Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing To Examine Genetic Diversity of Mycobacterium tuberculosis in Singapore

ABSTRACT Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.
Iterative Receiver Techniques for SC-FDMA Uplink Block Transmission: Design and Performance Evaluation

This paper deals with Cyclic Prefix (CP)-assisted block transmission solutions for future mobile broadband systems, in the context of a Single Carrier (SC)-Frequency Division Multiple Access (FDMA) uplink. Two alternative choices are considered regarding the subcarrier mapping rule: a "localized" subcarrier mapping where user's data occupy a set of consecutive subcarriers (Rule R1); a "distributed" subcarrier mapping where user's data occupy a set of uniformly spaced subcarriers (Rule R2). Detailed performance evaluations, in this paper, involve the consideration of two iterative FDE receiver techniques, with different complexity levels, which can be regarded as extensions of iterative receiver techniques proposed previously within a single user context. A selected class of multipath radio channels, providing a range of channel time dispersion levels, is assumed for performance evaluation purposes, and a set of matched filter bounds on receiver performance plays a relevant role in "achievable performance" comparisons. Both the impact of the mapping rules and that of the iterative receiver techniques considered here are evaluated in detail. This paper also studies the performance degradation due to a channel impulse response longer than the CP: such degradation is related to an "ICI (Inter-Channel Interference) effect" (possibly involving a multi-user interference component) which is inherent to the insufficient-CP conditions. The performance advantages under rule R2 are emphasized for a low or moderate channel time dispersion, and both specific iterative receiver techniques; for a higher time dispersion, receiver performances become very similar with both rules, at the BER values of practical interest (say, BER=10-5). Having in mind that rule R2 has a power efficiency advantage regarding transmitter implementation (due to the reduced envelope fluctuations), we can conclude that this rule provides a clear overall power efficiency advantage, regarding both transmitter and receiver issues, for the entire range of channel time dispersion levels.
Structure-Function Analyses Point to a Polynucleotide-Accommodating Groove Essential for APOBEC3A Restriction Activities

ABSTRACT Members of the human APOBEC3 family of editing enzymes can inhibit various mobile genetic elements. APOBEC3A (A3A) can block the retrotransposon LINE-1 and the parvovirus adeno-associated virus type 2 (AAV-2) but does not inhibit retroviruses. In contrast, APOBEC3G (A3G) can block retroviruses but has only limited effects on AAV-2 or LINE-1. What dictates this differential target specificity remains largely undefined. Here, we modeled the structure of A3A based on its homology with the C-terminal domain of A3G and further compared the sequence of human A3A to those of 11 nonhuman primate orthologues. We then used these data to perform a mutational analysis of A3A, examining its ability to restrict LINE-1, AAV-2, and foreign plasmid DNA and to edit a single-stranded DNA substrate. The results revealed an essential functional role for the predicted single-stranded DNA-docking groove located around the A3A catalytic site. Within this region, amino acid differences between A3A and A3G are predicted to affect the shape of the polynucleotide-binding groove. Correspondingly, transferring some of these A3A residues to A3G endows the latter protein with the ability to block LINE-1 and AAV-2. These results suggest that the target specificity of APOBEC3 family members is partly defined by structural features influencing their interaction with polynucleotide substrates.
Context, cortex, and associations: a connectionist developmental approach to verbal analogies

We present a PDP model of binary choice verbal analogy problems (A:B as C:[D1|D2], where D1 and D2 represent choice alternatives). We train a recurrent neural network in item-relation-item triples and use this network to test performance on analogy questions. Without training on analogy problems per se, the model explains the developmental shift from associative to relational responding as an emergent consequence of learning upon the environment's statistics. Such learning allows gradual, item-specific acquisition of relational knowledge to overcome the influence of unbalanced association frequency, accounting for association effects of analogical reasoning seen in cognitive development. The network also captures the overall degradation in performance after anterior temporal damage by deleting a fraction of learned connections, while capturing the return of associative dominance after frontal damage by treating frontal structures as necessary for maintaining activation of A and B while seeking a relation between C and D. While our theory is still far from being complete it provides a unified explanation of findings that need to be considered together in any integrated account of analogical reasoning.
Embolization of Intracranial Aneurysms With Hydrogel-Coated Coils Versus Inert Platinum Coils: Effects on Packing Density, Coil Length and Quantity, Procedure Performance, Cost, Length of Hospital Stay, and Durability of Therapy

Background and Purpose— The durability of aneurysm coil embolization is thought to depend on packing density. The expansile property of hydrogel coating on coils increases volumetric packing per coil length. We describe our experience using hydrogel-coated coils (HydroCoils) compared with inert platinum coils in intracranial aneurysm embolization. Methods— Fifty aneurysms embolized primarily using HydroCoils from 2003 to 2004 were compared with 57 volume- and shape-matched aneurysms treated with standard platinum coils from 2000 to 2003. Outcome measures included volumetric percentage occlusion (VPO), length and number of coils used, procedure time, fluoroscopy time, contrast volume, coil cost, length of hospital stay, and durability of therapy. Results— Seventeen/26/5 small/medium/large aneurysms treated with HydroCoils were matched with 29/24/4 small/medium/large aneurysms treated with inert platinum. HydroCoil embolization yielded significantly greater VPO (84.8% versus 29.8%; P<0.001), decreased average total coil length used per aneurysm (33.2 versus 44.3 cm), reduced fluoroscopy time (53.2 versus 65.2 minutes; P=0.016), but increased contrast volume used (174.8 versus 112.9 cc; P<0.001). There were no differences in length of hospital stay. Procedure-related morbidity and mortality rates in the HydroCoil cohort were 4% and 0%, respectively. Follow-up angiography at mean 12.3 months revealed lower aneurysm recurrence rates (17% versus 24%; number-needed-to-treat [NNT] 14.3). Initial costs associated with HydroCoil embolization were higher ($5835 versus $4017; P=0.004) but countered by lower retreatment rates (10% versus 17%; NNT 14.3). Conclusions— HydroCoil embolization achieves greater aneurysm packing density with decreased coil length. Initial durability data favor HydroCoils, with lower recurrence and retreatment rates.
Focused training of emergency medicine residents in goal-directed echocardiography: a prospective study.

OBJECTIVES To determine if a focused transthoracic echocardiography (TTE) training course would improve the accuracy of completion and interpretation of a goal-directed TTE by emergency medicine residents. METHODS This was a prospective, observational, educational study of the impact of a focused training course on the change in physician performance on pre- and postcourse examinations testing competency in goal-directed TTE defined by five criteria: 1). image orientation, 2). anatomy identification, 3). chamber size grading, 4). ventricular function estimation, and 5). pericardial effusion identification. Subjects included were emergency medicine residents with between ten and 20 hours of noncardiac ultrasound didactics and between 20 and >150 proctored noncardiac ultrasound examinations. All underwent five hours of focused echocardiography didactics and one hour of proctored practical echocardiography training designed and implemented by an emergency physician ultrasound director and a cardiologist. Before the start of the training course, participants completed two examinations: 1) written 23-question test on the above concepts and 2) performance of a TTE on a healthy subject testing 16 elements that define a properly performed examination. After the training course, participants again completed both examinations. RESULTS A total of 21 emergency medicine residents qualified for and underwent standardized testing and training. The percentage correct on the precourse written examination was 54% (95% CI = 50% to 59%), and the postcourse examination score was 76% (95% CI = 71% to 80%) (p < 0.005, paired t-test). The percentage correct on the precourse practical examination was 56% (95% CI = 51% to 60%), and the postcourse examination score was 94% (95% CI = 91% to 96%) (p < 0.005). CONCLUSIONS A focused six-hour echocardiography training course significantly improved emergency medicine residents' percentage scores on both written and practical examinations testing essential components required for correct goal-directed TTE performance and interpretation.
THE ROLE OF INTERMEDIARIES IN FACILITATING E- GOVERNMENT DIFFUSION IN SAUDI ARABIA

Recent studies of e-government activity have highlighted adoption and diffusion issues as important subjects for rating e-government success. However in developing countries inadequate resources and limited citizens’ capabilities regarding new e-government have resulted in low diffusion and adoption of e-government services. This paper examines the role of intermediaries, which can be played by a third party; in bridging the gap between e-government implementation and social reality, and looks at the roles a third party can add within the e-government services mechanism. This paper uses a case study approach in order to reflect e-government progress within the context of the Kingdom of Saudi Arabia (KSA) as one developing country. The result of this paper shows that intermediaries play an important role in the diffusion of e-services in relation to improving the availability, accessibility and enhancing privacy and security.
Community Design and Crime: The Impact of Housing and the Built Environment

Crime is influenced by the built environment. Broken windows, crime prevention through environmental design, situational crime prevention, and economic theories of the supply of and demand for criminal opportunities offer explanations. Zoning, designs of streets and housing, locations of public transit, and land uses shape the built environment in ways that can increase or reduce crime. Cross-sectional research shows that elements of the built environment are associated with crime rates in particular places. Quasi-experimental studies show that changes in zoning and street configurations, configuration and design of housing, and access to public transit can help manage crime. The mechanisms by which such changes influence crime are not well understood, though shifts in the supply of criminal opportunities most likely play a role. This evidence is promising. It suggests that the built environment can be modified to reduce both crime and reliance on criminal justice sanctions. Place-based experiments that manipulate features of the built environment will provide evidence for policy makers to use in designing cities in ways that reduce crime.
Specification of cell morphology by endogenous determinants

We are studying the mechanisms by which cells elaborate their differentiated morphologies. Here we discuss one aspect of this issue: the specification of the detailed shape of individual cells. We describe an experimental system in which endogenous determinants of morphology are expressed. These determinants originally were detected in the morphological relationships between sister neuroblastoma cells. Approaches to analyzing these relationships are presented. The properties and behavior of the endogenous determinants have been partially characterized by further experiments, which are also described. The significance and the prospects for further analysis of our findings are discussed.
PENGEMBANGAN TES DIAGNOSTIK TWO-TIER UNTUK MENGIDENTIFIKASI MISKONSEPSI PADA MATERI KIMIA SISWA SMA

Penelitian ini dikembangkan untuk menghasilkan instrumen diagnostik two tier yang dapat mendeteksi miskonsepsi siswa pada materi stoikiometri, hidrokarbon, dan laju reaksi. Metode deskriptif digunakan untuk mengembangkan instrumen pada materi stoikiometri dan laju reaksi sedangkan metode R&D digunakan untuk mengembangkan instrumen pada materi hidrokarbon. Kualitas instrumen diagnostik two-tier diuji dengan validitas dan reliabilitas. Uji validitas instrumen menunjukkan bahwa jumlah butir soal yang dinilai valid, yaitu 15 butir soal pada materi stoikiometri, 18 dari 39 butir soal pada materi hidrokarbon, dan 21 dari 56 butir soal pada materi laju reaksi. Instrumen tersebut kemudian diujikan kepada siswa SMA kelas X dan XI. Hasil tes tersebut dianalisis dan diinterpretasikan, sehingga miskonsepsi dapat teridentifikasi. Temuan dari penelitian ini menunjukkan bahwa miskonsepsi siswa pada materi stoikiometri meliputi hukum-hukum dasar kimia dan konsep mol. Miskonsepsi siswa pada materi hidrokarbon meliputi kekhasan atom karbon, ikatan atom dalam rantai karbon, dan rantai tertutup. Sementara itu, miskonsepsi siswa pada materi laju reaksi meliputi pengertian laju reaksi dan faktor-faktor yang mempengaruhi laju reaksi.
Closed-Form Crosstalk Noise Metrics for Physical Design Applications

In this paper we present efficient closed-form formulas to estimatecapacitive coupling-induced crosstalk noise for distributedRC coupling trees. The efficiency of our approach stemsfrom the fact that only the five basic operations are used in theexpressions: addition ( x + y), subtraction (x - y), multiplication(x × y), division (x / y) and square root ( /sqrt x). The formulasdo not require exponent computation or numericaliterations. We have developed closed-form expressions for thepeak crosstalk noise amplitude, the peak noise occurring timeand the width of the noise waveform. Our approximations areconservative and yet achieve acceptable accuracy. The formulasare simple enough to be used in the inner loops of performanceoptimization algorithms or as cost functions to guide routers.They capture the influence of coupling direction (near-end andfar-end coupling) and coupling location (near-driver and near-receiver).
A scan matching method using Euclidean invariant signature for global localization and map building

This work presents a new scan matching method for mobile robot localization and mapping. The proposed method is based on the geometric hashing scheme, which utilizes Euclidean invariant features in order to match an input scan with reference scans without an initial alignment The method is applicable to global localization in an environment having curved objects. Experimental results show that a map of a large cyclic environment was built with high accuracy using the proposed method.
Sexual Cognitive Predictors of Sexual Communication in Junior College Adolescents: Medical Student Perspectives

Background: Further understanding the relationship between sexual cognition and sexual communication in adolescents may facilitate sexual health promotion in this population. Purpose: This study was designed to investigate associations between sexual cognitive variables and sexual communication in adolescents. Methods: This study used a cross-sectional research design with conventional sampling. Data were collected from one medical college in central Taiwan. A total of 900 questionnaires were dispatched, with 748 copies returned, giving a response rate of 83.1%. Structural questionnaires were designed to collect demographic data, sexual self-concept inventory, sexual risk cognition, sexual self-efficacy, and sexual communication scale. This study applied statistical methods, including descriptive statistics, Pearson product-moment correlation, and multiple regression analysis. Results: Major findings revealed that (a) adolescents talked about sexual activity and sexual issues with their parents at a moderate level (mean = 2.52, SD = 1.24), (b) all sexual cognitive variables (sexual self-concept, sexual risk cognitions, and sexual self-efficacy) correlated positively with sexual communication, and (c) predictors of sexual communication were supported by demographic data (having heterosexual friends, satisfaction with heterosexual friends, and duration of relationships with heterosexual friends) and sexual cognitive variables, which accounted for 62.0% of variance. Conclusions/Implications for Practice: Study results can contribute to the development of safe sexual health programs and improve healthcare provider knowledge of sexual communication among adolescents. More sexual communication between adolescents and their parents is encouraged. Moreover, sexual health programs must give increased focus on the issue of adolescent sexual cognition to help encourage increased discussion between adolescents and their parents regarding sexual activity and issues.
The effect of intergroup contact on secondary group attitudes and social dominance orientation

The current study tested the extent to which intergroup contact reduces social dominance orientation (SDO), producing secondary transfer effects. Participants were first-year undergraduate students randomly assigned to live with either a same-race roommate or a roommate of a different race in university housing. Participants completed a feeling thermometer and a measure of SDO at the beginning and end of the fall semester. Participants in interracial rooms reported lower levels of SDO and more positive attitudes toward secondary groups (i.e., racial/ethnic groups other than their roommates’ group) than participants in same-race rooms at the end of the semester. Those in interracial rooms exhibited a significant change in SDO levels and attitudes across time, whereas those in same-race rooms exhibited no change. Furthermore, SDO fully mediated the effect of intergroup contact on attitudes toward secondary groups. These findings provide causal evidence of secondary transfer effects and indicate SDO as an underlying mechanism.
Reflexive research: Investigating the process of growth in recognition of self-awareness and affect

This article examines shifting thoughts and feelings throughout the interview process. More specifically, it draws on subjective, affective responses that occurred in relation to interviews with men about their fathering experiences. All of the fathers had records of criminal behaviour and severe adjustment problems in their adolescence. The discussion revolves around the reflexive process that took place from a researcher’s viewpoint, investigating shifting feelings throughout the analytical progression in (i) looking forward to the interviews, (ii) meeting and interacting with the interviewees, and (iii) reflecting upon the interviews. To examine these affective responses, the article relies on psychosocial theories that view the use of feelings as essential to interview analysis. The article draws on reflections on different interview meetings with a sample of 15 men. The discussion suggests that feelings are valuable ‘research tools’ in exploring methodological possibilities which can potentially make the research process transparent, thereby validating the findings.
U0126 prevents ERK pathway phosphorylation and interleukin-1beta mRNA production after cerebral ischemia.

OBJECTIVE To study the role of extracellular signal-regulated kinase (ERK) in cerebral ischemia and the mechanism of protective effects of U0126 (1,4-diamino-2,3-dicyano-1,4-bis[2-aminophenylthio] butadiene) on ischemic brain. METHODS Mice underwent left middle cerebral artery occlusion (MCAO) by introducing a suture in the lumen. U0126 was injected intravenously through the internal jugular vein. The immuno-activity of phosphorylated ERK1/2 (pERK1/2), phosphorylated mitogen activated protein kinase kinase (pMEK), and phosphorylated Elk-1 (pElk-1) was assessed by Western blot analysis and immunohistochemistry. Interleukin (IL)-1beta mRNA level was measured by ribonuclease protection assay. RESULTS Phosphorylated ERK1/2 in 2 hours MCAO mice was down-regulated after intravenous injection of U0126. The inhibition was dose dependent and treatment time related. pMEK and pElk-1 were also reduced in a similar fashion after U0126 treatment. IL-1beta mRNA increased after 1 and 2 hours of MCAO. After injection of U0126, it was down-regulated during 1 to 4 hours after MCAO. CONCLUSION Intravenous administration of the MEK inhibitor U0126 inhibits pMEK, pERK1/2, and pElk-1 up-regulation induced by cerebral ischemia. The protective effect of U0126 against ischemic injury is probably resulted from the reduction of IL-1beta mRNA via the inhibition of ERK pathway.
Evaluating an instrument to measure mental load and mental effort considering different sources of validity evidence

Abstract This study evaluates a 12-item instrument for subjective measurement of mental load (ML) and mental effort (ME) by analysing different sources of validity evidence. The findings of an expert judgement (N = 8) provide evidence based on test content that the formulation of the items corresponds to the meaning of ML and ME. An empirical study was conducted in which secondary school students (N = 602) worked on multiple choice (mc)-tasks and thereafter using the developed instrument to self-report ML and ME. The findings show that the instrument reliably measures the two positively correlated constructs ML and ME (evidence based on internal structure). Students working on mc-tasks with high complexity self-reported higher amounts of ML and ME than students working on mc-tasks with low complexity, and there is a negative relation between test performance and ML (evidence based in relation to other variables). Implications for educational assessment and limitations of the study are discussed.