gebhart/patrepeval huggingface dataset:
Expression of N‐Methyl‐D‐Aspartate receptor subunit mRNA in the human brain: Mesencephalic dopaminergic neurons (1998)

Evidence is accumulating that glutamate-mediated excitotoxicity plays an important role in neuronal degeneration in Parkinson's disease (PD). In addition, alterations in excitatory amino acid neurotransmission in the basal ganglia contribute to the clinical manifestations of motor dysfunction. However, detailed knowledge of the anatomical distribution and subtype specificity of glutamate receptors in the dopamine neurons of human substantia nigra (SN) has been lacking. In order to test the hypothesis that selective expression of particular N-methyl-D-aspartate receptor (NR) subunit mRNA contributes to the differential vulnerability of specific neuronal populations to excitotoxic injury in PD, we have used a quantitative dual label, in situ hybridization technique with ribonucleotide probes to examine the cellular distribution of NR subunit mRNA in postmortem human mesencephalic dopaminergic neurons from subjects with no known neurological disorder. Analysis of both film autoradiograms and emulsion-dipped sections demonstrated significant labeling of nigral neurons for each NR subunit. Neuronal labeling was most intense for the NR1 and NR2D subunits, with low level labeling for the remaining subunits. In addition, we examined four subregions of the ventral mesencephalon for differential expression of NR subunit mRNA. For all NR subunits, the pars lateralis (PL) exhibited the most intense signal, while neurons of the ventral tier substantia nigra pars compacta (SNpc) failed to demonstrate a preponderance of a particular subunit. These results demonstrate that NRs are expressed to a significant degree in dopaminergic neurons of the SN and that their distribution does not correlate with the characteristic pattern of neuronal degeneration in PD. J. Comp. Neurol. 390:91–101, 1998. © 1998 Wiley-Liss, Inc.
Resistance Mechanisms inPseudomonas aeruginosaand Other Nonfermentative Gram‐Negative Bacteria (1998)

Nonfermentative gram-negative bacilli are still a major concern in compromised individuals. By far the most important of these organisms is Pseudomonas aeruginosa, although Acinetobacter baumannii (previously Acinetobacter calcoaceticus), Stenotrophomonas maltophilia (previously Pseudomonas and Xanthomonas maltophilia), and Burkholderia cepacia (previously Pseudomonas cepacia) are also of substantative concern because of their similar high intrinsic resistances to antibiotics. The basis for the high intrinsic resistance of these organisms is the lower outer-membrane permeability of these species, coupled with secondary resistance mechanisms such as an inducible cephalosporinase or antibiotic efflux pumps, which take advantage of low outer-membrane permeability. Even a small change in antibiotic susceptibility of these organisms can result in an increase in the MIC of a drug to a level that is greater than the clinically achievable level. In this review, the major mechanisms of resistance observed in the laboratory and clinic are summarized.
ALIX/AIP1 Is Required for NP Incorporation into Mopeia Virus Z-Induced Virus-Like Particles (2011)

During virus particle assembly, the arenavirus nucleoprotein (NP) associates with the viral genome to form nucleocapsids, which ultimately become incorporated into new virions at the cell membrane. Virion release is facilitated by the viral matrix Z protein through its interaction with the cellular endosomal sorting complex required for transport (ESCRT) machinery. However, the mechanism of nucleocapsid incorporation into virions is not well understood. Here, we demonstrate that ALIX/AIP1, an ESCRT-associated host protein, is required for the incorporation of the NP of Mopeia virus, a close relative of Lassa virus, into Z-induced virus-like particles (VLPs). Furthermore, we show that the Bro1 domain of ALIX/AIP1 interacts with the NP and Z proteins simultaneously, facilitating their interaction, and we identify residues 342 to 399 of NP as being necessary for its interaction with ALIX/AIP1. Our observations suggest a potential role for ALIX/AIP1 in linking Mopeia virus NP to Z and the budding apparatus, thereby promoting NP incorporation into virions.
<title>Tunneling tip protection for a bulk micromachined accelerometer</title> (1995)

Ultrasensitive accelerometers are needed by NASA for the measurement of orbital drag. We have designed an accelerometer capable of measuring 10<SUP>-8</SUP>. In this paper, a method for fabricating a bulk micromachined accelerometer which incorporates a tunneling tip is presented. To meet sensitivity sepcifications, a weak spring and large mass are needed. However, these represent a delicate mechanism and a method of protection is provided by electrostatically clamping the proof mass in a fixed position. The effectiveness of the electrostatic clamp has been measured. It is found that clamping against an acceleration of 200 g is possible with voltages as low as 30 volts.
Reliable hopping sequence design for highly interfered wireless sensor networks (2017)

Guaranteeing reliability in highly interfered environments is a challenging requirement of current and future wireless applications. A promising state-of-the-art solution for low-power wireless technologies, e.g., wireless sensor networks (WSNs), is frequency hopping aided with black- and white-listing of channels. Both methods, although increase reliability, sacrifice frequency resources. Extensive measurements of channels' packet drop probabilities show that interfered channels are not fully blocked. Motivated by this discovery, we propose the whitening - a methodology for reliable hopping sequence design without resource sacrifice. We model the efficiency of interfered ISM band channels, and study the gains and trade-offs of applying whitening in different scenarios. Application reliability is achieved by granting re-transmissions within a time deadline. Simulations and measurements, performed on the exemplary use case of Time Slotted Channel Hopping WSNs, show that the proposed methods outperform state-of-the-art solutions in the presence of interference in terms of reliability.
Towards Multimodal Depth Estimation from Light Fields (2022)

Light field applications, especially light field rendering and depth estimation, developed rapidly in recent years. While state-of-the-art light field rendering methods handle semi-transparent and reflective objects well, depth estimation methods either ignore these cases altogether or only deliver a weak performance. We argue that this is due current methods only considering a single "true" depth, even when multiple objects at different depths contributed to the color of a single pixel. Based on the simple idea of outputting a posterior depth distribution instead of only a single estimate, we develop and explore several different deep-learning-based approaches to the problem. Additionally, we contribute the first "multimodal light field depth dataset" that contains the depths of all objects which contribute to the color of a pixel. This allows us to supervise the multimodal depth prediction and also validate all methods by measuring the KL divergence of the predicted posteriors. With our thorough analysis and novel dataset, we aim to start a new line of depth estimation research that overcomes some of the long-standing limitations of this field.
Even Faster SNN Simulation with Lazy+Event-driven Plasticity and Shared Atomics (2021)

We present two novel optimizations that accelerate clock-based spiking neural network (SNN) simulators. The first one targets spike timing dependent plasticity (STDP). It combines lazy- with event-driven plasticity and efficiently facilitates the computation of pre- and post-synaptic spikes using bitfields and integer intrinsics. It offers higher bandwidth than event-driven plasticity alone and achieves a 1.5×–2× speedup over our closest competitor. The second optimization targets spike delivery. We partition our graph representation in a way that bounds the number of neurons that need be updated at any given time which allows us to perform said update in shared memory instead of global memory. This is 2×–2.5× faster than our closest competitor. Both optimizations represent the final evolutionary stages of years of iteration on STDP and spike delivery inside "Spice" (/spaIk/), our state of the art SNN simulator. The proposed optimizations are not exclusive to our graph representation or pipeline but are applicable to a multitude of simulator designs. We evaluate our performance on three well-established models and compare ourselves against three other state of the art simulators.
Investigation of Reactive Transport and Coupled THMC Processes in the EBS (2013)

Geological repositories for disposal of high-level nuclear waste generally rely on a multibarrier system to isolate radioactive waste from the biosphere. The multi-barrier system typically consists of the natural barrier system (NBS), which includes the repository host rock and its surrounding subsurface environment, and the engineered barrier system (EBS). The EBS represents the man-made, engineered materials placed within a repository, including the waste form, waste canisters, buffer materials, backfill, and seals (OECD, 2003). The EBS plays a significant role in the containment and long-term retardation of radionuclide release.
Viral Load and Acute Otitis Media Development After Human Metapneumovirus Upper Respiratory Tract Infection (2012)

The role of human metapneumovirus (hMPV) in acute otitis media complicating upper respiratory tract infection (URI) was studied. Nasopharyngeal specimens from 700 URI episodes in 200 children were evaluated; 47 (7%) were positive for hMPV, 25 (3.6%) with hMPV as the only virus. Overall, 24% of URI episodes with hMPV only were complicated by acute otitis media, which was the lowest rate compared with other respiratory viruses. hMPV viral load was significantly higher in children with fever, but there was no difference in viral load in children with hMPV-positive URI with or without acute otitis media complication.
Outdoor Operation of Structured Light in Mobile Phone (2017)

Active Depth Camera is about to be integrated into a mobile phone and now beginning to be introduced into the market. It is expected that this technology will enable brand-new and meaningful user experiences in egocentric ecosystems. In view of practical usage, however, Active Depth Camera does not operate well especially outdoors because signal light is much weaker than ambient sunlight. To overcome this problem, Spectro-Temporal Light Filtering, adopting a light source of 940nm wavelength, has been designed. In order to check and improve outdoor depth quality, mobile phones for proof-of-concept have been implemented with structured light depth camera enclosed. We present its outdoor performance, featuring a 940nm vertical cavity surface emitting laser as a light source and an image sensor with a global shutter to reduce ambient light noise. The result makes us confident that this functionality enables mobile camera technology to step into another stunning stage.
DM-SCOPE, bilan d’étape et atouts des bases de données pour les maladies neuromusculaires (2015)

Il y a 7 ans, l’Observatoire français des dystrophies myotoniques, DM-Scope, était lancé pour améliorer la connaissance et la prise en charge des dystrophies myotoniques dont l’expression clinique extrêmement variable représente un frein pour la recherche et la prise en charge. Quel bilan d’étape peut-on formuler aujourd’hui ? Plus particulièrement, quelles catégories d’avancées des connaissances et de prise en charge sont susceptibles de bénéficier d’un tel outil ?
A Farm on Broiler Chickens' Welfare in Korea (2013)

We conducted investigations of the information and welfare of broiler chickens in Korea. The livestock housing of all broiler chicken farms were windowless type, bell feeder and nipple waterer were used, and stocking density was relatively higher (ranging from 18.2 <TEX>$birds/m^2$</TEX> to 24.2 <TEX>$birds/m^2$</TEX>) than RSPCA's welfare standards for chicken hens (less than 19 <TEX>$birds/m^2$</TEX>). The ratios of sandwich panel, urethane form, slate, and steel plate in roofing materials were 61%, 21%, 13%, and 5%, respectively. The ratios of sandwich panel, urethane form, brick, and steel plate in wall materials were 61%, 21%, 13%, and 5%, respectively. The ratios of soil and concrete in flooring materials were 10% and 90%. The mist spray, fan, and cooling pad in cooling facilities were 42%, 32%, and 26%, respectively. Thus we believe that present data contribute to develop the animal welfare certification for broiler chickens and to improve animal welfare in Korea.
Density of grammar forms. part I (1986)

We give two characterizations for dense intervals consisting of grammatical families. These results are general enough to cover the eases of context-free grammar forms, general grammar forms and synchronized EOL forms. By means of the characterizations it is proved that denseness is undecidable for context-free forms. The characterization theorems also enable us to investigate the maximality of dense intervals. The paper is divided into two parts. The results mentioned above are presented in Part II. This first part contains definitions and preliminary results. Also in Part I, we investigate language families defined by subregular forms and clarify the role of the empty word in form theory.
Identification of Novel CD4+ T Cell Subsets in the Target Tissue of Sjögren’s Syndrome and Their Differential Regulation by the Lymphotoxin/LIGHT Signaling Axis (2016)

Despite being one of the most common rheumatologic diseases, there is still no disease-modifying drug for primary Sjögren's syndrome (pSS). Advancing our knowledge of the target tissue has been limited by the low dimensionality of histology techniques and the small size of human salivary gland biopsies. In this study, we took advantage of a molecularly validated mouse model of pSS to characterize tissue-infiltrating CD4<sup>+</sup> T cells and their regulation by the lymphotoxin/LIGHT signaling axis. Novel cell subsets were identified by combining highly dimensional flow and mass cytometry with transcriptomic analyses. Pharmacologic modulation of the LTβR signaling pathway was achieved by treating mice with LTβR-Ig, a therapeutic intervention currently being tested in pSS patients (Baminercept trial NCT01552681). Using these approaches, we identified two novel CD4<sup>+</sup> T cell subsets characterized by high levels of PD1: Prdm1<sup>+</sup> effector regulatory T cells expressing immunoregulatory factors, such as Il10, Areg, Fgl2, and Itgb8, and Il21<sup>+</sup> effector conventional T cells expressing a pathogenic transcriptional signature. Mirroring these observations in mice, large numbers of CD4<sup>+</sup>PD1<sup>+</sup> T cells were detected in salivary glands from Sjögren's patients but not in normal salivary glands or kidney biopsies from lupus nephritis patients. Unexpectedly, LTβR-Ig selectively halted the recruitment of PD1<sup>-</sup> naive, but not PD1<sup>+</sup>, effector T cells to the target tissue, leaving the cells with pathogenic potential unaffected. Altogether, this study revealed new cellular players in pSS pathogenesis, their transcriptional signatures, and differential dependency on the lymphotoxin/LIGHT signaling axis that help to interpret the negative results of the Baminercept trial and will guide future therapeutic interventions.
Promoter hypermethylation of tumor‐related genes in the progression of colorectal neoplasia (2004)

Gene promoter hypermethylation is increasingly recognized to play an important role in cancer development through silencing of gene transcription. This study determined the methylation profiles of primary colorectal cancers and adenomas to elucidate the role of epigenetic changes in different stages of colorectal carcinogenesis. We examined the methylation profiles of 47 sporadic colorectal cancers, 36 colonic adenomas from patients without cancer and 34 colonic biopsies from patients without colonic lesions. Paired adjacent dysplasia tissues obtained from 17 cancer patients were also examined. Promoter hypermethylation in 10 tumor-related genes (APC, ATM, GSTP1, HLTF, MGMT, hMLH1, p14, p15, SOCS-1 and TIMP-3) were studied by methylation-specific PCR. Promoter hypermethylation was frequently detected in more than 40% of colonic cancers and adenomas in APC, ATM, HLTF, MGMT and hMLH1 genes (p < 0.0001 vs. normal). While low level of methylation was detected in p14, p15 and TIMP-3, there was no methylation detected in GSTP1 and SOCS-1. The frequencies of methylation were comparable between tumors and adenomas, and advanced and nonadvanced adenoma. In contrast, K-ras mutation was only detected in advanced adenomas and cancers. Concurrent methylation in >/= 3 genes was found in 66.7% adenomas and 68.1% cancers but not in normal colonic tissues. Methylation was associated with reduced protein expressions in colorectal adenomas and cancers. Moreover, methylation in ATM was more common in older cancer patients (p = 0.002), but there was no significant association between promoter hypermethylation and other clinicopathologic characteristics of cancer. Our study demonstrated the early and specific involvement of promoter hypermethylation in the colorectal adenoma-carcinoma sequence.
Phenotypic variation and host interactions of Xenorhabdus bovienii SS‐2004, the entomopathogenic symbiont of Steinernema jollieti nematodes (2011)

Xenorhabdus bovienii (SS-2004) bacteria reside in the intestine of the infective-juvenile (IJ) stage of the entomopathogenic nematode, Steinernema jollieti. The recent sequencing of the X. bovienii genome facilitates its use as a model to understand host - symbiont interactions. To provide a biological foundation for such studies, we characterized X. bovienii in vitro and host interaction phenotypes. Within the nematode host X. bovienii was contained within a membrane bound envelope that also enclosed the nematode-derived intravesicular structure. Steinernema jollieti nematodes cultivated on mixed lawns of X. bovienii expressing green or DsRed fluorescent proteins were predominantly colonized by one or the other strain, suggesting the colonizing population is founded by a few cells. Xenorhabdus bovienii exhibits phenotypic variation between orange-pigmented primary form and cream-pigmented secondary form. Each form can colonize IJ nematodes when cultured in vitro on agar. However, IJs did not develop or emerge from Galleria mellonella insects infected with secondary form. Unlike primary-form infected insects that were soft and flexible, secondary-form infected insects retained a rigid exoskeleton structure. Xenorhabdus bovienii primary and secondary form isolates are virulent towards Manduca sexta and several other insects. However, primary form stocks present attenuated virulence, suggesting that X. bovienii, like Xenorhabdus nematophila may undergo virulence modulation.
InGaN blue light-emitting micro-diodes with current path defined by tunnel junction (2022)

In this paper, we try to resolve problems related to decreasing the size of an LED, and find a solution that would let us preserve optoelectronics parameters. The main idea is to use tunnel junctions to define the current path and, therefore, define the size of µLED. This way, during fabrication, there is no need to etch the active region. That way, it does not introduce any degradation nor problems related to surface states or differences in electrical fields inside the device. We have fabricated such devices with sizes ranging from 100 µm-5 µm. In the characterization of these devices, it became apparent that, both electrical and optical parameters, are fully scalable with size. Most importantly, we do not observe an increase in the non-radiative recombination coefficient even for the smallest device. In addition, we observe excellent thermal stability of their light emission characteristics.
A Preprocessing Algorithm Applicable to the Multiuser Detection Problem (2005)

In this paper a preprocessing algorithm for binary quadratic programming problems is presented. For some types of binary quadratic programming problems, the algorithm can compute the optimal value for some or all integer variables without approximations in polynomial time. When the optimal multiuser detection problem is formulated as a maximum likelihood problem, a binary quadratic programming problem has to be solved. Fortunately, the low correlation between different users in the multiuser detection problem enables the use of the preprocessing algorithm. Simulations show that the preprocessing algorithm is able to compute almost all variables in the problem, even though the system is heavily loaded and affected by noise.
Aortic valve and ascending aortic root modeling from 3D and 3D+t CT (2010)

Aortic valve disorders are the most frequent form of valvular heart disorders (VHD) affecting nearly 3% of the global population. A large fraction among them are aortic root diseases, such as aortic root aneurysm, often requiring surgical procedures (valve-sparing) as a treatment. Visual non-invasive assessment techniques could assist during pre-selection of adequate patients, planning procedures and afterward evaluation of the same. However state of the art approaches try to model a rather short part of the aortic root, insufficient to assist the physician during intervention planning. In this paper we propose a novel approach for morphological and functional quantification of both the aortic valve and the ascending aortic root. A novel physiological shape model is introduced, consisting of the aortic valve root, leaflets and the ascending aortic root. The model parameters are hierarchically estimated using robust and fast learning-based methods. Experiments performed on 63 CT sequences (630 Volumes) and 20 single phase CT volumes demonstrated an accuracy of 1.45mm and an performance of 30 seconds (3D+t) for this approach. To the best of our knowledge this is the first time a complete model of the aortic valve (including leaflets) and the ascending aortic root, estimated from CT, has been proposed.
Esterase D Is Essential for Protection ofNeisseria gonorrhoeaeagainst Nitrosative Stress and for Bacterial Growth during Interaction with Cervical Epithelial Cells (2009)

estD encodes a carboxylic ester hydrolase and is part of the NmlR regulon in Neisseria gonorrhoeae. An estD mutant was found to be susceptible to nitrite and to S-nitrosoglutathione. This mutant was also unable to infect and survive within human cervical epithelial cells, and it showed reduced ability to form a biofilm on these cells. We conclude that esterase D is an integral part of the nitrosative stress defense system of N. gonorrhoeae and that it has potential importance in pathogenesis.
Observing molecular motions of a fluorinated ferroelectric liquid crystal using fluorine-19 NMR (1993)

Abstract Fluorine-19 NMR spectra have been recorded for both the phases (cholesteric and smectic C∗) of the ferroelectric liquid crystal 2,3-difluoro-4-octyloxybiphenyl-4′(-4″-oxycarbonyl-(S)-1-chloro-3-methylbutyl)benzoate, using a conventional high-resolution NMR probe. The magnitude of the dipolar coupling constant, D FF0, was found to increase with decreasing temperature in the cholesteric phase with a sudden increase (of approximately 1 000 Hz) at the cholesteric-smectic C∗ transition, whereafter a more gradual change was observed. The order parameter, was S FF, subsequently calculated for each temperature.