gebhart/patrepeval huggingface dataset:
Co-Infection of Cattle withFasciola hepaticaandMycobacterium bovis- Immunological Consequences (2009)

Fasciola hepatica, the liver fluke, is a common parasite of cattle in much of the world. Previously, we have shown that cattle infected with F. hepatica have altered responsiveness (delayed type hypersensitivity reaction and cytokine responses) to M. bovis BCG infection. We hypothesized that co-infection with F. hepatica would, likewise, alter the immune response of cattle to virulent M. bovis infection, with possible implications for disease diagnosis and disease progression. Our previous work with F. hepatica/M. bovis BCG-infected cattle demonstrated a reduction in interferon (IFN)-gamma responsiveness in co-infected animals. Similar findings are reported here with virulent M. bovis following aerosol infection. The epidemiological significance of these findings, also, require exploration, particularly in view of the considerable resources devoted to the diagnosis and eradication of bovine tuberculosis, and the high prevalence of F. hepatica infection in areas where eradication has proved difficult.
Artificial Retina Using Thin-Film Photodiodes and Thin-Film Transistors (2006)

An artificial retina using thin-film photodiodes (TFPDs) and thin-film transistors (TFTs) is proposed, which is expected to be suitable for living bodies, low-emitting and cost-effective, and which is an improvement of the system-on-panel devices in which the in-pixel and pixel-to-pixel operations are executed using TFTs. The characteristics of a TFPD and TFTs are measured, and their models are made for a circuit simulator. Circuits of the retina pixel and retina array with some improvements are invented, and it is confirmed using a circuit simulator that the artificial retina using TFPDs and TFTs can operate. Edge enhancement is also confirmed, and its dependence on the characteristic deviations of TFTs is analyzed.
P413 A simple scoring tool predicts exposure–response relationship, onset of action, response to interval shortening, and surgical risk with vedolizumab therapy for Crohn’s disease (2019)

We previously created and validated a clinical decision support tool (CDST) for predicting response to vedolizumab (VDZ) in Crohn’s disease (CD). We now aim to further validate this tool in an additional CD cohort and assess its performance for predicting other health outcomes. Using GEMINI II data, we explored correlations between VDZ exposure and onset of action across CDST-predicted probability of response groups (low, intermediate, high). The operating properties of the CDST for prediction of clinical remission and onset of action in the GETAID VDZ cohort were evaluated. In the GETAID and VICTORY cohorts, response to dose optimisation was assessed, and in the VICTORY cohort, we assessed the ability of the CDST to predict risk of surgery while on active therapy. A linear relationship was observed between CDST-predicted probability of response groups, VDZ exposure, onset of action, and efficacy in the GEMINI cohort for Week 2 through Week 52 (p < 0.001). In the GETAID cohort, the CDST predicted clinical remission at Week 14 (AUC 0.68), and a significant difference in speed of onset of action was observed between low- and intermediate–high-probability groups (p = 0.04). In both the GETAID and VICTORY cohorts, only patients in the low-probability group significantly benefited from shortening of VDZ intervals to Q4 weeks for non-response. In the GETAID cohort, a single infusion at Week 10 for patients in the low-probability group overcame differences in speed of onset of action seen between this group and the intermediate–high-probability group. In the VICTORY cohort, the CDST predicted a 2-fold increase in risk for surgery over 12 months of VDZ therapy among low–intermediate-probability patients compared with high-probability patients (HR 2.06, 95% CI 1.33–3.21). The CD VDZ CDST demonstrated good performance during external validation in the GETAID cohort. This tool was able to prognosticate VDZ exposure-efficacy relationships and speed of onset of action, identify patients who would most benefit from interval shortening for lack of response, and stratify patients at greatest risk for surgery while on active therapy.
Hormone Regulation of Tissue-Type Plasminogen Activator Gene Expression and Plasminogen Activator-Mediated Proteolysis (1991)

Hormone regulation of tissue-type plasminogen activator gene expression and plasminogen activator-mediated proteolysis.
Enhancement-mode GaN hybrid MOS-HFETs on Si substrates with Over 70 A operation (2009)

We report on the demonstration of enhancement-mode n-channel GaN-based hybrid MOS-HFETs realized on AlGaN/GaN heterostructure on silicon substrates with a large drain current operation. The GaN-based hybrid MOS HFETs realized the threshold voltage of 2.8 V, the maximum drain current of over 70 A with the channel width of 340 mm. This is the best value for an enhancement-mode GaN-based FET. The specific on-state resistance was 16.5 mΩcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The breakdown voltage was over 500 V. These results suggest that this structure is a good candidate for power switching applications.
Ribozyme-catalyzed and nonenzymic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom (1991)

The L-21 ScaI ribozyme derived from the intervening sequence of Tetrahymena thermophila pre-rRNA catalyzes a guanosine-dependent endonuclease reaction that is analogous to the first step in self-splicing of this intervening sequence. We now describe pre-steady-state kinetic experiments, with sulfur substituting for the pro-RP (nonbridging) phosphoryl oxygen atom at the site of cleavage, that test aspects of a kinetic model proposed for the ribozyme reaction (Herschlag, D., & Cech, T. R. (1990) Biochemistry 29, 10159-10171). Thio substitution does not affect the reaction with subsaturating oligonucleotide substrate and saturating guanosine ((kcat/Km)S), consistent with the previous finding that binding of the oligonucleotide substrate limits this rate constant. In contrast, there is a significant decrease in the rate of single-turnover reactions of ribozyme-bound (i.e., saturating) oligonucleotide substrate upon thio substitution, with decreases of 2.3-fold for the reaction with guanosine ((kcat/Km)G) and 7-fold for hydrolysis [i.e., with solvent replacing guanosine; kc(-G)]. These "thio effects" are consistent with rate-limiting chemistry, as shown by comparison with model reactions. Nonenzymatic nucleophilic substitution reactions of the phosphate diester, methyl 2,4-dinitrophenyl phosphate monoanion, are slowed 4-11-fold by thio substitution for reactions with hydroxide ion, formate ion, fluoride ion, pyridine, and nicotinamide. In addition, we have confirmed that thio substitution has no effect on the nonenzymatic alkaline cleavage of RNA (Burgers, P. M. J., & Eckstein, F. (1979) Biochemistry 18, 592-596). Considering the strong preference of Mg2+ for binding to oxygen rather than sulfur, the modest thio effect on the chemical step of the ribozyme-catalyzed reaction and the absence of a thio effect on the equilibrium constant for binding of the oligonucleotide substrate suggest that the pro-RP oxygen atom is not coordinated to Mg2+ in the E.S complex or in the transition state. General implications of thio effects in enzymatic reactions of phosphate diesters are discussed.
PDTM-45. POSITIVE MODULATION OF NATIVE GABAA RECEPTORS IN MEDULLOBLASTOMA CANCER CELLS WITH BENZODIAZEPINES INDUCES RAPID MITOCHONDRIAL FRAGMENTATION AND TP53-DEPENDENT, CELL CYCLE-INDEPENDENT APOPTOSIS (2018)

Medulloblastoma is the most common childhood malignant brain tumor. Children with highest morbidity have tumors that are TP53 wild-type and express high levels of MYC and GABRA5, which codes for the α-5 subunit of the ligand (chloride) gated GABAA receptor. Previously, we have established that the α-5 subunit of the GABAA receptor contributes to the assembly of a functional receptor in a subset of medulloblastoma cells and benzodiazepines, synthesized to function as α-5 selective ligands with psychotropic activity, impair viability1,2. Utilizing a TP53 wild-type medulloblastoma cell line with amplified MYC, high GABRA5 expression, and a functional α-5 GABAA receptor, we provide insight into how benzodiazepines impair cell viability by positively modulating the native GABAA receptors. We screened benzodiazepines to assess impact of varying chemical group identity on cell viability. The most potent benzodiazepine binds with specificity to ~1000 native receptors per cell with EC50 and IC50 values of ~0.8 micromolar. This binding evokes a 2 x 109 ions.sec-1 chloride flux, which morphologically elicits mitochondrial fragmentation, nuclei distention, and cellular blebbing. The cascade of events culminates in a caspase-mediated activation of apoptosis through the intrinsic pathway and a localization of pro-apoptotic Bcl-2-associated death promoter (BAD) protein. Benzodiazepines may be efficacious as anti-cancer therapeutics for medulloblastoma patients exhibiting a GABAA receptor expression signature by driving a chloride imbalance that leads to cell apoptosis. References: 1Sengupta, et al. α5-GABAA receptors negatively regulate MYC-amplified medulloblastoma growth. Acta Neuropathol. 2014; 127(4): 593–603. 2Jonas, et al. First in vivo testing of compounds targeting Group 3 medulloblastomas using an implantable microdevice as a new paradigm for drug development. J. Biomed. Nanotechnol. 2016; 12(6): 1297–1302.
Pulmonary vaccine delivery (2007)

This review will discuss developments in the field of pulmonary vaccine delivery. The possibilities of adopting aerosol-generation technology and specific pharmaceutical formulations for the purpose of pulmonary immunization are described. Aerosol-generation systems might offer advantages with respect to vaccine stability and antigenicity. Adjuvants and their inclusion in vaccine-delivery systems are described. Other formulation components, such as surfactants, particulate systems and dispersion of the aerosols are detailed in this paper. The noninvasive, relatively safe and low-cost nature of pulmonary delivery may provide great benefits to the public health vaccination campaign.
Joint User Grouping, Scheduling, and Precoding for Multicast Energy\n Efficiency in Multigroup Multicast Systems (2020)

This paper studies the joint design of user grouping, scheduling (or\nadmission control) and precoding to optimize energy efficiency (EE) for\nmultigroup multicast scenarios in single-cell multiuser MISO downlink channels.\nNoticing that the existing definition of EE fails to account for group sizes, a\nnew metric called multicast energy efficiency (MEE) is proposed. In this\ncontext, the joint design is considered for the maximization of MEE, EE, and\nscheduled users. Firstly, with the help of binary variables (associated with\ngrouping and scheduling) the joint design problem is formulated as a\nmixed-Boolean fractional programming problem such that it facilitates the joint\nupdate of grouping, scheduling and precoding variables. Further, several novel\noptimization formulations are proposed to reveal the hidden difference of\nconvex/ concave structure in the objective and associated constraints.\nThereafter, we propose a convex-concave procedure framework based iterative\nalgorithm for each optimization criteria where grouping, scheduling, and\nprecoding variables are updated jointly in each iteration. Finally, we compare\nthe performance of the three design criteria concerning three performance\nmetrics namely MEE, EE, and scheduled users through Monte-Carlo simulations.\nThese simulations establish the need for MEE and the improvement from the\nsystem optimization.\n
Dopamine agonists and sleep in Parkinson’s disease (2002)

Dopaminergic therapy is increasingly recognized as a cause of excessive daytime sleepiness in patients with PD. This adverse effect may be a dose-related phenomenon that is somewhat more likely to occur with dopamine agonists than with levodopa, although all dopaminergic drugs can be sedating. However, medication effect is only one of several causes of somnolence in PD. Other factors include age-related changes in sleep quality, nocturnal motor disturbances, primary sleep disorders such as sleep apnea, medication-induced sleep disruption, and concurrent medical illnesses. There is also increasing evidence that the disease process itself may affect the control of the sleep-wake cycle. Although we have characterized the sleep disturbances in PD, further investigation is needed to define their prevalence and etiology, particularly with respect to the role of dopamine and dopaminergic agents. Clinicians should be alert to the complaint of excessive sleepiness in their patients and should attempt to identify and treat the underlying causes.
Direct Dielectric Barrier Discharge Ionization Promotes Rapid and Simple Lubricant Oil Fingerprinting (2020)

Petroleomics, which is the characterization, separation, and quantification of the components of petroleum and crude oil, is an emerging area of study. However, the repertoire of analytical methods available to understand commercial automotive lubricant oils (ALOs) is very limited. Ambient mass spectrometry is one of the most sensitive analytical methods for real-time and in situ chemical analysis. With this technique, the chemical fingerprinting of ALOs can be performed quickly and simply using dielectric barrier discharge ionization time-of-flight mass spectrometry. In this study, the mass spectra of 35 samples were obtained without any sample preparation in positive-ion mode, and no carryover was observed. To elucidate the similarities and differences between the ALO samples, the data generated from these spectra were analyzed using four chemometric techniques: principal component analysis, multivariate curve resolution, hierarchical cluster analysis, and pattern recognition entropy. The ALO samples were readily differentiated according to their American Petroleum Institute classification and base oil types: mineral, semisynthetic, and synthetic. The development of this new methodology will aid in the semiquantitative control analysis of ALOs and offers an improved ability to identify the components therein.
Hepatitis B Virus Infection triggers AP–1 dependent CD95Ligand expression in HepG2 cells (2012)

An acute Hepatitis B Virus (HBV)-infection is characterized by a vigorous, polyclonal and multi-specific CD8+ T cell response. CD8+ T cells are the main effector cells responsible for viral clearance and disease pathogenesis during an acute HBV-infection. CD95 Ligand (CD95L) expression is generally restricted to a few cell types, e.g. T cells, macrophages and NK cells. We have previously shown that an intact CD95 signalling pathway is required for elimination of HBV-infected hepatocytes. Furthermore, we have identified an AP–1 element in the CD95L promoter which is essential for the transactivation of the CD95L gene. The aim of this study was to analyze CD95L transactivation and -expression in HBV-infected hepatocytes. Adenoviral transfer of HBV constructs into the hepatoma cell line HepG2 resulted in the transactivation, transcription and expression of CD95L. Four different CD95L promoter constructs (CD95L –36, –220, –536, and –1204/+100) have been used to identify the binding site responsible for CD95L transactivation in HBV-infected hepatocytes. However, there was no particular difference in the induction of the different constructs. This led to the hypothesis that no binding site between –36 and –1204 functions as the major binding site responsible for CD95L transactivation in HBV-infected hepatocytes. Instead, inhibition of JNK resulted in a significant inhibition of CD95L transactivation. Since HBV infection resulted in the phosphorylation of JNK (Jun-NH2 kinase) and the subsequent activation of the transcription factor AP–1, we postulate that CD95L transactivation is triggered by Thr183/Tyr185 phosphorylation of JNK. We characterized the molecular mechanisms resulting in CD95L expression in HBV-infected hepatocytes. In this study we provide evidence that HBV infection leads to the phosphorylation of JNK, AP–1 dependent transactivation of CD95L and finally CD95L expression, suggesting a potential CD95L activation independent of CD8+ T cells in HBV infection.
Novel Preparation Steps and Imaging Procedures Suitable for Electronmicroscopical Characterization of Zeolite Structures (2007)

Extract Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007
Autodetection of ancient Arabian tombs in high-resolution satellite imagery (2013)

High circular tombs (HCTs) in southern Arabia provide valuable information for anthropologists who seek fundamental understanding of the transition of ancient peoples from a nomadic pastoral lifestyle, to agro-pastoralism, and eventually to the formation of ancient states. In particular, knowing the geographical distribution of HCTs across the region informs theories on patterns of territoriality and environmental and social factors that are implicated in the emergence of ancient civilizations. The small size of the HCTs, vast search regions, and rugged terrain make mapping them in the field difficult and costly. In this article, a detection algorithm is described and quantitatively evaluated and establishes the feasibility of automatically detecting these tombs in satellite imagery. By narrowing the search to a smaller set of candidate locations, wide area discovery and mapping can be performed much more effectively.
Rare loss-of-function mutation of a death receptor gene in head and neck cancer. (1998)

The chromosomal region 8p21 contains a number of putative tumor suppressor genes and is a frequent site of translocations in head and neck cancers. Recently, a novel tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) death receptor gene, KILLER/DR5, a member of the tumor necrosis factor receptor family, was identified as a potential mediator in p53-dependent apoptosis and mapped to 8p21 by fluorescence in situ hybridization. We have determined the genomic structure of KILLER/DR5 and performed sequence analysis of all 10 coding exons in 20 primary head and neck cancers with allelic loss of chromosome 8p. To screen for a subset of mutations localized to the functional cytoplasmic death domain, we sequenced this region in an additional 40 primary head and neck cancers. We found two alterations in this domain, including a 2-bp insertion at a minimal repeat site, introducing a premature stop codon and resulting in a truncated protein. This KILLER/DR5 mutation was also present in the germ line of the affected patient, and the tumor did not have a p53 mutation by sequence analysis. Transfection studies in head and neck squamous cell carcinoma and colon and ovarian carcinoma cell lines revealed loss of growth-suppressive function associated with the tumor-derived KILLER/DR5 truncation mutant. These observations provide the first evidence for mutation of a TRAIL death receptor gene in a human cancer, leading to loss of its apoptotic function.
GHz Erbium-Doped Mode-Locked Laser Dual-Frequency Comb Spectrometer (2022)

In dual-comb spectroscopy, the maximal spectral coverage and the minimal measurement time depend quadratically on the lasers’ pulse repetition rate. Here, we demonstrate a high-repetition rate 1 GHz dual-comb spectrometer based on low-noise Erbium-doped mode-locked lasers.
Coverage-directed validation of hardware models (1999)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.
Update on genetic and molecular markers associated with myelodysplastic syndromes (2009)

Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms defined by morphologic dysplasia, peripheral cytopenia and clonal instability with enhanced risk of transformation into acute myeloid leukemia. The prognosis and clinical picture in MDS vary depending on patient-related factors (age, gender, comorbidity), the disease variant, cell types affected and genes involved in the malignant process. In fact, more and more data suggest that cytogenetic and molecular defects and gene variants are associated with the clinical course and prognosis in MDS. Although certain molecular defects are indicative of distinct cytogenetic abnormalities, others represent point mutations in critical target genes (RUNX1, N-RAS, JAK2, KIT, others) and sometimes are associated with a particular type of MDS, an overlap disease, a co-existing hematopoietic neoplasm or disease progression. Although most are somatic mutations, germ line mutations and gene polymorphisms have also been described in MDS. Some of these mutations may influence the natural course of disease, iron accumulation or disease progression. The present article provides a summary of our current knowledge about molecular and genetic markers in MDS, with special reference to their potential prognostic and therapeutic implications.
High Performance for Labeling, Separation and Detection Methods for Genome Analysis 12 (2003)

OAK-B135 Our research efforts over the past year have focused on the development of advanced integrated PCR reactors on chips, the development of robust integrated valves, the development of integrated optical detectors, and the development of microdevices for performing integrated genetic analysis. The details of all the projects will be found in the listed papers.
Sub-wavelength resolution using apertureless terahertz near-field microscopy (2003)

We demonstrate apertureless near-field terahertz imaging by introducing a metallic probe above a sample surface. The amplitude of the scattered pulses is very sensitive to the tip-sample distance. A spatial resolution of /spl lambda//520 is demonstrated.
Alpha 2-macroglobulin from horse plasma. Purification, properties and interaction with certain serine proteinases. (1984)

alpha 2-macroglobulin was isolated by polyethylene glycol precipitation, gel filtration on Sephacryl S-300 and DE-52 cellulose chromatography, with 20% yield. The preparation obtained was homogenous as tested by biochemical and immunological criteria. Its molecular mass was estimated at 800,000, comprising of four identical subunits. The isoelectric point of our preparation was 4.8 and two molecules of serine proteinases per 1 molecule of inhibitor were bound.
Using Topological Analysis to Support Event-Guided Exploration in Urban Data (2014)

The explosion in the volume of data about urban environments has opened up opportunities to inform both policy and administration and thereby help governments improve the lives of their citizens, increase the efficiency of public services, and reduce the environmental harms of development. However, cities are complex systems and exploring the data they generate is challenging. The interaction between the various components in a city creates complex dynamics where interesting facts occur at multiple scales, requiring users to inspect a large number of data slices over time and space. Manual exploration of these slices is ineffective, time consuming, and in many cases impractical. In this paper, we propose a technique that supports event-guided exploration of large, spatio-temporal urban data. We model the data as time-varying scalar functions and use computational topology to automatically identify events in different data slices. To handle a potentially large number of events, we develop an algorithm to group and index them, thus allowing users to interactively explore and query event patterns on the fly. A visual exploration interface helps guide users towards data slices that display interesting events and trends. We demonstrate the effectiveness of our technique on two different data sets from New York City (NYC): data about taxi trips and subway service. We also report on the feedback we received from analysts at different NYC agencies.