Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic markers useful for distinguishing between organ‐confined and locally advanced prostate cancer

Prostate cancer is one of the most commonly diagnosed cancers and the second leading cause of cancer deaths among men in the United States. In this study, we performed comparative genomic hybridization (CGH) on 45 primary prostate adenocarcinomas to determine genetic markers that could be useful for distinguishing between organ‐confined and locally advanced prostate cancer. Of these tumors, 24 were pT2 stage, 21 were pT3b; 20 had low Gleason scores (GS), 25 had high GS. The most common chromosomal alterations in all 45 tumors included losses on 8p (57.8%), 10q21→qter (40.0%), 16q (35.6%), 11q21→qter (28.9%), 16p (22.2%), 6q22→24 (22.2%), 10p (20.0%), 5q31→qter (17.8%), 6p (17.8%), 15q22→qter (15.6%), and 17p (15.6%) as well as gains on 7cen→p14 (20.0%), 7cen→q22 (20.0%), and Xcen→q21 (17.8%). Contingency table analysis showed that losses of 8p, 10q25→qter, 6p21, 6q24→qter, and 15q22→qter were significantly increased in frequency (P < 0.05) with increasing stage and/or GS. A model was created following multivariate logistic regression analysis that was predictive of tumor stage in approximately 90% of the tumors studied. This model suggests that loss of 8p is the most valuable predictor of stage. These findings suggest that chromosomal regions identified in this study may be useful for distinguishing between organ‐confined and locally advanced prostate tumors. © 2003 Wiley‐Liss, Inc.
Transfer of the plasmid for exfoliative toxin B synthesis in mixed cultures on nitrocellulose membranes

Plasmid pRW002 carries genetic determinants for exfoliative toxin B and bacteriocin R1 synthesis. When a donor strain carrying plasmid pRW002 was mixed with a plasmidless recipient strain on a nitrocellulose membrane in accordance with the procedure used for staphylococcal conjugation, pRW002 was passed to the recipient by mixed-culture transduction. Transfer was inhibited by citrate and serotype B phage antisera but not by DNase I. Cell-to-cell contact was not required, and transfer frequencies increased more than 10-fold in the presence of small concentrations of mitomycin C. These results are consistent with pRW002 transfer in mixed cultures by transduction and not by conjugation or transformation. Immunodiffusion and DNA analyses after agarose gel electrophoresis demonstrated that transductants were exfoliative toxin B producers and housed pRW002. Since mixed-culture transfer has been reported to occur on skin, our results suggest that mixed-culture transduction might be a mechanism for the transfer of genetic determinants for pathogenicity in vivo.
Revealing academic web interlinking motives through webometrics and statistical techniques: Nigerian university websites as a case study

The websites of the universities of Africa's most populous country Nigeria were examined. The goal was to unearth the reasons why external hyperlinks are placed on these sites and identify any peculiarities by geographical location. Academic website interlinking motivations were formulated. Over 6,000 hyperlinks placed on the websites of 86 Nigerian universities were categorised under these interlinking motivations. Categorising the motivations by examining the source and target pages of each hyperlink was an arduous task. Statistical analysis offered a clearer picture of the interlinking motives. A chi-squared test revealed distinctive features, which are characteristic of specific geographical regions of Nigeria. The study serves as a route to further research on feasibility of findings in other developing countries. Results obtained could be of great importance for academic webpage developers and authors. The results could modify their work towards improving the use of hyperlinks as a major communication tool on the web.
Meta-heuristics in multidimensional systems stability study

Multidimensional systems, or n-D systems, are systems having several independent variables. Several topics, in particular stability, of n-D systems (n > 1) have attracted the interest of many researchers. The main reason, is because the extension stability theory of 1-D systems to systems with higher dimensions is not straightforward. In this paper, two adopted meta-heuristics algorithms are used for complementing the study of systems stability based on their polynomial characteristics over the variables boundaries. The two meta-heuristics are genetic algorithm and particle swarm optimization due to its popularity. Practical results of both meta-heuristics are compared and the better algorithm highlighted. The results demonstrate that meta-heuristics can be applied in studding multidimensional system stability.
Transmission of HCV in the Vietnamese community

and if positive for HCV RNA, the HCV genotype was determined. Genotyping was performed using the Inno-LiPA HCV II genotyping kit (Inno-LiPA, Innogenetics, Ghent, Belgium). We successfully recruited 11 male and 3 female Vietnameseborn patients whose median age was 48 years and who were HCV antibody positive. Half of the patients had no understanding of the routes of HCV transmission, while others confused transmission modes for HCV with those of other agents of viral hepatitis. Exposure to some medical and dental procedures during childhood in Vietnam may have increased the risk of HCV infection among these patients. For instance, mass dental procedures were reported to take place in some villages. A visiting dentist would extract teeth from successive patients with the same instrument, without cleaning or sterilising equipment between patients. Traditional treatment practices for pruritis would involve the village doctor incising the back of patients’ legs with a piece of glass. Again, the glass was used on successive patients. The HCV genotypes of 11 patients who provided a blood sample were genotype 1b (n=8), genotype 6a (n=2) and genotype 2a/c (n=1). This was consistent with the distribution of genotypes previously described for people living in Vietnam,8 but different to the distribution of genotypes of Australian-born people with HCV infection,9 supporting our assumption that Vietnamese immigrants acquired their HCV infection in Vietnam. In summary, this study has shown that previously unrecorded cultural/medical practices may be common throughout parts of Vietnam and further research is needed to understand the role that such practices play in the transmission of HCV. The evidence showing the same distribution of HCV genotypes among participants in this study with that identified in Vietnam suggests that infection occurred in Vietnam. Even though small, our study has identified an urgent need for the provision of culturally relevant information and education programs about HCV in this target population.
Commute mode diversity and income inequality: an inter-urban analysis of 148 midsize US cities

ABSTRACT Little is known about the relationship between multi-modal transportation environments and aspects of sustainable urban development, such as reduced income inequality and affordable housing. This study, adapted from Molotch and Appelbaum's inter-city differential method, studied 148 semi-isolated mid-size cities. Using U.S. Census data from 2013, we found that increased diversity in commute modality is associated with less income inequality between white and African-American households, as well as between men and women. Commute mode diversity is also associated with higher earnings for white women and African-American men. Our study also shows that cities with more commuter mode diversity are associated with higher home property values and affordable rental markets compared to automobile dependent cities. These results undercut the notion that increasing automobile ownership is a reasonable policy response to urban poverty, and suggest that sustainable transportation policy can produce positive economic gains for cities. This work adds to the growing literature identifying fundamental differences between multimodal and automobile dependent cities.
Characterization of high-energy optical-parametric oscillation by using periodically poled Mg-doped congruent LiTaO3

Quasi phase matching (QPM), realized by periodic inversion of crystal polarization, have been used for highly efficient nonlinear wavelength conversion, such as second harmonic generation and optical parametric oscillation (OPO). Last several years, we have reported high-energy OPO by using periodically poled Mg-doped congruent LiNbO3 (MgLN) to generate high-energy mid-IR light [1, 2]. Also, we have reported on Mg-doped congruent LiTaO3 (MgLT) as a new material for high power/energy QPM device [3, 4]. MgLT has improved properties on thermal conductivity and absorption edge in UV region compared to MgLN, although nonlinear coefficient of MgLT is smaller than MgLN, and we expect that MgLT is suitable for higher power/energy QPM device compared to MgLN. In this study, characterization of high-energy OPO using periodically poled MgLT (PPMgLT) will be presented, and compared to that of conventional periodically poled MgLN (PPMgLN).
State Control Versus Hybrid Land Markets: Planning and Urban Development in Transitional Hanoi, Vietnam

During the post-reform period since 1986, land-use systems in Vietnam have been reformed in terms of the regulation of land markets and the built environment. This study analyzes the changing role of urban planning and the policy of state intervention in land markets to manage spatial changes in Vietnamese cities. Theoretical and empirical approaches are used to analyze urban development and planning practices in Hanoi. The study further describes the constraints of planning systems in hybrid land markets that include both formal and informal land development. We argue that in Vietnam, where the role of the state in market construction has not been fully developed and land market institutions are incomplete, urban planning is used as a passive tool of state control and is no longer relevant to the process of spatial development, which is driven by the speculative activities of interest actors. This situation challenges state regulations for the effective management of spatial resources. The empirical results suggest the utility of further reforms to the land-use system and planning institutions in Vietnam, and of strengthening the capacity of the state in land administration.
Polarization- and Phase-Sensitive Low-Coherence Interferometry Setup for the Characterization of Integrated Optical Components

A novel phase-sensitive and polarization-sensitive scheme to implement an optical low-coherence interferometry (OLCI) system is presented. With respect to conventional phase-sensitive OLCI, in our system the interference fringes of the coherent light used to recover phase information are conveniently detected by the same photodetector acquiring the low-coherence signal. This strategy guarantees the intrinsic synchronization of the two signals at any acquisition speed, makes measurements more robust against long-term fluctuations in the experimental setup, and reduces the measurement time without affecting phase accuracy. The residual phase error after the phase recovery procedure is less than 0.01 rad, to the authors' knowledge one of the best results reported so far for OLCI measurements. Polarization sensitivity is achieved in the same setup by means of polarization selective retarders (PSRs) employed to couple light into and out of the device under test. This scheme enables to retrieve the time and frequency domain response of an optical device for both the polarization states from a single data acquisition. The presented technique is extremely versatile; it can be implemented by using either fiber or free space optics and applied to the characterization of generic optical devices. Its effectiveness is demonstrated by reporting the measurement of the amplitude and phase response of integrated optical devices based on ring resonators.
Pure-tone audiometric threshold assessment with in-ear monitoring of noise levels

Abstract Objective: Our objective was to obtain reliable threshold measurements without a sound booth by using a passive noise-attenuating hearing protector combined with in-ear 1/3-octave band noise measurements to verify the ear canal was suitably quiet. Design: We deployed laptop-based hearing testing systems to Tanzania as part of a study of HIV infection and hearing. An in-ear probe containing a microphone was used under the hearing protector for both the in-ear noise measurements and threshold audiometry. The 1/3-octave band noise spectrum from the microphone was displayed on the operator's screen with acceptable levels in grey and unacceptable levels in red. Operators attempted to make all bars grey, but focused on achieving grey bars at 2000 Hz and above. Study sample: 624 adults and 197 children provided 3381 in-ear octave band measurements. Repeated measurements from 144 individuals who returned for testing on three separate occasions were also analysed. Results: In-ear noise levels exceeded the maximum permissible ambient noise levels (MPANL) for ears not covered, but not the dB SPL levels corresponding to 0 dB HL between 2000–4000 Hz. In-ear noise measurements were repeatable over time. Conclusions: Reliable audiometry can be performed using a passive noise-attenuating hearing protector and in-ear noise measurements.
State Finances after Fiscal Responsibility Legislation: Genuine Improvement or Illusion?

ABSTRACT Getting subnational governments to behave in a fiscally responsible manner is a challenge in federations. Fiscal Responsibility Legislation (FRL), which binds subnational governments to fiscal prudence, has been seen as a way of meeting this challenge. We examine this issue in the context of states in the Indian federation. We seek to investigate the extent to which states have tried to improve their fiscal health in the post-FRL period.The fiscal performance of 15 Indian states, both before and after the enactment of FRLs, is examined. Initially, we compare a measure of fiscal performance (e.g., gross fiscal deficit as percentage of each state’s output) for specified number of years after enacting the FRL with the performance over the same number of years prior to enacting the FRL. We then employ GMM estimation approach to estimate a dynamic panel data model to study the impact of the FRLs. Our analysis suggests that federal transfers have likely played a much more important role in the process of restoring states’ fiscal health as compared to their own-efforts at such improvement. This paper thus signals the need to re-look at the quantum and design of intergovernmental transfer such that states are encouraged to boost their own-revenue collection efforts.
HOP-1 Presenilin Deficiency Causes a Late-Onset Notch Signaling Phenotype That Affects Adult Germline Function in Caenorhabditis elegans

Functionally redundant genes present a puzzle as to their evolutionary preservation, and offer an interesting opportunity for molecular specialization. In Caenorhabditis elegans, either one of two presenilin genes (sel-12 or hop-1) facilitate Notch activation, providing the catalytic subunit for the γ secretase proteolytic enzyme complex. For all known Notch signaling events, sel-12 can mediate Notch activation, so the conservation of hop-1 remains a mystery. Here, we uncover a novel “late-onset” germline Notch phenotype in which HOP-1-deficient worms fail to maintain proliferating germline stem cells during adulthood. Either SEL-12 or HOP-1 presenilin can impart sufficient Notch signaling for the establishment and expansion of the germline, but maintenance of an adult stem cell pool relies exclusively on HOP-1-mediated Notch signaling. We also show that HOP-1 is necessary for maximum fecundity and reproductive span. The low-fecundity phenotype of hop-1 mutants can be phenocopied by switching off glp-1/Notch function during the last stage of larval development. We propose that at the end of larval development, dual presenilin usage switches exclusively to HOP-1, perhaps offering opportunities for differential regulation of the germline during adulthood. Additional defects in oocyte size and production rate in hop-1 and glp-1 mutants indicate that the process of oogenesis is compromised when germline Notch signaling is switched off. We calculate that in wild-type adults, as much as 86% of cells derived from the stem cell pool function to support oogenesis. This work suggests that an important role for Notch signaling in the adult germline is to furnish a large and continuous supply of nurse cells to support the efficiency of oogenesis.
Genetic and Epigenetic screening for gene alterations of the chromatin‐remodeling factor, SMARCA4/BRG1, in lung tumors

The SMARCA4/BRG1 gene product is a component of the SWI‐SNF chromatin‐remodeling complex and regulates gene expression by disrupting histone‐DNA contacts in an ATP‐dependent manner. Inactivating mutations of the SMARCA4 gene, on chromosome arm 19p, are present in several human cancer cell lines, including cell lines derived from lung cancers. Interestingly, loss of heterozygosity (LOH) at 19p and absence of the SMARCA4 protein have been reported in lung tumors. To evaluate further the possible contribution of SMARCA4 gene inactivation to lung carcinogenesis, we performed a complete analysis of the SMARCA4 gene to search for (a) point mutations in all 35 coding exons, including an existing splicing variant and the intron–exon boundaries, and (b) abrogation of gene expression through promoter hypermethylation by using the methylation‐specific polymerase chain reaction (MSP) assay. We selected genomic DNA from 20 lung primary tumors with LOH on 19p for the screening of point mutations and 10 lung cancer cell lines and 52 lung primary tumors for the MSP analysis. Through our mutational screening, we identified an in‐frame and germ‐line insertion of 24 bp in exon 4 whose biological relevance is unknown. This variant was not detected in the germ line of the 62 additional individuals analyzed, indicating it is not a common polymorphism. Moreover, two missense alterations were identified in the tumors of 2 patients, a somatic Gly1160Arg mutation and a Ser1176Cys mutation. Neither was present in the germ line of the 51 additional lung cancer individuals tested. Because these mutations lead to substitution of highly conserved amino acids, they may affect the ATPase function of the protein. Finally, no promoter hypermethylation was observed in any lung primary tumor or cancer cell line, indicating that this is not a major mechanism for SMARCA4 inactivation during lung carcinogenesis. In conclusion, our data revealed that somatic point mutations of the SMARCA4 gene are present in a small subset of lung tumors, although mutations affecting the ATPase domain may be a hot‐spot for SMARCA4 gene inactivation. We cannot rule out that other mechanisms, such as complete or partial deletions of the SMARCA4 gene, are contributing to the loss of the SMARCA4 protein in lung cancer. © 2004 Wiley‐Liss, Inc.
Observer agreement for respiratory signs and oximetry in infants hospitalized with lower respiratory infections.

To determine observer agreement for a clinical score and oximetry in lower respiratory infection in children less than 2 yr of age, a convenience sample of 56 infants hospitalized with bronchiolitis or pneumonia was assessed independently by two observers. A total of 12 infants had chronic lung disease of prematurity or congenital heart disease. Infants in whom oxygen supplementation could not be discontinued for at least 5 min were excluded. A severity score was assigned for each of four categories (respiratory rate, retractions, wheeze, and general appearance). A total for each patient was obtained by summing the score for each category. Oxygen saturation was measured using a Nellcor oximeter. Agreement beyond chance was measured using the kappa statistic. The relationship between observers for total score and oximetry and the mean total score and mean oximetry value for each patient was expressed as a Pearson correlation coefficient. A total of 56 infants and children were studied: 2 had pneumonia, 11 had an exacerbation of pulmonary signs and symptoms with their underlying cardiac or pulmonary disease, and 43 had bronchiolitis. Kappa was 0.48 for general assessment, 0.38 for respiratory rate, 0.31 for wheeze, and 0.25 for retractions. All values were statistically significantly greater than 0 at p less than 0.01. Correlations for total score and for oximetry were 0.68 and 0.88, respectively. The median difference between oximetry readings was 1. The correlation coefficient between total score and oximetry was -0.04. The limited agreement for clinical signs makes comparison of patient illness severity between studies difficult. (ABSTRACT TRUNCATED AT 250 WORDS)
Second hand smoke in alfresco areas.

ISSUE ADDRESSED There are moves to ban smoking in outdoor areas of pubs, restaurants and cafes. Some argue that this is unnecessary as exposure to second hand smoke (SHS) is minimal. The aim of this study was to determine potential exposure of patrons to SHS in outdoor areas of eating and drinking venues. METHODS Concentrations of fine particulate matter (PM2.5) were measured in the alfresco areas of 28 cafes and pubs. Data were collected on the number of smokers present during sampling and factors that could influence PM2.5concentrations. PM2.5concentrations for periods with and without smokers were compared using paired and independent sample tests. RESULTS PM2.5 concentrations were significantly increased when there was at least one smoker compared to periods with no smoking (14.25 microg/m3 and 3.98 g/m3, respectively). There was evidence of a dose response increase with mean concentrations for none, one and two or more smokers of 3.98, 10.59and 17.00microg/m3, respectively. The differences remained significant after controlling for other factors. When two or more people were smoking, average PM2.5reached levels the US Environmental Protection Agency warns may put particularly sensitive people at risk of respiratory symptoms. CONCLUSIONS Smoking increases PM2.5concentrations in outdoor areas to levels that are potentially hazardous to health.
Differential distribution of the KCl cotransporter KCC2 in thalamic relay and reticular nuclei

In the thalamus of the rat the reversal potential of GABA‐induced anion currents is more negative in relay cells than in neurones of the reticular nucleus (nRt) due to different chloride extrusion mechanisms operating in these cells. The distribution of KCl cotransporter type 2 (KCC2), the major neuronal chloride transporter that may underlie this effect, is unknown in the thalamus. In this study the precise regional and ultrastructural localization of KCC2 was examined in the thalamus using immunocytochemical methods. The neuropil of all relay nuclei was found to display intense KCC2 immunostaining to varying degrees. In sharp contrast, the majority of the nRt was negative for KCC2. In the anterior and dorsal part of the nRt, however, KCC2 immunostaining was similar to relay nuclei and parvalbumin and calretinin were found to colocalize with KCC2. At the ultrastructural level, KCC2 immunoreactivity was mainly located in the extrasynaptic membranes of thick and thin dendrites and the somata of relay cells but was also found in close association with asymmetrical synapses formed by cortical afferents. Quantitative evaluation of KCC2 distribution at the electron microscopic level demonstrated that the density of KCC2 did not correlate with dendritic diameter or synaptic coverage but is 1.7 times higher on perisynaptic membrane surfaces than on extrasynaptic membranes. Our data demonstrate that the regional distribution of KCC2 is compatible with the difference in GABA‐A reversal potential between relay and reticular nuclei. At the ultrastructural level, abundant extrasynaptic KCC2 expression will probably play a role in the regulation of extrasynaptic GABA‐A receptor‐mediated inhibition.