. These three building blocks were employed together with methyl 4'-hydroxybiphenyl-4-carboxylate in a convergent iterative strategy to synthesize seven libraries containing up to three generations of 3',4'-, 3',5'-, and 3',4',5'-substituted biphenyl-4-methyl ether based amphiphilic dendrons. These dendrons self-assemble into supramolecular dendrimers that self-organize into periodic assemblies. Structural and retrostructural analysis of their assemblies demonstrated that these dendrons self-assemble into hollow and non-hollow supramolecular dendrimers exhibiting dimensions of up to twice those reported for architecturally related dendrons based on benzyl ether repeat units. These new dendrons expand the structural diversity and demonstrate the generality of the concept of self-assembling dendrons based on amphiphilic arylmethyl ethers.
Apparatus And Methods For Launching And Receiving A Broad Wavelength Range Source (2023)

An apparatus and method for simultaneous detection of N gas species through laser radiation attenuation techniques is disclosed. Each of the N species has a spectral absorption band. N laser sources operate at a wavelength ?N in a spectral absorption band separated by the cutoff wavelength for single-mode transmission. Each laser source corresponds to a gas species and transmits radiation through an optical fiber constructed and arranged to provide single-mode transmission with minimal power loss.
GOLD ATOM CHEMISTRY; SYNTHESIS AND CHARACTERIZATION OF BINARY GOLD CARBONYLS Au(CO)$^{n} (WHERE n = 1 OR 2)$ IN LOW TEMPERATURE MATRICES; SPECTROSCOPIC EVIDENCE FOR ISOCARBONYL-CAR BONYL GOLD, A LINKAGE ISOMER OF BIS-CARBONYL GOLD (1976)

Author Institution: Lash Miller Chemistry Laboratory and Erindale College, University of Toronto
Time over Threshold based digital animal PET (TODPET) (2011)

We have developed Time over Threshold (ToT) based Pr:LuAG-APD PET (TODPET) tomograph with a mixed signal front-end. The tomograph consists of 8 block detectors, each of which is composed of a 12 × 12 array of 2 × 2 x 10mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> Pr:LuAG crystals individually coupled with 12 × 12 UV-enhanced APD arrays. The APDs are individually read out with a custom-designed Time over Threshold ASIC and FPGA readout system. Developed PET tomograph has the energy resolution of 10% and the time resolution of 4.2ns. The 1.76 mm spatial resolution (FWHM) is achieved for the first result.
Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica (2019)

Abstract Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica . A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should provide a broader understanding of Salmonella biology and virulence and contribute to the practical applications of phages as vectors and antibacterial agents. Results: Comparative analysis of the full genome sequences of 142 prophages of Salmonella enterica subsp. enterica retrieved from public databases revealed an extensive variation in genome sizes (6.4- 358.7 kb) and guanine plus cytosine (GC) content (35.5-65.4%) and a linear correlation between the genome size and the number of open reading frames (ORFs). We used three approaches to compare the phage genomes. The NUCmer/MUMmer genome alignment tool was used to evaluate linkages and correlations based on nucleotide identity between genomes. Multiple sequence alignment was performed to calculate genome average nucleotide identity using the Kalgin program. Finally, genome synteny was explored using dot plot analysis. We found that 90 phage genome sequences grouped into 17 distinct clusters while the remaining 52 genomes showed no close relationships with the other phage genomes and are identified as singletons. We generated genome maps using nucleotide and amino acid sequences which allowed protein-coding genes to be sorted into phamilies (phams) using the Phamerator software. Out of 5796 total assigned phamilies, one phamily was observed to be dominant and was found in 49 prophages, or 34.5% of the 142 phages in our collection. A majority of the phamilies, 4330 out of 5796 (74.7%), occurred in just one prophage underscoring the high degree of diversity among Salmonella bacteriophages. Conclusions: Based on nucleotide and amino acid sequences, a high diversity was found among Salmonella bacteriophages which validate the use of prophage sequence analysis as a highly discriminatory subtyping tool for Salmonella. Thorough understanding of the conservation and variation of prophage genomic characteristics will facilitate their rational design and use as tools for bacterial strain construction, vector development and as anti-bacterial agents.
Evidence for Viscoelastic Effects in Surface Capillary Waves of Molten Polymer Films (2007)

The surface dynamics of supported ultrathin polystyrene films with thickness comparable to the radius of gyration were investigated by surface sensitive x-ray photon correlation spectroscopy. We show for the first time that the conventional model of capillary waves on a viscous liquid has to be modified to include the effects of a shear modulus in order to explain both static and dynamic scattering data from ultrathin molten polymer films.
Bit Patterned Media at 1 Tdot/in2 and Beyond (2013)

Bit patterned media (BPM) provide an alternative to conventional granular thin film recording media, circumventing the challenges of managing grain size and its associated noise and thermal stability issues in granular media. A viable fabrication strategy involves creation of a master pattern by rotary-stage e-beam lithography and directed self-assembly of block copolymers, followed by pattern replication via UV-cure nanoimprint lithography and pattern transfer to a magnetic thin film by ion beam etching. These steps have been demonstrated for 150 Gdot/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (1 Tdot/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) hcp patterns, achieving a dot placement tolerance of 1.2 nm 1σ and a defect rate of <; 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . Media samples fabricated in this manner from continuous CoCrPt alloy films have achieved a 1σ switching field distribution of 4% of H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> . A 2T medium SNR of nearly 14 dB and a write bit error rate of 2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> have been shown using a static tester with a conventional product read/write head. Modeling and experiment suggest that higher recording density can be achieved using BPM with a bit aspect ratio (BAR) >; 1. A master pattern generation generation strategy for BAR>; 1 with rectangular islands is shown using intersecting lines generated by directed self-assembly of lamellar block copolymers in combination with spacer-defined line doubling.
Demonstration of planar waveguides on thick LD-3 polymer films for true-time-delay applications (1996)

The successful synthesis of the LD-3 electrooptic polymer has resulted in a highly reliable nonlinear organic material. However, further progress has been impeded due to the fact that LD-3 films produced thus far are too thin to form useful waveguide devices. Here the formation of thick LD-3 films ranging from 1.2 micrometers to 2.4 micrometers by using cyclopentanone as the new solvent are reported. Preliminary waveguide loss studied shows a guide loss of approximately 3 dB/cm. Aimed at forming true-time-delay lines for phased- array antenna applications, optical heterodyne detection is conducted using various waveguide lengths. A heterodyne signal of a base bandwidth of 25 GHz is demonstrated with signal-to-noise ratio of 15 dB.
Dynamic analysis of current regulators for AC motors using complex vectors (2002)

The analysis and design of current regulators for polyphase AC loads is presented using complex vector notation. The AC motor current regulation problem is analyzed by studying both the command tracking and disturbance rejection capability of the current regulator. The use of complex vector notation and the generalization of classical control tools like root locus, frequency response functions, and dynamic stiffness functions to complex vectors provide a way of comparing the performance of different controller topologies. Limitations in the performance of the synchronous frame PI current regulator are outlined and several ways of improving its performance are suggested and investigated.
Normal-metal hot-electron bolometer with Andreev reflection from superconductor boundaries (1999)

This paper describes the design and experimental testing of a high-sensitivity hot-electron bolometer based a film of normal metal, exploiting the Andreev reflection from superconductor boundaries, and cooled with the help of a superconductor-insulator-normal metal junction. At the measured thermal conductivity, G≈6×10−12 W/K, and a time constant of τ=0.2 μs, and a temperature of 300 mK, the estimated noise-equivalent power NEP=5×10−18 W/Hz1/2, assuming that temperature fluctuations are the major source of noise. At a temperature of 100 mK, the thermal conductivity drops to G≈7×10−14 W/K, which yields NEP=2×10−19 W/Hz1/2 at a time constant of τ=5 μs. The microbolometer has been designed to serve as a detector of millimeter and FIR waves in space-based radio telescopes.
Patterns of Long Acting Injectable Antipsychotic Prescription During Criminal Acts in a Portuguese Psychiatric Hospital (2016)

Introduction Under the Portuguese law, criminal offenders that are designated as non-criminal responsible – “inimputáveis”, similar those in the United States of America found “not guilty by reason of insanity”, are forced to be committed to inpatient forensic units either in psychiatric hospitals or prison hospitals for mandatory security measures. Objectives/aims To evaluate if patients committed in a regional forensic inpatient unit (RFIU) who had a psychiatric history preceding the crime, were under long acting injectable antipsychotic (LAIA) in during the period of the crime. Methods During September/October 2015, patients committed to the RFIU in Centro Hospitalar Psiquiátrico de Lisboa were characterized using medical and court records regarding clinical and demographic variables. The type of crime and previous number of criminal acts were also accounted for. Results We included 33 patients in the study. During time of the crime, 25 patients (75.8%) had history of previous psychiatric appointments, with an average of 3 commitments to the psychiatric inpatient units. The majority ( n = 17; 68%) had a diagnose of “schizophrenia, schizotypal and delusional disorders” (F20–29; ICD 10) and committed “crimes against life” ( n = 13; 52%). They had an average of 0.8 previous criminal acts. During the crime, 7 patients (28%) were taking LAIA. Those, 16% ( n = 4) were doing an unknown antipsychotic and 12% ( n = 3) were doing Haloperidol. Conclusions Despite several studies showing the clinical and rehabilitative benefit of using LAIA early in the disease course, most of the patients in our study, who were already being followed in outpatient psychiatric units, did not benefit from them. Disclosure of interest The authors have not supplied their declaration of competing interest.