Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of histological changes after calibrated crush of the intraorbital optic nerve in rats

Background: Traumatic optic nerve lesions (TONL) are probable but unpredictable consequence after severe midface or skull base trauma. Based on a previously described rat model, the authors developed a new model in order to simulate optic nerve crush during trauma on the optic canal. Methods: To achieve a calibrated TONL, a microinjuring device was designed that made it possible to assess the correlation between a defined trauma and the neuronal degeneration in the rat retinal ganglion cell (RGC) layer. This device is based on a small dynamometer mounted onto a conventional micromanipulator. The supraorbital approach was chosen to expose the extracranial optic nerve. Results: In this rat model (n=100, Wistar strain) the parameters of “force” and “time” could be precisely monitored during the experiment. The decrease in the mean number of retinal neurons (N) according to the pressure exerted (2–30 cN•mm−2) on the optic nerve was linear for 1, 6, and 15 minutes of injuring time; the decrease in N for varying injuring forces also appears to be nearly linear. Conclusion: The results show that this model provides a reliable method for studying quantitatively the anatomical effects of TONL on the RGC layer and the optic nerve itself, and may allow the design of treatment strategies following TONL.
Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum

Increasing evidence shows that the spatial organization of transcription is an important epigenetic factor in eukaryotic gene regulation. The malaria parasite Plasmodium falciparum shows a remarkably complex pattern of gene expression during the erythrocytic cycle, paradoxically contrasting with the relatively low number of putative transcription factors encoded by its genome. The spatial organization of nuclear subcompartments has been correlated with the regulation of virulence genes. Here, we investigate the nuclear architecture of transcription during the asexual cycle of malaria parasites. As in mammals, transcription is organized into discrete nucleoplasmic sites in P. falciparum, but in a strikingly lower number of foci. An automated analysis of 3D images shows that the number and intensity of transcription sites vary significantly between rings and trophozoites, although the nuclear volume remains constant. Transcription sites are spatially reorganized during the asexual cycle, with a higher proportion of foci located in the outermost nuclear region in rings, whereas in trophozoites, foci are evenly distributed throughout the nucleoplasm. As in higher eukaryotes, transcription sites are predominantly found in areas of low chromatin density. Immunofluorescence analysis shows that transcription sites form an exclusive nuclear compartment, different from the compartments defined by the silenced or active chromatin markers. In conclusion, these data suggest that transcription is spatially contained in discrete foci that are developmentally regulated during the asexual cycle of malaria parasites and located in areas of low chromatin density.
Bored to death?

Have you ever felt bored (Fig 1)? Ever found yourself with nothing engaging to do? Experienced a lack of interest in everything and everyone around you? Although not a pleasant state in which to find oneself, is boredom bad for health? In a rare moment of idleness one day, we pondered whether the expression ‘bored to death’ has any basis. Are people who are bored more likely to die earlier than those who are not? Boredom levels were reported in the later versions of the baseline questionnaire (1985–88) of the Whitehall II cohort study. Participants were civil servants, based in London, aged 35–55 years. They were asked in a self-completed questionnaire about boredom during the past 4 weeks (response options were ‘not at all’, ‘a little’, ‘quite a lot’, ‘all the time’). At the risk of participants becoming bored of answering this question, it was repeated at Phase 2 some 3 years later, but not since. Information on mortality was ascertained through the NHS Central Registry, by using their unique NHS identification number. Follow-up for total mortality was available up to the end of April 2009. Excluding those with prevalent cardiovascular disease (CVD) at baseline, gave a sample size of 7524 men and women. We found that those who report quite a lot or a great deal of boredom are more likely to be younger, to be women, to rate their health worse, to be in low employment grades and to report lower physical activity levels (Table 1). We also found that those with a great deal of boredom were more likely to die during follow-up than those not bored at all (Table 2). In particular, they were more likely to die from a CVD fatal event [hazard ratio (HR) 2.53; confidence interval (CI) 1.23–5.21]. Furthermore, we found some suggestive evidence of cumulative effects in the mortality after Phase 2, as those still reporting boredom at Phase 2 had slightly higher risks than those reporting it once or never. With further adjustments for employment grade, physical activity levels and poor self-rated health, the hazard ratios for CVD for those with a great deal of boredom were reduced and did not reach statistical significance (1.96; CI 0.94–4.05). We conclude that those who report being bored are more likely to die younger than those who are not bored. However, the state of boredom is almost certainly a proxy for other risk factors. Whilst some aspects of life may not be so easily modified (e.g. disease status or position in society), proneness to boredom, particularly in younger populations, could be indicative of harmful behaviours such as excessive drinking, smoking, taking drugs and low psychological profiles. Finding renewed interest in social and physical activities may alleviate boredom and improve health, thus reducing the risk of being ‘bored to death’.
Possible Roles of Spontaneous Waves and Dendritic Growth for Retinal Receptive Field Development

Several models of cortical development postulate that a Hebbian process fed by spontaneous activity amplifies orientation biases occurring randomly in early wiring, to form orientation selectivity. These models are not applicable to the development of retinal orientation selectivity, since they neglect the polarization of the retina's poorly branched early dendritic trees and the wavelike organization of the retina's early noise. There is now evidence that dendritic polarization and spontaneous waves are key in the development of retinal receptive fields. When models of cortical development are modified to take these factors into account, one obtains a model of retinal development in which early dendritic polarization is the seed of orientation selectivity, while the spatial extent of spontaneous waves controls the spatial profile of receptive fields and their tendency to be isotropic.
Managing massive trajectories on the cloud

With advances in location-acquisition techniques, such as GPS- embedded phones, an enormous volume of trajectory data is generated, by people, vehicles, and animals. This trajectory data is one of the most important data sources in many urban computing applications, e.g., traffic modeling, user profiling analysis, air quality inference, and resource allocation. To utilize large scale trajectory data efficiently and effectively, cloud computing platforms, e.g., Microsoft Azure, are the most convenient and economic way. However, traditional cloud computing platforms are not designed to deal with spatio-temporal data, such as trajectories. To this end, we design and implement a holistic cloud-based trajectory data management system on Microsoft Azure to bridge the gap between trajectory data and urban applications. Our system can efficiently store, index, and query large trajectory data with three functions: 1) trajectory ID-temporal query, 2) trajectory spatio-temporal query, and 3) trajectory mapmatching. The efficiency of the system is tested and tuned based on real-time trajectory data feeds. The system is currently used in many internal urban applications, as we will illustrate using case studies.
Study of the demographic criteria and management of adolescents referred with abnormal cervical smears

Summary This observational study was conducted on the adolescents referred to a colposcopy clinic in a UK general hospital over a period of 10 years (1996 – 2005). It included 155 newly referred adolescents (age ≤ 20 years) with abnormal smear results. The aim of the study was to define the demographic risk factors associated with the development of abnormal cervical smears and identify the incidence of high-grade cervical lesions in this age group. All the risk factors associated with development of HPV infection were found among this group, particularly early age of sexual contact and number of sexual partners. A total of 52.9% of the cases had a smear showing moderate or severe dyskaryosis. The incidence increased to 66.7% among those who had their first sexual contact before the age of 16. Colposcopy and histology confirmed the presence of CIN II and CIN III in 40.6% of cases. The study showed that patients can develop high-grade cervical lesions in their early teens. Delaying the age of onset of cervical screening to 25, as it is currently recommended in UK, will delay the detection and treatment of these cases. A new approach is required to deal with this problem.
Hardware Performance Evaluation of SHA-3 Candidate Algorithms

Secure Hashing Algorithms (SHA) showed a significant importance in today’s information security applications. The National Institute of Standards and Technology (NIST), held a competition of three rounds to replace SHA1 and SHA2 with the new SHA-3, to ensure long term robustness of hash functions. In this paper, we present a comprehensive hardware evaluation for the final round SHA-3 candidates. The main goal of providing the hardware evaluation is to: find the best algorithm among them that will satisfy the new hashing algorithm standards defined by the NIST. This is based on a comparison made between each of the finalists in terms of security level, throughput, clock frequancey, area, power consumption, and the cost. We expect that the achived results of the comparisons will contribute in choosing the next hashing algorithm (SHA-3) that will support the security requirements of applications in todays ubiquitous and pervasive information infrastructure.
Motivating students, improving schools : the legacy of Carol Midgley

The need for sensation as a prerequisite for motivation to engage in academic tasks (E.M. Anderman et al.). Students' sense of belonging in school (L.H. Anderman, T.M. Freeman). The significance of motivational culture in schools serving African American adolescents: a goal theory approach (K.E. Freeman). Achievement goals and intergroup relations (A. Kaplan). Multicultural education and achievement goal theory: school reforms for education in a culturally pluralistic society (R. Kumar). Person and context: theoretical and practical concerns in achievement goal theory (E.A. Linnenbrink). Developing adolescent literacy in high poverty middle schools: the impact of talent development's reforms across multiple years and sites (D. Mac Iver et al.). Motivating through challenge: promoting a positive press for learning (M. Middleton). Re-examining classroom mastery goal structure (H. Patrick). Competing schools of thought in achievement goal theory? (R.W. Roeser). Young adolescents' social motivation: an achievement goal theory perspective (A.M. Ryan et al.). Are challenge and caring compatible in middle school mathematics classrooms? (J.C. Turner, D.K. Meyer). Can achievement goal theory guide school reform? (T. Urdan).
The good preschool teacher : six teachers reflect on their lives

This important book is the result of an in-depth inquiry into the lives and work of six outstanding preschool teachers. Through a creative, original combination of interviews, letters, vignettes, interpretive analysis, and reflections, the author describes and links together the events, people, and experiences that have made these women the excellent teachers they are.
Toxicokinetics of Dothiepin: 2 Case Reports

In this article, 2 cases of intentional dothiepin intoxication are presented. Both patients survived after receiving appropriate supportive care. The dothiepin and metabolite levels were measured at different times after ingestion. The initial levels of dothiepin were 1900 μg/L in case 1 and 5500 μg/L in case 2. In case 1, a toxicokinetic model was fitted, suggesting a higher peak level, corresponding with the QRS duration and clinical symptoms. In case 2, a combined dothiepin-ethanol intoxication was seen, complicating the interpretation of clinical parameters, such as the QRS duration. In conclusion, the severity of dothiepin intoxication is poorly predicted by plasma levels alone, as time of ingestion can be critical for interpretation. However, especially in combined intoxications, interpretation of the QRS duration may also fail. Therefore, it is important to evaluate the whole range of clinical parameters, QRS duration, clinical symptoms, dothiepin concentration(s), and other possible intoxications.
Query-Oriented Data Cleaning with Oracles

As key decisions are often made based on information contained in a database, it is important for the database to be as complete and correct as possible. For this reason, many data cleaning tools have been developed to automatically resolve inconsistencies in databases. However, data cleaning tools provide only best-effort results and usually cannot eradicate all errors that may exist in a database. Even more importantly, existing data cleaning tools do not typically address the problem of determining what information is missing from a database. To overcome the limitations of existing data cleaning techniques, we present QOCO, a novel query-oriented system for cleaning data with oracles. Under this framework, incorrect (resp. missing) tuples are removed from (added to) the result of a query through edits that are applied to the underlying database, where the edits are derived by interacting with domain experts which we model as oracle crowds. We show that the problem of determining minimal interactions with oracle crowds to derive database edits for removing (adding) incorrect (missing) tuples to the result of a query is NP-hard in general and present heuristic algorithms that interact with oracle crowds. Finally, we implement our algorithms in our prototype system QOCO and show that it is effective and efficient through a comprehensive suite of experiments.
A randomized controlled clinical multicenter trial comparing the clinical and histological performance of a new, modified polylactide-co-glycolide acid membrane to an expanded polytetrafluorethylene membrane in guided bone regeneration procedures.

OBJECTIVES To compare the clinical and histological outcomes of a resorbable modified polylactide/polyglycolide acid (PLGA) test membrane and a titanium-reinforced expanded polytetrafluorethylene (ePTFE) control membrane used for guided bone regeneration (GBR) around dental implants. MATERIALS AND METHODS A total of 40 patients with peri-implant dehiscence-type defects were randomly allocated to a GBR procedure using either a modified PLGA test or an ePTFE control membrane. Soft tissue condition, implant integration, adverse events and quality of life were recorded during the 6-month healing period. At re-entry peri-implant bone defect dimensions were measured and compared with values recorded at implant/GBR surgery. A biopsy was retrieved for qualitative and quantitative histological analyses. A comparison between the groups was conducted using non-parametric statistical tests. RESULTS Soft tissue complications were observed in five test patients and two control patients. Except for soft tissue complications and incomplete regeneration, no procedure- or device-related adverse events were observed. The vertical bone defect component was, in mean, reduced by-5.1 mm (95% CI -6.8, -3.3) in the test group and -6.9 mm (95% CI -8.2, -5.5 mm) in the control group. The mean residual vertical defect height measured 1.2 ± 2.4 mm in the test group and 0.3 ± 1.1 mm in the control group meaning a mean defect resolution of 81% in the test group and 96% in the control group (P = 0.161). The horizontal bone thickness at implant shoulder level decreased from a mean of 3.2 mm to 1.4 mm (-56%, mean -1.7 mm, 95% CI -2.3, -1.1) in the test group and from 3.3 mm to 2.5 mm (-24%, mean -0.8 mm, 95% CI -1.3, -0.3) in the control group (P = 0.022). Qualitative and quantitative histological analyses did not show significant differences in the tissue composition between groups. CONCLUSION Peri-implant GBR was successfully performed using either of the membranes. The control membrane was able to better maintain the horizontal thickness of regenerated bone and revealed less soft tissue complications. No statistically valid evidence about the superiority of one membrane was found in any other parameters. Soft tissue dehiscences occur with both types of membranes and can impair the amount of regenerated bone.
A general language model for information retrieval

Statistical language modeling has been successfully used for speech recognition, part-of-speech tagging, and syntactic parsing. Recently, it has also been applied to information retrieval. According to this new paradigm, each document is viewed as a language sample, and a query as a generation process. The retrieved documents are ranked based on the probabilities of producing a query from the corresponding language models of these documents. In this paper, we will present a new language model for information retrieval, which is based on a range of data smoothing techniques, including the Good-Turning estimate, curve-fitting functions, and model combinations. Our model is conceptually simple and intuitive, and can be easily extended to incorporate probabilities of phrases such as word pairs and word triples. The experiments with the Wall Street Journal and TREC4 data sets showed that the performance of our model is comparable to that of INQUERY and better than that of another language model for information retrieval. In particular, word pairs are shown to be useful in improving the retrieval performance.
Incomplete peripheral CD4+ cell count restoration in HIV-infected patients receiving long-term antiretroviral treatment.

BACKGROUND Although antiretroviral therapy has the ability to fully restore a normal CD4(+) cell count (>500 cells/mm(3)) in most patients, it is not yet clear whether all patients can achieve normalization of their CD4(+) cell count, in part because no study has followed up patients for >7 years. METHODS Three hundred sixty-six patients from 5 clinical cohorts who maintained a plasma human immunodeficiency virus (HIV) RNA level 1000 copies/mL for at least 4 years after initiation of antiretroviral therapy were included. Changes in CD4(+) cell count were evaluated using mixed-effects modeling, spline-smoothing regression, and Kaplan-Meier techniques. RESULTS The majority (83%) of the patients were men. The median CD4(+) cell count at the time of therapy initiation was 201 cells/mm(3) (interquartile range, 72-344 cells/mm(3)), and the median age was 47 years. The median follow-up period was 7.5 years (interquartile range, 5.5-9.7 years). CD4(+) cell counts continued to increase throughout the follow-up period, albeit slowly after year 4. Although almost all patients (95%) who started therapy with a CD4(+) cell count 300 cells/mm(3) were able to attain a CD4(+) cell count 500 cells/mm(3), 44% of patients who started therapy with a CD4(+) cell count <100 cells/mm(3) and 25% of patients who started therapy with a CD4(+) cell count of 100-200 cells/mm(3) were unable to achieve a CD4(+) cell count >500 cells/mm(3) over a mean duration of follow-up of 7.5 years; many did not reach this threshold by year 10. Twenty-four percent of individuals with a CD4(+) cell count <500 cells/mm(3) at year 4 had evidence of a CD4(+) cell count plateau after year 4. The frequency of detectable viremia ("blips") after year 4 was not associated with the magnitude of the CD4(+) cell count change. CONCLUSIONS A substantial proportion of patients who delay therapy until their CD4(+) cell count decreases to <200 cells/mm(3) do not achieve a normal CD4(+) cell count, even after a decade of otherwise effective antiretroviral therapy. Although the majority of patients have evidence of slow increases in their CD4(+) cell count over time, many do not. These individuals may have an elevated risk of non-AIDS-related morbidity and mortality.
Variability of the preC/C region of hepatitis B virus genotype A from a South African cohort predominantly infected with HIV

Hepatitis B virus (HBV) is a serious global health problem, and HBV genotype is an important determinant of disease progression and treatment outcome. The aim of this study was to assess variations of the precore/core (preC/C) region in HBV genotype A. Sequencing of the preC/C and surface (S) genes of HBV was performed on plasma samples from 20 HBV/HIV co‐infected and 5 HBV mono‐infected individuals. All preC/C study sequences clustered with subgenotype A1, except for two which clustered with subgenotype D4 reference strains. The nucleotide and amino acid variability was far higher in the preC/C region than in the S region. Mutations associated with reduction or failure of HBV e‐antigen (HBeAg) production were observed, with a preC start codon mutation being common (24%). Other mutations (e.g., P5H/L and I97L) associated with severe liver disease were also noticed, some of which were located in the major histocompatibility restricted sites. PreC/C intergenotype nucleotide divergence was >7%, while subgenotypes differed by 2.5–7%. Several study sequences were highly divergent from other African subgenotype A1 strains. This study showed that HBeAg‐negative chronic hepatitis B is underestimated in subgenotype A1, and also highlighted the variant South African A1 strains. The major advantage of preC/C sequencing is that it informs patient management as HBeAg‐negative chronic hepatitis B responds poorly to conventional interferon‐α therapy, and some guidelines treat HBeAg‐negative chronic hepatitis B differently from HBeAg‐positive chronic hepatitis B. These data suggest that subgenotype A1 may be more involved in severe HBV‐related diseases. J Med. Virol. 85:1883–1892, 2013. © 2013 Wiley Periodicals, Inc.