gebhart/patrepeval huggingface dataset:
Hexagonal voids and the formation of micropipes during SiC sublimation growth (2001)

Hexagonal voids observed in sublimation grown SiC boules were examined using optical microscopy, atomic force microscopy (AFM), scanning electron microscopy, KOH etching, and synchrotron white-beam x-ray topography. Voids formed at imperfections in the attachment layer between the seed and crucible cap. They are platelet-like in shape with lateral sizes between 50 and 750 μm and thickness along the c axis between 5 and 25 μm. Growth steps were observed on the void facets closest to the seed and evaporation steps were observed on void facets closest to the growth surface, providing evidence for void movement during crystal growth. AFM images revealed that growth steps nucleate at a void sidewall, flow across the bottom of the void, and terminate in a trench-like depression. KOH etching of waters between the void and seed revealed dislocations lining up along the trace of the void path, often with higher densities corresponding to the location of the trench. X-ray topographs showed a random distribution of screw dislocations in the crystal volume above the void, and an absence of screw dislocations in the volume directly below the void. Hollow-core superscrew dislocations, called micropipes, were found at the corners of the void trace. Image forces associated with growth steps and void sidewalls are used to explain the formation of micropipes.
Rapid identification of Arabidopsis insertion mutants by non‐radioactive detection of T‐DNA tagged genes (2002)

Summary To assist in the analysis of plant gene functions we have generated a new Arabidopsis insertion mutant collection of 90 000 lines that carry the T‐DNA of Agrobacterium gene fusion vector pPCV6NFHyg. Segregation analysis indicates that the average frequency of insertion sites is 1.29 per line, predicting about 116 100 independent tagged loci in the collection. The average T‐DNA copy number estimated by Southern DNA hybridization is 2.4, as over 50% of the insertion loci contain tandem T‐DNA copies. The collection is pooled in two arrays providing 40 PCR templates, each containing DNA from either 4000 or 5000 individual plants. A rapid and sensitive PCR technique using high‐quality template DNA accelerates the identification of T‐DNA tagged genes without DNA hybridization. The PCR screening is performed by agarose gel electrophoresis followed by isolation and direct sequencing of DNA fragments of amplified T‐DNA insert junctions. To estimate the mutation recovery rate, 39 700 lines have been screened for T‐DNA tags in 154 genes yielding 87 confirmed mutations in 73 target genes. Screening the whole collection with both T‐DNA border primers requires 170 PCR reactions that are expected to detect a mutation in a gene with at least twofold redundancy and an estimated probability of 77%. Using this technique, an M 2 family segregating a characterized gene mutation can be identified within 4 weeks.
jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units (2011)

jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/.
Emission spectroscopy analysis of carbonaceous molecules involved in dust particle growth by plasma (2015)

International audience
A Virtual Reality Test for the Assessment of Cognitive Deficits: Usability and Perspectives (2013)

The assessment of cognitive deficits, such as executive functions, can be critical in neuropsychology because is not easy to catch all the important cues of real-life behavior using the classic paper and pensil tests or even sophisticated laboratory tasks. On the other hand, using virtual simulation
Modern sand provenance and transport across the western Gulf of Mexico margin (2023)

Petrographic and detrital zircon U-Pb analysis of modern beach sands and river sands from major catchments in northeastern Mexico draining to the Gulf of Mexico provides evidence for a minimum of 650 km of littoral sand transport southward from the mouth of the Rio Grande at the Mexico-U.S. border to the central part of the state of Veracruz, Mexico. Principal tracers of Rio Grande sand include: (1) quartzose composition that contrasts with lithic compositions of sand in eastern Mexico rivers and (2) detrital zircon ages with Mesoproterozoic modes at 1.8−1.5 Ga and 1.4 Ga, age groups that are typical of basement and derivative sediment of the SW United States but are uncommon to rare in Mexican river catchments. In contrast, abundant Miocene and younger grains in beach sands of Veracruz indicate primary sediment derivation from active and recently active volcanoes in the Trans-Mexican volcanic belt in central Mexico. A proportional decrease in sand of Rocky Mountain provenance with distance southward along the coast from the mouth of the Rio Grande and absence of Miocene and younger zircon grains in beaches north of rivers draining the Trans-Mexican volcanic belt indicate net littoral sand transport southward along the eastern coast of Mexico, demonstrating that wintertime shoreline-parallel surface currents rather than north-directed summertime currents dominate sediment transfer. Sand samples of Tamaulipas beaches in northeastern Mexico commonly have equal or higher proportions of U.S.-derived Mesoproterozoic zircon grains than are present in river bar sand of the lower Rio Grande and the Rio Grande delta, and thus require that littoral processes rework and incorporate coastal dune and beach sands of northeastern Mexico that are enriched in predam Rio Grande sediment. Implied coastal erosion may be related to Holocene transgression or interruption of sediment supply to the coastal sediment transport system by dams in the Rio Grande drainage basin. Such coastal erosion is impacting long-term shoreline stability and viability of the littoral environment.
Developments in Schizophrenia Treatment (2001)

Several years ago, a research group from the United Kingdom announced in the prestigious scientific journal Nature that a gene for schizophrenia had been located. This was greeted with widespread applause. Even the editors of Nature believed that a major piece of the puzzle for schizophrenia had at last been found. Sadly, the bubble soon burst. Despite many attempts, no one was able to replicate the initial finding, and it is now widely felt to have been a mistake. This is no longer surprising. Use of the restriction fragment length polymorphism approach to finding genes for complex disorders like schizophrenia has been notably unsuccessful. Currently, journal editors are alerted to the receipt of claims that a gene for some disorder has been found, only to be burnt by the next dozen failures to replicate the finding. The schizophrenia “finding” was a great disappointment.
The mitochondrial protein TSPO in Alzheimer’s disease: relation to the severity of AD pathology and the neuroinflammatory environment (2023)

The 18kD translocator protein (TSPO) is used as a positron emission tomography (PET) target to quantify neuroinflammation in patients. In Alzheimer's disease (AD), the cerebellum is the pseudo-reference region for comparison with the cerebral cortex due to the absence of AD pathology and lower levels of TSPO. However, using the cerebellum as a pseudo-reference region is debated, with other brain regions suggested as more suitable. This paper aimed to establish the neuroinflammatory differences between the temporal cortex and cerebellar cortex, including TSPO expression. Using 60 human post-mortem samples encompassing the spectrum of Braak stages (I-VI), immunostaining for pan-Aβ, hyperphosphorylated (p)Tau, TSPO and microglial proteins Iba1, HLA-DR and MSR-A was performed in the temporal cortex and cerebellum. In the cerebellum, Aβ but not pTau, increased over the course of the disease, in contrast to the temporal cortex, where both proteins were significantly increased. TSPO increased in the temporal cortex, more than twofold in the later stages of AD compared to the early stages, but not in the cerebellum. Conversely, Iba1 increased in the cerebellum, but not in the temporal cortex. TSPO was associated with pTau in the temporal cortex, suggesting that TSPO positive microglia may be reacting to pTau itself and/or neurodegeneration at later stages of AD. Furthermore, the neuroinflammatory microenvironment was examined, using MesoScale Discovery assays, and IL15 only was significantly increased in the temporal cortex. Together this data suggests that the cerebellum maintains a more homeostatic environment compared to the temporal cortex, with a consistent TSPO expression, supporting its use as a pseudo-reference region for quantification in TSPO PET scans.
TiN/TiSi2 Formation Using TiNx Layer and Its Feasibilities in ULSI (1994)

A new technique for the formation of the TiN/TiSi2 bilayer using a TiNx layer was described. The TiNx layer was deposited by sputtering in a mixed gas atmosphere of argon and nitrogen, wherein the concentration of nitrogen was controlled to be lower than that required in the formation of stoichiometric TiN. The nitrogen atoms in the Ti matrix relaxed the mechanical stress of the deposited film and also limited the number of Ti atoms available for the interaction with the Si substrate (i.e., silicidation reaction). Upon thermal annealing, TiNx changed to the bilayer structure of TiN/TiSi2, in which the thickness of the overlying TiN was so great that only a rather thin TiSi2 was formed between TiN and the Si substrate. Moreover, TiN had the (111) texture, and TiSi2 formed on the (100)Si substrate was found to show well-aligned epitaxial properties with an extremely uniform thickness.
Channel engineering for analog device design in deep submicron CMOS technology for system on chip applications (2002)

Scaling of analog CMOS in the deep submicron regime is challenging, particularly for mixed mode system on chip applications due to the tradeoff in design requirements for analog and digital applications. The conventional approach employing aggressive gate oxide and S/D junction scaling to suppress the two-dimensional (2-D) electrostatic coupling and related short channel effects that degrade the device behavior in the deep submicron regime, though, improves the digital performance. However, this approach is not sufficient to obtain a reasonable analog performance. This paper presents a comprehensive study on the analog performance of scaled MOSFETs and explores alternative ways for improving the analog performance of these devices. It is shown that an easily integrable innovative channel engineering scheme in the form of single pocket structures can be used in the standard logic CMOS process to significantly improve the device analog performance of the deep submicron devices.
Development and Performance of High-Speed SPM Synchronous Machine (2018)

This paper presents a performance evaluation for a 250 kW - 20,000 min <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> high-speed permanent magnet (PM) motor for high-speed applications such as industrial blowers and compressors. The utilization of a high-speed motor for a direct drive system can contribute to making the system size more compact when compared to a geared system. However, this could cause the motor loss density to be high due to the high output power density in the high-speed motor. At this time, we evaluated the electrical characteristics and efficiency of the prototype 250 kW - 20,000 min <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> high-speed PM motor and measured the temperature increase by carrying out a heat run test. Furthermore, loss separation was performed to improve the efficiency and design accuracy.
LIDAR and Monocular Based Overhanging Obstacle Detection (2015)

This paper presents an improved method for the detection of obstacles in the trajectory of autonomous ground vehicle (AGV). The novel approach requires fewer calculations, i.e. less computational time. Obstacle detection algorithms were investigated, in order to perform safe motion control, in an environment with unknown overhanging obstacles. We describe a two dimensional (2D) laser sensor application, and optimal sensor configurations for mounting a monocular camera to monitor path ahead clearance. Two different sensors are used, a vision sensor and a scanning laser, Light Detection and Ranging (LIDAR). While LIDAR measures the precise distance to the object, it cannot detect low objects and overhanging obstacles due to its predefined, constant, scanning height and angle. In contrast, vision sensor provides 2D scenery information with relatively poor distance information. To compensate for the drawbacks of these two sensors, the sensor fusion method for obstacle detection of AGV is proposed. Size expansion cue algorithm is deployed to achieve that goal. Proposed method is validated experimentally.
Folding correction of ABC‐transporter ABCB1 by pharmacological chaperones: a mechanistic concept (2017)

Point mutations of ATP-binding cassette (ABC) proteins are a common cause of human diseases. Available crystal structures indicate a similarity in the architecture of several members of this protein family. Their molecular architecture makes these proteins vulnerable to mutation, when critical structural elements are affected. The latter preferentially involve the two transmembrane domain (TMD)/nucleotide-binding domain (NBD) interfaces (transmission interfaces), formation of which requires engagement of coupling helices of intracellular loops with NBDs. Both, formation of the active sites and engagement of the coupling helices, are contingent on correct positioning of ICLs 2 and 4 and thus an important prerequisite for proper folding. Here, we show that active site compounds are capable of rescuing P-glycoprotein (P-gp) mutants ∆Y490 and ∆Y1133 in a concentration-dependent manner. These trafficking deficient mutations are located at the transmission interface in pseudosymmetric position to each other. In addition, the ability of propafenone analogs to correct folding correlates with their ability to inhibit transport of model substrates. This finding indicates that folding correction and transport inhibition by propafenone analogs are brought about by binding to the active sites. Furthermore, this study demonstrates an asymmetry in folding correction with cis-flupentixol, which reflects the asymmetric binding properties of this modulator to P-gp. Our results suggest a mechanistic model for corrector action in a model ABC transporter based on insights into the molecular architecture of these transporters.
Influence of lead and lag differences on localization (2002)

The precedence effect explains the ability of our hearing system to locate a sound source in a reverberant room. However, there are still many unknowns about how the occurrence of the effect depends on the differences of the lead and lag. In this paper, lead and lag signals were not reproduced only through one sound source, but simultaneously through two. Thus, the precedence effect was simulated using two phantom sound sources rather then two real sources. Cross-correlation function between left and right ear signals of a dummy head was calculated in order to find the relation to subjective tests.
A QUANTITATIVE MODELING METHOD OF BEHAVIOR AND CAUSE-AND-EFFECT RELATIONSHIPS AMONG PHYSICAL PHENOMENA FOR FAILURE DETECTION CONSIDERING WAYS OF USE (2016)

With recent globalization in industries, the number of failures and troubles of products caused by using them in unexpected ways has increased. In order to avoid such troubles, it is necessary not only to assume various ways of use thoroughly, but also to verify whether the design plan can fulfill required functions when the product is utilized in those ways. From this point of view, the authors proposed a functional verification method considering ways of use based on qualitative modeling of behavior and cause-and-effect relationships among physical phenomena using Petri nets. It is, however, impossible to detect failures concerning to specification which requires dealing with quantitative information. This paper provides a method for quantitative modeling of behavior and cause-and-effect relationships among physical phenomena. Two types of tokens were defined for dealing with positive and negative values and four types of arcs were for controlling changes of those values. These new elements of Petri net made it possible to represent behavior and cause-and-effect relationships quantitatively. Application of this new modeling method to the functional verification method enables automatic detection of failures concerning to both functions and specification. The verification method using this modeling method was applied to an example, and its effectiveness was proven.
Novel Spectrum Sensing Methods for OFDM Systems Using Deep Learning Networks (2018)

Spectrum sensing plays a critical role in dynamic spectrum sharing, a promising technology to address the radio spectrum shortage. In particular, sensing of Orthogonal frequency division multiplexing (OFDM) signals, a widely accepted multi-carrier transmission paradigm, has received paramount interest. Despite various efforts, most conventional OFDM sensing methods suffer from noise uncertainty, timing delay and carrier frequency offset (CFO) that significantly degrade the sensing accuracy. To address these challenges, this work develops two novel OFDM sensing frameworks drawing support from deep learning networks. Specifically, we first propose a stacked autoencoder based spectrum sensing method (SAE-SS), in which a stacked autoencoder network is designed to extract the inherent features of OFDM signals. Using these features to classify the OFDM user's activities, SAE-SS is much more robust to noise uncertainty, timing delay, and CFO than the conventional OFDM sensing methods. Moreover, SAE-SS doesn't require any prior information of signals (e.g., signal structure, pilot tones, cyclic prefix) which are essential for the conventional feature-based OFDM sensing methods. To further improve the sensing accuracy of SAE-SS, especially under low SNR conditions, we propose a stacked autoencoder based spectrum sensing method using time-frequency domain signals (SAE-TF). SAE-TF achieves higher sensing accuracy than SAW-SS at the cost of higher computational complexity. Extensive simulation results show that both SAE-SS and SAE-TF can achieve significantly higher sensing accuracy, compared with state of the art approaches that suffer from noise uncertainty, timing delay and CFO.
Defective phagocytosis leads to neurodegeneration through systemic increased innate immune signaling (2023)

In nervous system development, disease and injury, neurons undergo programmed cell death, leaving behind cell corpses that are removed by phagocytic glia. Altered glial phagocytosis has been implicated in several neurological diseases including Alzheimer's disease, Parkinson's disease, and traumatic brain injury. To untangle the links between glial phagocytosis and neurodegeneration, we investigated <i>Drosophila</i> mutants lacking the phagocytic receptor Draper. Loss of Draper leads to persistent neuronal cell corpses and age-dependent neurodegeneration. Here we investigate whether the phagocytic defects observed in <i>draper</i> mutants lead to chronic increased immune activation that promotes neurodegeneration. A major immune response in <i>Drosophila</i> is the activation of two NFκB signaling pathways that produce antimicrobial peptides, primarily in the fat body. We found that the antimicrobial peptide Attacin-A is highly upregulated in the fat body of aged <i>draper</i> mutants and that inhibition of the Immune deficiency (Imd) pathway in the glia and fat body of <i>draper</i> mutants led to reduced neurodegeneration, indicating that immune activation promotes neurodegeneration in <i>draper</i> mutants. Taken together, these findings indicate that phagocytic defects lead to neurodegeneration via increased immune signaling, both systemically and locally in the brain.
W-AKA: Privacy-enhanced LTE-AKA using secured channel over Wi-Fi (2013)

In this paper, we propose a privacy-enhanced LTE authentication and key agreement scheme, W-AKA. The scheme promises to improve privacy by employing a dynamic identity instead of the static IMSI. In order to exchange the IMSI and inform the user of the new randomized identity, we propose two methods. The first method uses a Wi-Fi secured side channel since Wi-Fi hotspots are becoming ubiquitous. The other method is incorporated as part of the mobile AKA. We also present a simple method through which a random temporary identity is generated. We studied the conditions where W-AKA outperforms the original AKA and where it underperforms. Our analysis shows that in the presence of Wi-Fi, and unless an attacker jams the Wi-Fi channel, W-AKA can sustain both active and passive attacks. On the other hand, in the absence of Wi-Fi, it can only mitigate risks of passive attacks. The difficulties and challenges of the proposed work are also analyzed. The scheme was implemented and compared with previously-published techniques in order to study the computational overhead to accomplish enhanced privacy.
Cone-like rhodopsin expressed in the all cone retina of the colubrid pine snake as a potential adaptation to diurnality (2017)

Colubridae is the largest and most diverse family of snakes, with visual systems that reflect this diversity, encompassing a variety of retinal photoreceptor organizations. The transmutation theory proposed by Walls postulates that photoreceptors could evolutionarily transition between cell types in squamates, but few studies have tested this theory. Recently, evidence for transmutation and rod-like machinery in an all-cone retina has been identified in a diurnal garter snake (<i>Thamnophis</i>), and it appears that the rhodopsin gene at least may be widespread among colubrid snakes. However, functional evidence supporting transmutation beyond the existence of the rhodopsin gene remains rare. We examined the all-cone retina of another colubrid, <i>Pituophis melanoleucus</i>, thought to be more secretive/burrowing than <i>Thamnophis</i> We found that <i>P. melanoleucus</i> expresses two cone opsins (SWS1, LWS) and rhodopsin (RH1) within the eye. Immunohistochemistry localized rhodopsin to the outer segment of photoreceptors in the all-cone retina of the snake and all opsin genes produced functional visual pigments when expressed <i>in vitro</i> Consistent with other studies, we found that <i>P. melanoleucus</i> rhodopsin is extremely blue-shifted. Surprisingly, <i>P. melanoleucus</i> rhodopsin reacted with hydroxylamine, a typical cone opsin characteristic. These results support the idea that the rhodopsin-containing photoreceptors of <i>P. melanoleucus</i> are the products of evolutionary transmutation from rod ancestors, and suggest that this phenomenon may be widespread in colubrid snakes. We hypothesize that transmutation may be an adaptation for diurnal, brighter-light vision, which could result in increased spectral sensitivity and chromatic discrimination with the potential for colour vision.