gebhart/patrepeval huggingface dataset:
Characterization of human astrovirus type 1 (1990)

The work described in this thesis identifies the structural polypeptide profile of human astrovirus type 1, grown in tissue culture in the presence of trypsin. Four major polypeptides were observed, of molecular weights: 34,000, 33.000, 26,500 and 6-8,000. A fifth of molecular weight 37,000 observed when the virus is prepared by PEG precipitation is considered to represent a precursor polypeptide. Of the four structural polypeptides, designated VP1, VP2, VP3 and VP4 respectively, VP1 and VP2 were found to be immunologically reactive with anti-astrovirus type 1 polyclonal antiserum. &#13;\n&#13;\nAstrovirus type 1 particles were found to have a buoyant density of 1.33-1.34 gm/ral in caesium chloride and a genome approximately 7,200 bases in length, corresponding to a molecular weight of 2.43 x 10° which is assumed to be RNA. &#13;\n&#13;\nThis data suggests a relationship between astroviruses and picornaviruses, most especially the enterovirus subgroup, which have similar structural polypeptide and physico-chemical properties to those described above. However, the use of trypsin for the propagation of astrovirus in tissue culture means that further analysis of the structural polypeptides is required to determine whether those observed in this analysis represent four individual proteins, similar to the profile of picornaviruses, or whether some are cleavage products of the larger proteins due to the action of trypsin. &#13;\n&#13;\nThe 3' terminal sequence of the astrovirus genome has been cloned and sequenced. It was found to have a poly (A) tail, stop codons in all three reading frames within the last 95 nucleotides and no polyadenylation signals. Several other astrovirus specific clones were obtained, but there is no suggestion as to which regions of the genome these represent. Comparisons between the astrovirus specific clones and the microgenie sequence databank has shown no significant homologies. The highest homology obtained for the 3' terminal sequence when compared to those of other picornaviruses was 47Z with coxsackie A21, this is not taken to confirm a relationship between the viruses. &#13;\n&#13;\nAssay systems were developed for astrovirus during the course of this study. An immunofluorescent end point titration, using type specific antisera, allowed the determination of the infectivity of a virus stock within 48 hours of infection. An immuno dot blot system was developed to assay for amounts of virus protein in samples, such as gradient fractions, and was used to determine the peak banding of virus in sucrose &#13;\n
Isomerizations of a Pt4 cluster revealed by spatiotemporal microscopic analysis (2019)

We now report the first direct observation of the fluxional nature in which the four-atomic platinum cluster (Pt4) randomly walks through several isomers. Time-lapse analysis by a Cs-corrected transmission electron microscope allowed us to acquire the atomic coordinates at a sub-angstrom space resolution and 0.2 s time resolution for each cluster isomer. The analysis revealed that the isomerization follows a simple first-order kinetic model.
Architectured helically coiled scaffolds from elastomeric poly(butylene succinate)(PBS) copolyester via wet electrospinning (2018)

Electrospinning is one of the most investigated methods used to produce polymeric fiber structures that mimic the morphology of native extracellular matrix. These structures have been extensively studied in the context of scaffolds for tissue regeneration. However, the compactness of materials obtained by traditional electrospinning, collected as two-dimensional non-woven scaffolds, can limit cell infiltration and tissue ingrowth. In addition, for applications in smooth muscle tissue engineering, highly elastic scaffolds capable of withstanding cyclic mechanical strains without suffering significant permanent deformations are preferred. In order to address these challenges, we report the fabrication of microscale 3D helically coiled structures (referred as 3D-HCS) by wet-electrospinning method, a modification of the traditional electrospinning process in which a coagulation bath (non-solvent system for the electrospun material) is used as the collector. The present study, for the first time, successfully demonstrates the feasibility of using this method to produce various architectures of 3D-HCS from segmented copolyester of poly(butylene succinate-co- dilinoleic succinate) (PBS-DLS), a thermoplastic elastomer. A mechanism for the HCS formation is proposed and verified with experimental data. Fabricated 3D-HCS showed high specific surface area, high porosity, and good elasticity. Further, the marked increase in cell proliferation on 3D-HCS confirmed the suitability of these materials as scaffolds for soft tissue engineering.
Prediction of trapping rates in mixtures of partially absorbing spheres (2002)

The combined effects of diffusion and reaction in heterogeneous media govern the behavior of a wide variety of physical and biological phenomena, including the consumption of nutrients by cells and the study of magnetic relaxation in tissues. We have considered the so-called “trapping problem,” in which diffusion takes place exterior to a collection of fixed traps while reaction occurs at their surface. A simulation technique for predicting the overall trapping rate for systems of partially absorbing spherical traps based on the first-passage spheres method is presented. Using data obtained by applying this simulation technique, we then consider the problem of mixtures of partially absorbing traps. By hypothesizing a method for reducing a general mixture of traps to a mixture of perfect absorbers and perfect reflectors (i.e., reducing the dimensionality of the space of variables), we are able to accurately predict the effective surface rate constant and the trapping rate for an arbitrary mixture of partially absorbing traps. Remarkably, we find that a single, nearly universal curve allows accurate predictions to be made over a wide range of trap volume fractions and even for different trap distributions.
Differential Regulation of Rat and HumanCYP7A1by the Nuclear Oxysterol Receptor Liver X Receptor-α (2003)

In rodent liver, transcription of the gene encoding cholesterol 7alpha-hydroxylase (CYP7A1), which catalyzes the rate-limiting step in the classic bile acid synthetic pathway, is stimulated by the liver X receptor alpha (LXRalpha), a nuclear receptor for oxysterol metabolites of cholesterol. This feed-forward regulatory loop provides a mechanism for the elimination of excess cholesterol from the body. In this report, we demonstrate that in primary cultures of human hepatocytes, activation of LXRalpha has the opposite effect, repressing CYP7A1 expression. This repression is mediated, at least in part, through induction of the orphan nuclear receptor, short heterodimer partner (SHP), which is also induced by bile acids. We demonstrate that SHP is regulated directly by LXRalpha through a DNA response element that overlaps with the previously characterized bile acid response element. Our data reveal a fundamental difference in the regulation of CYP7A1 in rodent and human hepatocytes and provide evidence that different species employ distinct molecular strategies to regulate cholesterol homeostasis.
PLA2G7 associates with hormone receptor negativity in clinical breast cancer samples and regulates epithelial‐mesenchymal transition in cultured breast cancer cells (2017)

Breast cancer is the leading cause of cancer-related deaths in women due to distinct cancer subtypes associated with early recurrence and aggressive metastatic progression. High lipoprotein-associated phospholipase A2 (<i>PLA2G7</i>) expression has previously been associated with aggressive disease and metastasis in prostate cancer. Here, we explore the expression pattern and functional role of <i>PLA2G7</i> in breast cancer. First, a bioinformatic analysis of genome-wide gene expression data from 970 breast samples was carried out to evaluate the expression pattern of <i>PLA2G7</i> mRNA in breast cancer. Second, the expression profile of <i>PLA2G7</i> was studied in 1042 breast cancer samples including 89 matched lymph node metastasis samples using immunohistochemistry. Third, the effect of <i>PLA2G7</i> silencing on genome-wide gene expression profile was studied and validated in cultured breast cancer cells expressing <i>PLA2G7</i> at high level. Last, the expression pattern of <i>PLA2G7</i> mRNA was investigated in 24 nonmalignant tissue samples and 65 primary and 7 metastatic tumour samples derived from various organs using qRT-PCR. The results from clinical breast cancer samples indicated that <i>PLA2G7</i> is overexpressed in a subset of breast cancer samples compared to its expression in benign breast tissue samples and that high <i>PLA2G7</i> expression associated with hormone receptor negativity as well as with poor prognosis in a subset of breast cancer samples. <i>In vitro</i> functional studies highlighted the putative role of <i>PLA2G7</i> in the regulation of epithelial-mesenchymal transition (EMT)-related signalling pathways, vimentin and E-cadherin protein expression as well as cell migration in cultured breast cancer cells. Furthermore, supporting the findings in breast and prostate cancer, high <i>PLA2G7</i> mRNA expression was associated with metastatic cancer in four additional organs of origin. In conclusion, our results indicate that <i>PLA2G7</i> is highly expressed in a subset of metastatic and aggressive breast cancers and in metastatic samples of various tissues of origin and promotes EMT and migration in cultured breast cancer cells.
The Fastrack Suborbital Platform for Microgravity Applications (2009)

The FASTRACK suborbital experiment platform has been developed to provide a capability for utilizing 2.5-5 minute microgravity flight opportunities anticipated from the commercial suborbital fleet (currently in development) for science investigations, technology development and hardware testing. It also provides express rack functionality to deliver payloads to ISS. FASTRACK fits within a 24 x 24 x 36 (61 cm x 61 cm x 91.4 cm) envelope and is capable of supporting either two single Middeck Locker Equivalents (MLE) or one double MLE configuration. Its overall mass is 300 lbs (136 kg), of which 160 lbs (72 kg) is reserved for experiments. FASTRACK operates using 28 VDC power or batteries. A support drawer located at the bottom of the structure contains all ancillary electrical equipment (including batteries, a conditioned power system and a data collection system) as well as a front panel that contains all switches (including remote cut-off), breakers and warning LEDs.
Estimation of tip shape for carrot classification by machine vision. (1990)

Tip shape has been identified as an important carrot feature which is a major concern to both consumers and in post harvest operations. A classification method can help carrot breeders to measure the success of their breeding operations. Based on the Freeman chain code, a curvature profile was developed. Using a non-linear least squares technique known as the Marquardt method, the curvature profile was reduced to six parameters describing the carrot tip. These parameters were used to develop a Bayes decision function which classified carrot tips into five classes (sharp tapered to extremely blunt tips). This method was tested on 250 carrots. Of the 250 carrots tested, 14% were misclassified.
The balance between neural and hemodynamic factors is abolished in hypertensive men (2013)

Bristol, Bristol, United Kingdom In normotensive men there is a balance among sympathetic nerve activity (SNA), peripheral resistance (TPR) and cardiac output (Q). Thus, the net effect that high resting levels of SNA has on blood pressure (BP) is minimal. SNA is elevated in resistant hypertensive men, despite treatment with three or more medications. We hypothesised that there would be an imbalance between SNA, TPR and Q in resistant hypertensive men. In 10 (age; 53 ± 4) resistant hypertensive men, we measured muscle SNA (peroneal microneurography), BP (cuff and Finapres) and heart rate (HR, ECG) during 10 minutes of supine rest. Stroke volume was calculated using Modelflow analysis on the Finapres BP waveform. Q was calculated as stroke volume × HR. MSNA was positively associated to TPR (r = 0.59, P&lt;0.05), but not Q (r = 0.13). Thus mean BP was directly related to MSNA (r = 0.56, P&lt;0.05). In summary, despite treatment with more than 3 anti‐hypertensive medications, high MSNA was related to high TPR, which was not balanced by lower Q (as it is in normotensive men). Consequently, sympathetic activity may continue to play a role in resistant hypertension despite treatments targeting the sympathetic nervous system. British Heart Foundation funded.
On Assessing and Developing Spoken ’Grammatical Error Correction’ Systems (2022)

Spoken 'grammatical error correction' (SGEC) is an important process to provide feedback for second language learning. Due to a lack of end-to-end training data, SGEC is often implemented as a cascaded, modular system, consisting of speech recognition, disfluency removal, and grammatical error correction (GEC). This cascaded structure enables efficient use of training data for each module. It is, however, difficult to compare and evaluate the performance of individual modules as preceeding modules may introduce errors. For example the GEC module input depends on the output of nonnative speech recognition and disfluency detection, both challenging tasks for learner data. This paper focuses on the assessment and development of SGEC systems. We first discuss metrics for evaluating SGEC, both individual modules and the overall system. The systemlevel metrics enable tuning for optimal system performance. A known issue in cascaded systems is error propagation between modules.
A Novel Thin Wafer Handling Technology to Enable Cost-Effective Fabrication of Through-Glass Via Interposers (2014)

Thin wafer handling technologies to fabricate silicon interposers have been widely discussed at conferences. Despite tremendous efforts to overcome several technical hurdles such as wafer chipping, cracking, and warpage, high manufacturing costs resulting from the complexity of the processes used to make silicon interposers remains a major concern. Fabricating a through-glass via (TGV) interposer using novel thin wafer handling (TWH) technology will be presented here as an example of a simple and cost-effective solution for realizing 2.5-D IC integration. Utilizing a simplified TWH technology, a TGV interposer with 30-μm-diameter vias to eliminate the isolation layer is combined with polymer-based polybenzoxazole (PBO) as passivation to build one to two redistribution layers (RDLs) with 20-μm line width on both sides after thinning to 100 μm. The simplified TWH requires only a release layer on the glass carrier and another layer of bonding material on the TGV wafer to enable fabrication of a TGV interposer. A process flow for fabricating a TGV interposer utilizing a simplified TWH technology will be presented in detail, including carrier treatment, bonding material, bonding, titanium/copper seed layer deposition, copper plating, RDL deposition, under-bump material (UBM) formation, debonding, and silicon chip stacking on a TGV interposer. The combination of TGV interposer and novel TWH technology will pave the way for cost-effective fabrication in 2.5-D IC.
IL‐18 Activity in Systemic Lupus Erythematosus (2009)

Interleukin-18 (IL-18) is an inflammation-related cytokine that plays a central role both in innate defense reactions and in Th1 activation and specific immune responses. Increased levels of IL-18 can be detected in biological fluids and organs of individuals affected by several autoimmune pathologies, as well as in autoimmune animal models. In this review, the role of IL-18 in systemic lupus erythematosus (SLE) is critically examined, including its possible role in the pathogenesis of disease. In SLE, increased levels of IL-18 have been found in serum/plasma of affected persons, which positively correlated with disease severity. The possibility that circulating IL-18 levels are predictive of renal damage has been proposed, suggesting that IL-18 may be a prognostic marker of renal involvement useful to identify patients at risk of renal failure. The evaluation of urinary levels of free active IL-18 indeed suggests a correlation with the degree of renal involvement. The possible pathogenic role of IL-18 in lupus has been studied in a mouse model of progressive disease, which makes possible the identification, at the level of the different affected organs, of IL-18 changes preceding disease development and those appearing after disease onset. It can be concluded that IL-18 has a multifaceted role in autoimmune lupus, being apparently involved both in the effector phases of the late organ damage and, in some organs, in the initial pathogenic events. Therapeutic strategies targeting IL-18 in autoimmunity are under development.
Nuclease-dead S. aureus Cas9 downregulates alpha-synuclein and reduces mtDNA damage and oxidative stress levels in patient-derived stem cell model of Parkinson’s disease (2023)

Parkinson's disease (PD) is one of the most common neurodegenerative diseases, but no disease modifying therapies have been successful in clinical translation presenting a major unmet medical need. A promising target is alpha-synuclein or its aggregated form, which accumulates in the brain of PD patients as Lewy bodies. While it is not entirely clear which alpha-synuclein protein species is disease relevant, mere overexpression of alpha-synuclein in hereditary forms leads to neurodegeneration. To specifically address gene regulation of alpha-synuclein, we developed a CRISPR interference (CRISPRi) system based on the nuclease dead <i>S. aureus</i> Cas9 (SadCas9) fused with the transcriptional repressor domain Krueppel-associated box to controllably repress alpha-synuclein expression at the transcriptional level. We screened single guide (sg)RNAs across the <i>SNCA</i> promoter and identified several sgRNAs that mediate downregulation of alpha-synuclein at varying levels. CRISPRi downregulation of alpha-synuclein in iPSC-derived neuronal cultures from a patient with an <i>SNCA</i> genomic triplication showed functional recovery by reduction of oxidative stress and mitochondrial DNA damage. Our results are proof-of-concept <i>in vitro</i> for precision medicine by targeting the <i>SNCA</i> gene promoter. The <i>SNCA</i> CRISPRi approach presents a new model to understand safe levels of alpha-synuclein downregulation and a novel therapeutic strategy for PD and related alpha-synucleinopathies.
Modulation Depth Enhancement for Randomly Arranged Tags in Passive RFID Tag to Tag Communications (2021)

In this paper, the performance evaluation of the tag to tag (T2T) communications using UHF (Ultra High Frequency) passive RFID (Radio Frequency Identification) tags is tackled. The T2T communication system is performed directly between a reader tag (RT) and a listener tag (LT) in the presence of an external electromagnetic (EM) field. Consequently, this kind of communication system implies the use of low RF signal levels, which makes it very sensitive to the noise, to the arrangement between the tags (i.e. spacing, tilt and shift) but also to the position of the source. The performance evaluation of this communication system is based on the study of the modulation depth, an indicator of the separation between the two modulation states and, indirectly, of the T2T communication quality. Considering scenarios in which the two tags are in the same plane but with the RT tilted and staggered with respect to the LT, our study demonstrates that the modulation depth can be kept higher for different separations between the tags by choosing the proper angle of incidence of the RF source with respect to the tag’s plane. The proposed approach is studied through electromagnetic simulations and the obtained results are confronted with measurements.
Optimizing Reciprocity-Based Backscattering with a Full-Duplex Antenna Array Reader (2018)

Backscatter communication (BSC) technology can enable ubiquitous deployment of low-cost sustainable wireless devices. In this work we investigate the efficacy of a full-duplex antenna array reader in overcoming the limited communication range bottleneck of monostatic BSCs. As performance is strongly influenced by the channel estimation (CE) quality, we first derive a novel least-squares estimator (LSE) for the forward and backward links between the reader and the tag, assuming that reciprocity holds. After defining the transceiver design at reader using this LSE, we optimize the energy allocation for the CE and information decoding phases, to maximize the average backscattered signal-to-noise ratio (SNR). The unimodality of this SNR in optimization variable along with a tight approximation for the global optimal design are also presented. Lastly, numerical results validate the proposed analysis and present key insights into the optimal LSE and energy allocation.
Generalized Grounding Graphs: A Probabilistic Framework for\n Understanding Grounded Commands (2017)

Many task domains require robots to interpret and act upon natural language\ncommands which are given by people and which refer to the robot's physical\nsurroundings. Such interpretation is known variously as the symbol grounding\nproblem, grounded semantics and grounded language acquisition. This problem is\nchallenging because people employ diverse vocabulary and grammar, and because\nrobots have substantial uncertainty about the nature and contents of their\nsurroundings, making it difficult to associate the constitutive language\nelements (principally noun phrases and spatial relations) of the command text\nto elements of those surroundings. Symbolic models capture linguistic structure\nbut have not scaled successfully to handle the diverse language produced by\nuntrained users. Existing statistical approaches can better handle diversity,\nbut have not to date modeled complex linguistic structure, limiting achievable\naccuracy. Recent hybrid approaches have addressed limitations in scaling and\ncomplexity, but have not effectively associated linguistic and perceptual\nfeatures. Our framework, called Generalized Grounding Graphs (G^3), addresses\nthese issues by defining a probabilistic graphical model dynamically according\nto the linguistic parse structure of a natural language command. This approach\nscales effectively, handles linguistic diversity, and enables the system to\nassociate parts of a command with the specific objects, places, and events in\nthe external world to which they refer. We show that robots can learn word\nmeanings and use those learned meanings to robustly follow natural language\ncommands produced by untrained users. We demonstrate our approach for both\nmobility commands and mobile manipulation commands involving a variety of\nsemi-autonomous robotic platforms, including a wheelchair, a micro-air vehicle,\na forklift, and the Willow Garage PR2.\n
Study of multiple hologram recording in lithium niobate (1974)

The results of a number of theoretical and experimental studies relating to multiple hologram recording in lithium niobate are reported. The analysis of holographic gratings stored in lithium niobate has been extended to cover a more realistic range of physical situations. A new successful dynamic (feedback) theory for describing recording, nondestructive reading, erasure, enhancement, and angular sensitivity has been developed. In addition, the possible architectures of mass data storage systems have been studied.