Xu: An Automated Query Expansion and Optimization Tool

The exponential growth of information on the Internet is a big challenge for information retrieval systems towards generating relevant results. Novel approaches are required to reformat or expand user queries to generate a satisfactory response and increase recall and precision. Query expansion (QE) is a technique to broaden users' queries by introducing additional tokens or phrases based on some semantic similarity metrics. The tradeoff is the added computational complexity to find semantically similar words and a possible increase in noise in information retrieval. Despite several research efforts on this topic, QE has not yet been explored enough and more work is needed on similarity matching and composition of query terms with an objective to retrieve a small set of most appropriate responses. QE should be scalable, fast, and robust in handling complex queries with a good response time and noise ceiling. In this paper, we propose Xu, an automated QE technique, using high dimensional clustering of word vectors and Datamuse API, an open source query engine to find semantically similar words. We implemented Xu as a command line tool and evaluated its performances using datasets containing news articles and human-generated QEs. The evaluation results show that Xu was better than Datamuse by achieving about 88% accuracy with reference to the human-generated QE.Comment: Accepted to IEEE COMPSAC 201

Smooth muscle archvillin: a novel regulator of signaling and contractility in vascular smooth muscle

The mechanisms by which protein kinase C (PKC) and extracellular-signal-regulated kinases (ERK1/2) govern smooth-muscle contractility remain unclear. Calponin (CaP), an actin-binding protein and PKC substrate, mediates signaling through ERK1/2. We report here that CaP sequences containing the CaP homology (CH) domain bind to the C-terminal 251 amino acids of smooth-muscle archvillin (SmAV), a new splice variant of supervillin, which is a known actin- and myosin-II-binding protein. The CaP-SmAV interaction is demonstrated by reciprocal yeast two-hybrid and blot-overlay assays and by colocalization in COS-7 cells. In differentiated smooth muscle, endogenous SmAV and CaP co-fractionate and co-translocate to the cell cortex after stimulation by agonist. Antisense knockdown of SmAV in tissue inhibits both the activation of ERK1/2 and contractions stimulated by either agonist or PKC activation. This ERK1/2 signaling and contractile defect is similar to that observed in CaP knockdown experiments. In A7r5 smooth-muscle cells, PKC activation by phorbol esters induces the reorganization of endogenous, membrane-localized SmAV and microfilament-associated CaP into podosome-like structures that also contain F-actin, nonmuscle myosin IIB and ERK1/2. These results indicate that SmAV contributes to the regulation of contractility through a CaP-mediated signaling pathway, involving PKC activation and phosphorylation of ERK1/2

AIDS-defining illnesses among patients with HIV in Singapore, 1985 to 2001: results from the Singapore HIV Observational Cohort Study (SHOCS)

BACKGROUND: The objective was to describe the causes of initial and overall AIDS-defining disease episodes among HIV patients in Singapore. METHODS: A retrospective observational cohort study was performed of all adult patients seen at the national HIV referral center between 1985 and 2001. Data were extracted from the patients' records by ten trained healthcare workers. AIDS-defining conditions were established using predefined criteria. RESULTS: Among 1504 patients, 834 had experienced one or more AIDS-defining diseases. The most frequent causes of the initial AIDS-defining episode were Pneumocystis carinii pneumonia (35.7%), Mycobacterium tuberculosis (22.7%) and herpes simplex (7.4%). In total 1742 AIDS-defining episodes occurred. The most frequent causes were Pneumocystis carinii pneumonia (25.1%), Mycobacterium tuberculosis (16.2%) and cytomegalovirus retinitis (9.5%). CONCLUSIONS: The most frequent causes of AIDS-defining illnesses in Singapore are similar to those reported in the West, prior to the introduction of anti-retroviral therapy. Opportunistic infections remain the most frequent AIDS-defining illnesses

The use of cosmic-ray muons in the energy calibration of the Beta-decay Paul Trap silicon-detector array

This article presents an approach to calibrate the energy response of double-sided silicon strip detectors (DSSDs) for low-energy nuclear-science experiments by utilizing cosmic-ray muons. For the 1-mm-thick detectors used with the Beta-decay Paul Trap, the minimum-ionizing peak from these muons provides a stable and time-independent in situ calibration point at around 300 keV, which supplements the calibration data obtained above 3 MeV from α sources. The muon-data calibration is achieved by comparing experimental spectra with detailed Monte Carlo simulations performed using GEANT4 and CRY codes. This additional information constrains the calibration at lower energies, resulting in improvements in quality and accuracy

Nuclear Localization of Cyclin B1 Controls Mitotic Entry After DNA Damage

Mitosis in human cells is initiated by the protein kinase Cdc2-cyclin B1, which is activated at the end of G2 by dephosphorylation of two inhibitory residues, Thr14 and Tyr15. The G2 arrest that occurs after DNA damage is due in part to stabilization of phosphorylation at these sites. We explored the possibility that entry into mitosis is also regulated by the subcellular location of Cdc2-cyclin B1, which is suddenly imported into the nucleus at the end of G2. We measured the timing of mitosis in HeLa cells expressing a constitutively nuclear cyclin B1 mutant. Parallel studies were performed with cells expressing Cdc2AF, a Cdc2 mutant that cannot be phosphorylated at inhibitory sites. Whereas nuclear cyclin B1 and Cdc2AF each had little effect under normal growth conditions, together they induced a striking premature mitotic phenotype. Nuclear targeting of cyclin B1 was particularly effective in cells arrested in G2 by DNA damage, where it greatly reduced the damage-induced G2 arrest. Expression of nuclear cyclin B1 and Cdc2AF also resulted in significant defects in the exit from mitosis. Thus, nuclear targeting of cyclin B1 and dephosphorylation of Cdc2 both contribute to the control of mitotic entry and exit in human cells

Cyclin A2 Mutagenesis Analysis: A New Insight into CDK Activation and Cellular Localization Requirements

Cyclin A2 is essential at two critical points in the somatic cell cycle: during S phase, when it activates CDK2, and during the G2 to M transition when it activates CDK1. Based on the crystal structure of Cyclin A2 in association with CDKs, we generated a panel of mutants to characterize the specific amino acids required for partner binding, CDK activation and subcellular localization. We find that CDK1, CDK2, p21, p27 and p107 have overlapping but distinct requirements for association with this protein. Our data highlight the crucial importance of the N-terminal α helix, in conjunction with the α3 helix within the cyclin box, in activating CDK. Several Cyclin A2 mutants selectively bind to either CDK1 or CDK2. We demonstrate that association of Cyclin A2 to proteins such as CDK2 that was previously suggested as crucial is not a prerequisite for its nuclear localization, and we propose that the whole protein structure is involved

The radio counterpart of the likely TeV binary HESS J0632+057

The few known gamma-ray binary systems are all associated with variable radio and X-ray emission. The TeV source HESS J0632+057, apparently associated with the Be star MWC148, is plausibly a new member of this class. Following the identification of a variable X-ray counterpart to the TeV source we conducted GMRT and VLA observations in June-September 2008 to search for the radio counterpart of this object. A point-like radio source at the position of the star is detected in both 1280 MHz GMRT and 5 GHz VLA observations, with an average spectral index, alpha, of ~0.6. In the VLA data there is significant flux variability on ~month timescales around the mean flux density of ~0.3 mJy. These radio properties (and the overall spectral energy distribution) are consistent with an interpretation of HESS J0632+057 as a lower power analogue of the established gamma-ray binary systems.Comment: Accepted for publication in MNRAS (7 pages, 4 figures, 1 table

The Beta-decay Paul Trap Mk IV: Design and commissioning

The Beta-decay Paul Trap is an open-geometry, linear trap used to measure the decays of $^8$Li and $^8$B to search for a tensor contribution to the weak interaction. In the latest $^8$Li measurement of Burkey et al. (2022), $\beta$ scattering was the dominant experimental systematic uncertainty. The Beta-decay Paul Trap Mk IV reduces the prevalence of $\beta$ scattering by a factor of 4 through a redesigned electrode geometry and the use of glassy carbon and graphite as electrode materials. The trap has been constructed and successfully commissioned with $^8$Li in a new data campaign that collected 2.6 million triple coincidence events, an increase in statistics by 30% with 4 times less $\beta$ scattering compared to the previous $^8$Li data set.Comment: 17 pages, 7 figure

Student Independent Projects Psychology Programs 2014:

The capstone course, Psychology 4950, in the Bachelor of Arts and Bachelor of Science psychology degree programs allows students to carry out research on a topic of their choice and to prepare reports on their findings. This compilation of papers represents the results of their efforts. The faculty and staff of the Psychology Program congratulate the members of the Year 2014 course on their accomplishment, and wish them continued succes