Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase transitions in biogenic amorphous calcium carbonate

Crystalline biominerals do not resemble faceted crystals. Current explanations for this property involve formation via amorphous phases. Using X-ray absorption near-edge structure (XANES) spectroscopy and photoelectron emission microscopy (PEEM), here we examine forming spicules in embryos of Strongylocentrotus purpuratus sea urchins, and observe a sequence of three mineral phases: hydrated amorphous calcium carbonate (ACC·H2O) → dehydrated amorphous calcium carbonate (ACC) → calcite. Unexpectedly, we find ACC·H2O-rich nanoparticles that persist after the surrounding mineral has dehydrated and crystallized. Protein matrix components occluded within the mineral must inhibit ACC·H2O dehydration. We devised an in vitro, also using XANES-PEEM, assay to identify spicule proteins that may play a role in stabilizing various mineral phases, and found that the most abundant occluded matrix protein in the sea urchin spicules, SM50, stabilizes ACC·H2O in vitro.
Retraction: Promoting the Safe and Strategic Use of Technology for Victims of Intimate Partner Violence: Evaluation of the Technology Safety Project

This article has been withdrawn because it is a redundant publication of an article that was published in the Journal of Family Violence, Issue 1, Volume 24. January 2009, DOI: 10.1007/s10896-008-9207-2. The article went through peer review for publication in Violence Against Women without the journal_s knowledge that a similar article was submitted to the Journal of Family Violence.
Conformal field theories in a periodic potential: results from holography and field theory

We study ( 2 + 1 )-dimensional conformal field theories (CFTs) with a globally conserved U(1) charge, placed in a chemical potential which is periodically modulated along the spatial direction x with zero average: μ ( x ) = V cos ( k x ) . The dynamics of such theories depends only on the dimensionless ratio V / k , and we expect that they flow in the infrared to new CFTs whose universality class changes as a function of V / k . We compute the frequency-dependent conductivity of strongly coupled CFTs using holography of the Einstein-Maxwell theory in four-dimensional anti–de Sitter space. We compare the results with the corresponding computation of weakly coupled CFTs, perturbed away from the CFT of free, massless Dirac fermions (which describes graphene at low energies). We find that the results of the two computations have significant qualitative similarities. However, differences do appear in the vicinities of an infinite discrete set of values of V / k : the universality class of the infrared CFT changes at these values in the weakly coupled theory, by the emergence of new zero modes of Dirac fermions which are remnants of local Fermi surfaces. The infrared theory changes continuously in holography, and the classical gravitational theory does not capture the physics of the discrete transition points between the infrared CFTs. We briefly note implications for a nonzero average chemical potential.
Simplifying size-specific radiation dose estimates in pediatric CT.

OBJECTIVE Size-specific dose estimates (SSDEs) require manual measurement of torso diameters for individual patients--anteroposterior (hereafter, D(AP)), lateral (hereafter, D(LAT)), and effective (hereafter, D(E))--which can be tedious in clinical settings. We aimed to determine whether body weight can be used as a surrogate for measuring diameter in children. MATERIALS AND METHODS D(AP) and D(LAT) were measured in 522 consecutive CT examinations (chest, 187 and abdomen-pelvis, 335) performed in 483 (± SD) children (13 ± 7 years). Effective diameter (D(E1)) was calculated as the square root of the product of D(AP) and D(LAT). A second measurement of effective diameter (D(E2)) was obtained using automated software. Correlation coefficients between patient body weight, age, and diameter were measured in addition to 95% prediction interval analysis for diameters corresponding to body weight. RESULTS Median body weight was 51 kg, and mean D(AP), D(LAT), D(E1), and D(E2) were 207.1 ± 50.8 mm, 289.8 ± 72.6 mm, 243.3 ± 62.0 mm, and 233.6 ± 55.4 mm, respectively. Overall body weight had a strong correlation with diameter (0.88, 0.85, 0.86, and 0.93 respectively; all p < 0.0001). SSDE measured using body weight was statistically not different than SSDE measured using effective diameters (p = 0.9). Children weighing less than 27 kg and between 46 and 100 kg had statistically significant correlations with torso diameters, whereas only anteroposterior and effective diameters were correlated with children weighing between 27 and 45 kg. Children less than 4 years old had strong correlation with all diameters. Adolescents (15-18 years) did not have statistically significant correlation with any of the diameters. CONCLUSION Body weight, instead of body diameter, can be used as a surrogate to estimate size-specific dose in children, making dose estimation clinically simpler and more rapid.
Improving posterior based confidence measures in hybrid HMM/ANN speech recognition systems

In this paper we define and investigate a set of confidence measures based on hybrid Hidden Markov Model/Artificial Neural Network (HMM/ANN) acoustic models. All these measures are using the neural network to estimate the local phone posterior probabilities, which are then combined and normalized in different ways. Experimental results will indeed show that the use of an appropriate duration normalization is very important to obtain good estimates of the phone and word confidences. The different measures are evaluated at the phone and word levels on both an isolated word task (PHONEBOOK) and a continuous speech recognition task (BREF). It will be shown that one of those confidence measures is well suited for utterance verification, and that (as one could expect) confidence measures at the word level perform better than those at the phone level. Finally, using the resulting approach on PHONEBOOK to rescore the N-best list is shown to yield a 34% decrease in word error rate.
On the Performance Advantage of Relaying Under the Finite Blocklength Regime

We consider a two-phase relaying system with finite blocklengths. We study the performance difference of relaying under the finite blocklength regime as well as under the Shannon capacity regime. Most importantly, we are interested in the conditions that lead to a higher performance of relaying under the finite blocklength regime. We find that these situations are characterized by error probabilities of relaying, e.g., the overall error probability of relaying and the error probability of the bottleneck link of relaying. We identify scenarios where relaying outperforms direct transmission under the finite blocklength regime even if their performances are similar under the Shannon capacity regime. Moreover, we prove that under these scenarios the performance advantage of relaying is more significant with short blocklengths. Finally, numerical results are provided and discussed.
Cloud Storage Cost Modeling for Cryptographic File Systems

Nowadays, data security is a demand for companies when adopting storage services on public clouds. From long term persistence services, such as Amazon Glacier, to online block storage systems for virtual machines disks, security principles can be part of the cloud context, especially for customer's sensitive data. The confidentiality of storage services considers aspects such as data life-cycle, location, and size, besides that, this principle is often provided by a cryptography mechanism applied in one of the persistence layers, such as in the File-System (FS). However, to add cryptography for data security demands extra CPU cycles for ciphering the data during its persistence. Although these extra CPU cycles are not considered on current cloud costs estimations, it should be part of the total application execution's costs. This paper presents the architectures for Cryptography File Systems (CFS) adoption for data storing in cloud computing. Furthermore, a mathematical model is presented and discussed as an estimation tool of cryptography overhead when using CFSs in the cloud storage stack. The model is verified in a real scenario for estimating the total cost when adding security for storage in a cloud environment. As main result, the model could estimate the overhead within 90% to 92% of accuracy for the AES algorithm, according to real cases traces, considering available memory, {I/O} throughput and workload size.
Exploring Perceived Value in Social Networking Sites: The Mediation of Customer Satisfaction

— As users increasingly participate in the community, social networking sites (SNS) are gaining attention in academic research. This study aims to explore perceived value influencing usage intention in SNS, and examines the mediation of customer satisfaction between perceived value and usage intention. Mediated regression analysis was used and 205 savvy SNS users in Taiwan were investigated. The findings reveal that perceived value, including information value, sociable value, and hedonic value, has a positive impact on usage intention, but the mediation effect of customer satisfaction is only significant for social value and hedonic value, excluding information value. Thus, this study suggests that marketers need sincerely concern the importance of customer satisfaction when users perceive the values in SNS, especially for social value and hedonic value.
Let's go to the whiteboard: how and why software developers use drawings

Software developers are rooted in the written form of their code, yet they often draw diagrams representing their code. Unfortunately, we still know little about how and why they create these diagrams, and so there is little research to inform the design of visual tools to support developers' work. This paper presents findings from semi-structured interviews that have been validated with a structured survey. Results show that most of the diagrams had a transient nature because of the high cost of changing whiteboard sketches to electronic renderings. Diagrams that documented design decisions were often externalized in these temporary drawings and then subsequently lost. Current visualization tools and the software development practices that we observed do not solve these issues, but these results suggest several directions for future research.
Biased signalling and proteinase‐activated receptors (PARs): targeting inflammatory disease

Although it has been known since the 1960s that trypsin and chymotrypsin can mimic hormone action in tissues, it took until the 1990s to discover that serine proteinases can regulate cells by cleaving and activating a unique four‐member family of GPCRs known as proteinase‐activated receptors (PARs). PAR activation involves the proteolytic exposure of its N‐terminal receptor sequence that folds back to function as a ‘tethered’ receptor‐activating ligand (TL). A key N‐terminal arginine in each of PARs 1 to 4 has been singled out as a target for cleavage by thrombin (PARs 1, 3 and 4), trypsin (PARs 2 and 4) or other proteases to unmask the TL that activates signalling via Gq, Gi or G12/13. Similarly, synthetic receptor‐activating peptides, corresponding to the exposed ‘TL sequences’ (e.g. SFLLRN—, for PAR1 or SLIGRL— for PAR2) can, like proteinase activation, also drive signalling via Gq, Gi and G12/13, without requiring receptor cleavage. Recent data show, however, that distinct proteinase‐revealed ‘non‐canonical’ PAR tethered‐ligand sequences and PAR‐activating agonist and antagonist peptide analogues can induce ‘biased’ PAR signalling, for example, via G12/13‐MAPKinase instead of Gq‐calcium. This overview summarizes implications of this ‘biased’ signalling by PAR agonists and antagonists for the recognized roles the PARs play in inflammatory settings.
Clinicalpathological and prognostic significance of survivin expression in renal cell carcinoma: a meta-analysis

Background In recent years, survivin expression had been investigated as a prognostic biomarker for renal cell carcinoma (RCC), however, the results were conflicting. This study was aimed to explore the association between survivin expression and clinicalpathological features and the prognostic value for cancer-specific survival (CSS) and overall survival (OS) in RCC. Results Eleven studies with 1,697 subjects were included in this meta-analysis. The results showed that survivin expression was associated with higher tumor grade (OR=4.25, 95%CI: 3.04-5.95, p<0.001), advanced tumor stage (OR=3.83, 95%CI: 2.01-7.3, p<0.001) and lymph node metastasis (OR=4.19, 95%CI: 2.34-7.52, p<0.001), but had no association with age, gender or distant metastasis. In addition, survivin expression was also correlated with poor CSS (HR=2.08, 95%CI: 1.07-4.05, p=0.032) and poor OS (HR=2.28, 95%CI: 1.57-3.33, p<0.001). Materials and Methods Literature was searched by PubMed, Embase and Web of Science. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were extracted from eligible studies. Fixed or random effects model were used to calculate pooled HRs and 95%CIs according to heterogeneity. Conclusions This study demonstrated that survivin expression was associated with more aggressive clinical features and predicted poor CSS and OS in patients with RCC.
THE FEAR FACTOR: BULLYING AND STUDENTS WITH DISABILITIES

This article provides an overview of research addressing bullying and students with disabilities. The studies are discussed within two disability categories: visible and non-visible. Disabilities that are overt and observable were determined by the researchers to be categorized as visible. In contrast, disabilities that are less obvious and would require more time to observe and differentiate were categorized as non-visible. Results from the eleven studies published from 1989 to 2003 indicated students with disabilities, both visible and non-visible, experienced bullying more than their non-disabled general education peers and that boys were bullied more often than girls (Dawkins, 1996; O’Moore & Hillery (1989). Reported forms of bullying included name-calling, teasing, physical attacks, severe verbal bullying, verbal aggression, threats, taking belongings, imitating, and making fun of the students with disabilities. The students with disabilities also tended to be less popular, have fewer friends, and struggle with loneliness. Implications for future research are discussed.
Dynamic State Alteration Techniques for Automatically Locating Software Errors

Software does not always behave as expected due to errors. These errors can potentially lead to disastrous consequences. Unfortunately, debugging software errors can be difficult and time-consuming. Many techniques to automatically locate errors have been developed, but the results are far from ideal. Unlike other techniques that analyze existing state information from program executions, dynamic state alteration techniques modify the state of program executions to gain deeper insight into the potential locations of errors. However, prior state alteration techniques are generally no more effective than other techniques, and come at the expense of increased computation time. This dissertation shows that aggressive and well-targeted state alteration techniques can be both highly effective and reasonably efficient. The Value Replacement technique performs aggressive state alterations to locate software errors by replacing the set of values used in different statement instances in failing program executions. In a set of benchmarks, Value Replacement precisely identifies a faulty statement in 39 out of 129 cases, whereas the most effective technique previously known does so in 5 cases. Value Replacement can be generalized to iteratively locate multiple errors. A brute-force implementation of Value Replacement can require hours to locate a single error, but techniques are developed that can reduce this timing requirement to minutes to locate multiple errors. The Execution Suppression technique performs targeted state alterations to locate memory errors by iteratively suppressing (avoiding) the effects of statements involving known memory corruption during failing executions. The technique is able to precisely identify the first point of memory corruption in all analyzed benchmark programs; this point is typically at or close to the location of a memory error. Execution Suppression can be generalized to locate multithreading errors including data races. While a software-only implementation of suppression incurs an overhead of 7.2x on average, this overhead can be reduced to 1.8x using hardware support. Finally, a machine learning technique called BugFix is developed that provides automated assistance in modifying a faulty statement to fix an error. A case study illustrates the potential benefit of the technique.
dsg, a gene required for cell-cell interaction early in Myxococcus development

dsg mutants of Myxococcus xanthus are conditionally defective in fruiting body development, including sporulation. Unable to develop on their own, these mutants can assemble fruiting bodies with spores if they are mixed with wild-type cells. To elucidate the developmental defect in dsg mutants by close comparison with wild type, such mutants have been backcrossed by transduction, using a closely linked insertion of transposon Tn5 for selection. Backcrossed dsg mutants form aggregates that are larger, less compact, and less symmetrical than dsg+ fruiting bodies. Also, the starvation-induced sporulation in dsg aggregates is delayed and reduced. However, dsg mutants can be induced by glycerol or dimethyl sulfoxide to sporulate at levels approaching those of wild type. dsg mutants may thus have a primary defect early in development which diminishes their capacity to aggregate and which indirectly decreases the number of fruiting body spores. The linked insertion of Tn5 also facilitated cloning the dsg gene. The cloned dsg+ allele was shown to be dominant to both the dsg-429 and dsg-439 alleles, and both mutant alleles were shown to belong to the same genetic complementation group. Subcloning of restriction fragments, deletions, and insertions of transposon Tn5 agree in locating the dsg gene to an 850-base-pair segment of the cloned region.
Optimization of Mass Storage Hierarchies

Optimization is often a question of where one should put one’s money in improving performance. As far as large storage hierarchies go, intuition suggests (and common practice supports) adding as much as is affordable of the fastest technology available. Many cache hierarchy studies have shown that this is often not the optimal approach, and we show that for mass storage hierarchies it always tends to be the wrong approach. For large data sets, as is the case for network file servers, a machine with no RAM and several gigabytes of disk performs 30% faster than a machine with no disk and a cost-equivalent amount of RAM.
Modeling of In-Utero and Intra-Partum Transmissions to Evaluate the Efficacy of Interventions for the Prevention of Perinatal HIV

Background Antiretroviral treatments decrease HIV mother-to-child transmission through pre/post exposure prophylaxis and reduction of maternal viral load. We modeled in-utero and intra-partum HIV transmissions to investigate the preventive role of various antiretroviral treatments interventions. Methods We analysed data from 3,759 women-infant pairs enrolled in 3 randomized clinical trials evaluating (1) zidovudine monotherapy, (2) zidovudine plus perinatal single-dose nevirapine or (3) zidovudine plus lopinavir/ritonavir for the prevention of mother-to-child transmission of HIV in Thailand. All infants were formula-fed. Non-linear mixed effect modeling was used to express the viral load evolution under antiretroviral treatments and the probability of transmission. Results Median viral load was 4 log10 copies/mL (Interquartile range: 3.36–4.56) before antiretroviral treatments initiation. An Emax model described the viral load time-course during pregnancy. Half of the maximum effect of zidovudine (28% decrease) and lopinavir/ritonavir (72% decrease) were achieved after 98 and 12 days, respectively. Adjusted on viral load at baseline (Odds ratio = 1.50 [95% confidence interval: 1.34, 1.68] per log10 copies/mL increment), antiretroviral treatments duration (OR = 0.80 [0.75, 0.84] per week increment) but not the nature of antiretroviral treatments were associated with in-utero transmission. Adjusted on gestational age at delivery (<37 weeks, OR = 2.37 [1.37, 4.10]), baseline CD4 (Odds ratio = 0.79 [0.72, 0.88] per 100 cells/mm3 increment) and predicted viral load at delivery (OR = 1.47 [1.25, 1.64] per log10 copies/mL increment), single-dose nevirapine considerably reduced intra-partum transmission (OR = 0.32 [0.2, 0.51]). Conclusion These models determined the respective contributions of various antiretroviral strategies on prevention of mother-to-child transmission. This can help predict the efficacy of new antiretroviral treatments and/or prevention of mother-to-child transmission strategies particularly for women with no or late antenatal care who are at high risk of transmitting HIV to their offspring. Trial Registration This analysis is based on secondary data obtained from three clinical trials. ClinicalTrials.gov. NCT00386230, NCT00398684, NCT00409591.
When Status Hurts: Dimensions of Women’s Status and Domestic Abuse in Rural Northern India

This study is a multiple logistic regression analysis of the relationship between dimensions of women’s status and domestic abuse in rural Uttar Pradesh, India, using the 1998-1999 National Family Health Survey (NFHS-2). Findings indicate that the effects of a woman’s status on her likelihood of experiencing abuse depend on the social realm within which status operates. Specifically, more “public” dimensions of status are associated with a greater probability of abuse, while “domestic” dimensions are protective. The findings are interpreted in terms of transitioning gender norms in Uttar Pradesh and provide clarity to the literature on the complex relationship between status and abuse.
Use of allopurinol for prevention and control of hyperuricemia in patients with neoplastic disease.

UROLITHIASIS and renal insufficiency, associated with hyperuricemia, are well known complications of certain neoplastic disorders, particularly leukemia and lymphoma.1 , 2 Irradiation or chemotherapy, by increasing elevated serum levels of uric acid, may precipitate acute uric acid nephropathy. This has been cited as the most frequent cause of acute renal failure in patients with leukemia,3 and occasionally may be the presenting manifestation of the disease.4 In the past, prevention and treatment of this complication were attempted by increasing the solubility of the increased uric acid load presented to the renal tubules with vigorous hydration, urinary alkalinization and osmotic diuresis. In desperate situations .