gebhart/patrepeval huggingface dataset:
Synaptojanin 1-linked phosphoinositide dyshomeostasis and cognitive deficits in mouse models of Down's syndrome (2008)

Phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P(2)] is a signaling phospholipid implicated in a wide variety of cellular functions. At synapses, where normal PtdIns(4,5)P(2) balance is required for proper neurotransmission, the phosphoinositide phosphatase synaptojanin 1 is a key regulator of its metabolism. The underlying gene, SYNJ1, maps to human chromosome 21 and is thus a candidate for involvement in Down's syndrome (DS), a complex disorder resulting from the overexpression of trisomic genes. Here, we show that PtdIns(4,5)P(2) metabolism is altered in the brain of Ts65Dn mice, the most commonly used model of DS. This defect is rescued by restoring Synj1 to disomy in Ts65Dn mice and is recapitulated in transgenic mice overexpressing Synj1 from BAC constructs. These transgenic mice also exhibit deficits in performance of the Morris water maze task, suggesting that PtdIns(4,5)P(2) dyshomeostasis caused by gene dosage imbalance for Synj1 may contribute to brain dysfunction and cognitive disabilities in DS.
Ontologies and Artificial Intelligence Systems for the Cooperative Smart Farming Ecosystem (2020)

Cyber-Physical Systems (CPS) and Internet of Thing (IoT) generate large amounts of data spurring the rise of Artificial Intelligence (AI) based smart applications. Driven by rapid advancements in technologies that support smart devices, agriculture and farming sector is shifting towards IoT connected ecosystem to balance the increase in demand for food supply. As the number of smart farms reach critical mass, it is now possible to include AI assisted systems at a cooperative (co-op) farming level. Today, in the United States alone there are about 1,871 co-ops serving 1,890,057 member farmers. Hence, such advanced technologies and infrastructure when incorporated in the co-op farming ecosystem can immensely benefit small member farmers who operate and maintain these independent co-op entities. In this paper, we develop a connected cooperative ecosystem which defines sensors and their communication among different entities along with cloud supported co-op hub. We develop member farm and co-op ontologies to capture data and various interactions that happen between shared resources, member farms, and the co-op that are stored in the cloud. These can then help generate AI supported insights for farmers and the cooperative. Several co-op farming use case scenarios have been discussed to demonstrate the functioning of our smart cooperative ecosystem. Finally, the paper describes various AI applications that can be deployed at the co-op level to aid member farmers.
<i>Toxoplasma gondii</i> autophagy-related protein ATG9 is crucial for the survival of parasites in their host (2016)

Autophagy is a conserved, life-promoting, catabolic process involved in the recycling of nonessential cellular components in response to stress. The parasite Toxoplasma gondii is an early-diverging eukaryote in which part of the autophagy machinery is not exclusively involved in a catabolic process but instead has been repurposed for an original function in organelle inheritance during cell division. This function, depending essentially on protein TgATG8 and its membrane conjugation system, is crucial for parasite survival and prevented an in depth study of autophagy in the mutants generated so far in Toxoplasma. Thus, in order to decipher the primary function of canonical autophagy in the parasites, we generated a cell line deficient for TgATG9, a protein thought to be involved in the early steps of the autophagy process. Although the protein proved to be dispensable for the development of these obligate intracellular parasites in vitro, the absence of TgATG9 led to a reduced ability to sustain prolonged extracellular stress. Importantly, depletion of the protein significantly reduced parasites survival in macrophages and markedly attenuated their virulence in mice. Altogether, this shows TgATG9 is important for the fate of Toxoplasma in immune cells and contributes to the overall virulence of the parasite, possibly through an involvement in a canonical autophagy pathway.
Continuous Flow as Enabling Technology: Synthesis of Heteroaromatic Sulfinates as Bench Stable Cross-Coupling Partners (2020)

An enabling continuous flow setup for handling of unstable organolithium intermediates and synthesis of heteroaryl sulfinates on a multigram scale is described. The developed continuous flow process allows for the synthesis and simple isolation of heteroaryl sulfinates which are otherwise challenging to access in classical batch mode. The lithium sulfinate salts prepared by this method were shown to be efficient reaction partners in palladium catalyzed C(<i>sp</i><sup>2</sup>)-C(<i>sp</i><sup>2</sup>) cross-coupling to access medicinally relevant bis-heteroaryl motifs.
Global proteomics dataset of miR-126 overexpression in acute myeloid leukemia (2016)

A deep proteomics analysis was conducted on a primary acute myeloid leukemia culture system to identify potential protein targets regulated by miR-126. Leukemia cells were transduced either with an empty control lentivirus or one containing the sequence for miR-126, and resulting cells were analyzed using ultra-high performance liquid chromatography (UHPLC) coupled with high resolution mass spectrometry. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD001994. The proteomics data and statistical analysis described in this article is associated with a research article, "miR-126 regulates distinct self-renewal outcomes in normal and malignant hematopoietic stem cells" (Lechman et al., 2016) [1], and serves as a resource for researchers working in the field of microRNAs and their regulation of protein levels.
Slew-down: analysis of slew relaxation for low-impact clock buffers (2017)

In the conventional ASIC design flow, slew constraints are imposed on clock sinks and clock buffers uniformly. The slew constraint has a significant affect not only on the timing but also on power in high performance designs. This paper investigates relaxing tight slew constraints for the reduction of low-impact buffers in clock trees. This is motivated by the observation that buffers in a clock tree that directly drive clock sinks have a high impact on meeting timing constraints. Buffers that drive other buffers in the clock tree do not directly impact the sink timing within some bound. These buffers can be considered low-impact, but still consume significant power. In order to reduce this power, the slew design constraint can be relaxed for low-impact buffers. Benchmarks from the ISPD2010 benchmark suite are synthesized to demonstrate the impact of a "slew-down" at the non-sink clock buffers of a clock tree with power and timing results from HSPICE. Results using a 20nm PTM FinFET technology at 4GHz shows that power savings of up to 50% (~10% on average) can be achieved compared to the minimum slew constraint while satisfying the same global slew constraint by a methodical slew-down process.
Skin absorption of actinides: influence of solvents or chelates on skin penetration <i>ex vivo</i> (2017)

Skin penetration and fixation profiles are different depending on the chemical actinide form. Altered behavior of Pu-TBP and actinide-DTPA complexes reinforces the need to address decontamination protocols.
Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature (2019)

Gliosarcoma is a very rare brain tumor reported to be a variant of glioblastoma (GBM), IDH-wildtype. While differences in molecular and histological features between gliosarcoma and GBM were reported, detailed information on the genetic background of this tumor is lacking. We intend to fill in this knowledge gap by the complex analysis of somatic mutations, indels, copy number variations, translocations and gene expression patterns in gliosarcomas. Using next generation sequencing, we determined somatic mutations, copy number variations (CNVs) and translocations in 10 gliosarcomas. Six tumors have been further subjected to RNA sequencing analysis and gene expression patterns have been compared to those of GBMs. We demonstrate that gliosarcoma bears somatic alterations in gene coding for PI3K/Akt (<i>PTEN</i>, <i>PI3K</i>) and RAS/MAPK (<i>NF1</i>, <i>BRAF</i>) signaling pathways that are crucial for tumor growth. Interestingly, the frequency of <i>PTEN</i> alterations in gliosarcomas was much higher than in GBMs. Aberrations of PTEN were the most frequent and occurred in 70% of samples. We identified genes differentially expressed in gliosarcoma compared to GBM (including collagen signature) and confirmed a difference in the protein level by immunohistochemistry. We found several novel translocations (including translocations in the <i>RABGEF1</i> gene) creating potentially unfavorable combinations. Collected results on genetic alterations and transcriptomic profiles offer new insights into gliosarcoma pathobiology, highlight differences in gliosarcoma and GBM genetic backgrounds and point out to distinct molecular cues for targeted treatment.
Tissue-specific macrophages: how they develop and choreograph tissue biology (2023)

Macrophages are innate immune cells that form a 3D network in all our tissues, where they phagocytose dying cells and cell debris, immune complexes, bacteria and other waste products. Simultaneously, they produce growth factors and signalling molecules - such activities not only promote host protection in response to invading microorganisms but are also crucial for organ development and homeostasis. There is mounting evidence of macrophages orchestrating fundamental physiological processes, such as blood vessel formation, adipogenesis, metabolism and central and peripheral neuronal function. In parallel, novel methodologies have led to the characterization of tissue-specific macrophages, with distinct subpopulations of these cells showing different developmental trajectories, transcriptional programmes and life cycles. Here, we summarize our growing knowledge of macrophage diversity and how macrophage subsets orchestrate tissue development and function. We further interrelate macrophage ontogeny with their core functions across tissues, that is, the signalling events within the macrophage niche that may control organ functionality during development, homeostasis and ageing. Finally, we highlight the open questions that will need to be addressed by future studies to better understand the tissue-specific functions of distinct macrophage subsets.
Behavioral reflexion models for software architecture (2010)

Developing and maintaining software is difficult and error prone. This can at least partially be attributed to its constantly evolving nature. Requirements are seldom finalized before the development begins, but evolve constantly as new details about the system become known and stakeholder objectives change. As requirements are altered, the software architecture must be updated to accommodate these changes. This includes updating the architecture documentation, which serves as the design specification as well as a means of comprehending complex systems. Furthermore, the software architecture of the implementation must be adapted in order to ensure that the system complies with both functional and non-functional requirements.
In practice, however, software changes are often applied in an ad-hoc manner. As a result, the implementation frequently deviates from the architecture documentation, rendering the latter useless for supporting system engineers in comprehending the system and aiding maintenance tasks. Furthermore, errors that are introduced during the implementation lead to discrepancies between the system and the intended architecture design. Consequently, it cannot be guaranteed that the system meets the desired quality objectives, such as reliability and dependability.
We present the behavioral reflexion model approach, which aims to support the system engineer in identifying and resolving discrepancies between software architecture representations. In our approach, the system engineer is supported in producing architecture documentation that reflects the intended architecture. Furthermore, discrepancies between the implementation and documentation are identified. These discrepancies are then illustrated graphically in a reflexion model, which guides debugging activities.
In this research, we are concerned with architecture representations of system behaviors and focus in particular on distributed systems. In this thesis, we describe how architecture discrepancies are introduced and the implications for the reliability and maintainability of the system. We then discuss the individual components of the behavioral reflexion model approach in detail. Finally, we provide an evaluation of our approach in the form of two case studies. In these studies, we applied the behavioral reflexion model approach to two space-mission systems with the goal to resolve problems in their reliability and maintainability.
On anonymizing query logs via token-based hashing (2007)

In this paper we study the privacy preservation properties of aspecific technique for query log anonymization: token-based hashing. In this approach, each query is tokenized, and then a secure hash function is applied to each token. We show that statistical techniques may be applied to partially compromise the anonymization. We then analyze the specific risks that arise from these partial compromises, focused on revelation of identity from unambiguous names, addresses, and so forth, and the revelation of facts associated with an identity that are deemed to be highly sensitive. Our goal in this work is two fold: to show that token-based hashing is unsuitable for anonymization, and to present a concrete analysis of specific techniques that may be effective in breaching privacy, against which other anonymization schemes should be measured.
Model-Based Ocean Acoustic Signal Processing (2011)

James V. Candy Abstract 5-1
University o f California 5.1 Introduction 5-2Edmund I. Sullivan 5'2 Model-Based Process^ 5-5
Motivation • Overview • Gauss-Markov Model • Model-5.3 State-Space Ocean Acoustic Forward Propagators 5-16
5.4 Ocean Acoustic Model-Based5.5 Summary 5-50
References 5-51Abstract
Signal processing can simply be defined as a technique or set o f techniques to extract the useful infor­
mation from noisy measurement data while rejecting the extraneous. These techniques can range from 
simple, non-physical representations of the measurement data such as the Fourier or wavelet transforms 
to parametric black-box models used for data prediction to lumped mathematical physical representations 
usually characterized by ordinary differential equations to full physical partial differential equation 
models capturing the critical details o f wave propagation in a complex medium. The determination o f 
which approach is the most appropriate is usually based on how severely contaminated the measurements 
are with noise and underlying uncertainties. If the signal-to-noise (SNR) of the measurements is high, 
then simple non-physical techniques can be used to extract the desired information. However, if the SNR 
is extremely low and/or the propagation medium is uncertain, then more of the underlying propagation 
physics must be incorporated somehow into the processor to extract the information. Model-based signal 
processing is an approach that incorporates propagation, measurement, and noise/uncertainty models 
into the processor to extract the required signal information while rejecting the extraneous data even inhighly uncertain environments — like the ocean. This chapter outlines the motivation and development 
of model-based processors (MBP) for ocean acoustic applications. We discuss the generic development 
o f MBP schemes and then concentrate specifically on those designed for application in the hostile ocean 
environment. Once the MBP is characterized, we then discuss a set of ocean acoustic applications 
demonstrating this approach.
Movement of grain to control stored-product insects and mites (2005)

The movement of stored grain by auger or pneumatic conveyor was evaluated for control of stored-product insects and mites. In a pilot scale test using nine welded steel bins each holding 322 kg of wheat ( Triticum aestivum ), movement of grain using an auger in three bins caused 89% mortality of red flour beetle, Tribolium castaneum adults and 94% mortality of rusty grain beetle, Cryptolestes ferrugineus adults. Larval mortality of both species, based on grain samples placed in Berlese funnels, was 100%. Pneumatic conveyance of grain in three bins caused 100% mortality of all stages of both insects based on grain samples and grain-probe insect traps. In field tests, infested wooden bins of wheat and corn ( Zea mays ) were moved by pneumatic conveyor to a truck and then hand-poured into welded steel bins. A parallel test on wheat and corn was done using a screw auger to move the grain. Pneumatic wheat movement killed 100% of mites ( Aeroglyphus robustus ), T. castaneum adults and larvae, and C. ferrugineus adults. Mortality of C. ferrugineus larvae and psocids was 79% and 83%, respectively. Augering wheat killed 98% of mites, 84% T. castaneum adults, 70% T. castaneum larvae, 14% C. ferrugineus adults, and 0% C. ferrugineus larvae. Pneumatic movement of corn killed 97% T. castaneum adults, 72% C. ferrugineus adults and 100% of the fungus beetle Cartodere constricta . Augering corn had less effects than pneumatic movement on insect mortality. Pneumatic conveyance of grain, especially wheat, offers an effective physical control for common stored-product insects.
Catalytic Enantioselective Alkylations with Allylic Alcohols (2012)

Allylic alcohols have recently risen to prominence as a valuable synthetic alternative to classic activated alkylating agents\nin asymmetric catalysis. The intrinsic drawbacks that limited their\nemployment in catalytic enantioselective transformations, until recently, have been efficiently addressed providing elegant solutions.\nThis short review intends to summarize the most salient and recent\noutcomes in this emerging research area, highlighting the scope and\nlimitations of the most selective catalytic methodologies.
Identification of Core Genes Involved in the Progression of Cervical Cancer Using an Integrative mRNA Analysis (2020)

In spite of being a preventable disease, cervical cancer (CC) remains at high incidence, and it has a significant mortality rate. Although hijacking of the host cellular pathway is fundamental for developing a better understanding of the human papillomavirus (HPV) pathogenesis, a major obstacle is identifying the central molecular targets involved in HPV-driven CC. The aim of this study is to investigate transcriptomic patterns of HPV-infected and normal tissues to identify novel prognostic markers. Analyses of functional enrichment and interaction networks reveal that altered genes are mainly involved in cell cycle, DNA damage, and regulated cell-to-cell signaling. Analysis of The Cancer Genome Atlas (TCGA) data has suggested that patients with unfavorable prognostics are more likely to have DNA repair defects attributed, in most cases, to the presence of HPV. However, further studies are needed to fully unravel the molecular mechanisms of such genes involved in CC.
&lt;title&gt;Compact HMD optics based on multiplexed aberration-compensated holographic optical elements&lt;/title&gt; (2001)

Head and helmet mounted displays (HMDs) can benefit greatly from new wide field-of-view, compact visor optics to project very high resolution (e.g., 5k X 4k) imagery. Physical Optics Corporation (POC) is developing novel, compact, lightweight wide field-of-view optics based on three-color multiplexed aberration-compensated holographic optical elements (MAC-HOEs). Taking advantage of the flexibility of holography, the HMD optics can be made compact using waveguide projection through the curved visor substrate, so that the see-through visor can have a wide field-of-view without large, bulky optical components. Using narrowband red-green-blue hologram multiplexing, MAC-HOEs can significantly reduce the chromatic and geometrical aberration introduced by conventional HOEs and refractive optics. In the initial phase of development, POC demonstrated the feasibility of the HMD optics through computer design and analysis, and by fabricating and demonstrating a MAC-HOE component.
Effect of molecular size of 125I-labelled poly(vinylpyrrolidone) on its pinocytosis by rat visceral yolk sacs and rat peritoneal macrophages (1981)

Rates of pinocytosis of different molecular-weight distributions of 125I-labelled poly(vinylpyrrolidone) by rat visceral yolk sacs and rat peritoneal macrophages were measured in vitro. Four preparations of mean molecular weights 50 000, 84 000, 700 000 and 7 000 000, were used. Macrophages captured the highest-molecular-weight preparation more rapidly than the other preparations. In contrast, rate of capture by the yolk sac decreased with increasing molecular weight. Incubations with a very-high-molecular-weight fraction derived from the 7 000 000-average-mol. wt. preparation clearly demonstrated that very large polymer molecules are not accumulated by the yolk sac, but are preferentially captured by macrophages. Analysis of the 125I-labelled poly(vinylpyrrolidone) internalized by the two cell types confirmed that low-molecular-weight material is preferred by the yolk sac, whereas the macrophage is less discriminating.
Hydrophobic microporous and mesoporous oxides as Brønsted and Lewis acid catalysts for biomass conversion in liquid water (2014)

Microporous and mesoporous silicates with internal or external hydrophobic surfaces show differences in catalytic reactivity and stability in liquid water.
The Construction of Boolean Permutations in Cryptosystems (2003)

Boolean permutations are in very important applications in cryptosystems. In the design of block cipher,those of high degree are needed. In this paper,a method of constructing boolean permutations of high degree by combining some boolean permutations of low degree is provided,and an example is given. The results are useful to the construction of boolean permutations.
Application of Iso-Strain Boundary Conditions to Deduce Orthotropic Elastic Constants of Biomineralized Fish Scale (2016)

The Atractosteus spatulas (Alligator gar) was used as the model structure for computational analysis to estimate elastic properties. The Alligator gar possesses a flexible dermal armor consisting of overlapping ganoid scales. Each scale is a bilayer hydroxyapatite and collagen-based biocomposite and is thought to be used for protection against predators. The exoskeleton fish scale is comprised of a stiff outer ganoine layer, a characteristic “sawtooth” pattern at the interface and a compliant bone inner layer with all materials exhibiting a decreasing elastic modulus from the external to the internal layers. Scanning electron microscopy (SEM) images of the cross section of gar fish scales revealed a two-layered structure. Nanoindentation measured modulus was correlated to structural changes across the scale’s layers. Piecewise linear grading functions were used to vary the properties within and between layers as well as explicit modeling of the sawtooth interface geometry. The fish scale composite was computationally modeled using a representative volume element (RVE). The model used iso-strain boundary conditions to determine the full elastic tensor for the composite system. Using isotropic behavior for individual elements, the results show that the RVE exhibits orthotropic symmetry with slight variations due to the sawtooth interface.
Cerebral activation during withholding urine with full bladder in healthy men using 99mTc-HMPAO SPECT. (2006)

Our results suggest that the right inferior frontal gyrus plays an important role in brain control of urinary continence. This study also suggests that brain control of continence can be confirmed by statistical image analysis software using SPECT.