Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutation Spectrum of the p 53 Gene in Bone and Soft Tissue Sarcomas 1

We present here an analysis of the spectrum of mutations of the p53 gene seen in 127 bone and soft tissue sarcomas of various histolÃ3gica! classifications. Gross rearrangements were analyzed by Southern blot ting using a complementary DNA probe from the p53 gene, and subtle alterations in the entire coding sequence (exons 2 through 11) were identified by a combination of single-strand conformation polymor phism analysis and direct genomic sequencing. A total of 42 somatic alterations of the p53 gene were found, of which 21 were gross rear rangements and 21 were subtle alterations. These included 17 cases of a single base substitution, 3 small deletions, and one single base inser tion. In contrast to reported findings for other types of cancer, we found that mutations of the p53 gene in sarcomas are quite heterogeneous both in their distribution throughout the gene and in the type of genetic alterations that result. All 13 missense mutations we found occurred at highly conserved residues, whereas 8 nonsense mutations occurred at sites that spanned the gene from codons 46 to 316. Surprisingly, approximately one-half of the osteosarcomas with allelic deletions on 17p did not have detectable alterations in the coding sequence of the p53 gene.
Rapid plasticity of visually evoked responses in rat monocular visual cortex

Sensory cortical circuits are shaped by experience during sensitive periods in development. In the primary visual cortex (V1) altered visual experience results in changes in visual responsiveness of cortical neurons. The experience-dependent refinement of the circuit in V1 is thought to rely on competitive interactions between feedforward circuits driven by the two eyes. However, recent data have provided evidence for an additional role of cortico-cortical circuits in this process. Indeed, experience-dependent changes in intracortical circuits can be induced rapidly and may result in rapid-onset functional changes. Unilateral occlusion of vision rapidly alters visual responsiveness, synaptic strength and connectivity of local circuits in the binocular region of V1 (V1b), where the inputs from the two eyes converge. In the monocular region of rodent V1 (V1m), where feedforward inputs from the ipsilateral eye are virtually absent, visual deprivation induces rapid plasticity in local circuits; however, functional changes seem to occur only after long periods of deprivation. In V1m there is currently no evidence for functional changes occurring within a time window compatible with that of local circuit plasticity. Here, we probed the visual responsiveness of neurons in rat V1m and assessed the effect of one day unilateral eye lid suture on single neuron visual responses. We report a novel form of plasticity within V1m that occurs on a timescale consistent with the earliest known changes in synaptic strength. Our data provide new insights into how sensory experience can rapidly modulate neuronal responses, even in the absence of direct competition between feedforward thalamocortical inputs.
The Role of Contextual Framing : Assessments , Classroom Practice , and Student Perceptions

Contextual framing in physics problems has been shown to generally affect student performance on assessments. This study seeks to identify some of the main influences of this effect, and to characterize how contextual framing may vary within a classroom. Students in summer introductory physics courses (algebra based and calculus based) are administered surveys that assess performance on problems that are contextually rich (more “real world”) vs. contextually bland (more abstract, “laboratory” descriptions). Initially females perform worse than do males on the contextually rich versions of the assessments when performance was equal on the contextually bland versions of the test. However further assessment reveals no clear trend how explicit contextual framing influences male and females differently. Students were polled on Attitudes and beliefs regarding the use of different kinds of context in the classroom, and the researcher’s observations of instructor practice correlated well with students’ opinions. Other roles of problem contextualization are identified, including the triggering of intuition and reasoning, albeit sometimes incorrect.
Eating Disorders in Adolescent Girls and Young Adult Women With Type 1 Diabetes

Dennis Daneman, MB, BCh, FRCPC Teens with type 1 diabetes face two clashing realities. On the one hand, the results of studies such as the Diabetes Control and Complications Trial (DCCT) provide irrefutable evidence of the link between diabetes control and the onset and progression of diabetes-related microvascular complications.1 The DCCT message was loud and clear: Control counts! On the other hand, there are numerous studies, including the DCCT, demonstrating that, during adolescence, metabolic control tends to be poorest and that the goals of intensive diabetes management are more difficult to achieve.2,3 What are the reasons for poor glycemic control in adolescents with type 1 diabetes? I believe that it results from the complex interplay between biological (e.g., insulin resistance of puberty) and psychosocial (e.g., noncompliance, family environment) factors. Our group has focused on one specific contributing factor, namely, eating disorders in teenage girls with type 1 diabetes. This From Research to Practice section offers a review of this topic by our research group at the University of Toronto. This is a departure from the usual format of Diabetes Spectrum research sections in that the entire section comprises contributions from a single research group. A number of groups around the world have made substantial contributions to this field, and we have been as diligent as possible in citing their enormous contributions. However, we do hope that our group has been able to provide a unifying view of the pathophysiology and impact of eating disturbances in girls and young women with type 1 diabetes. Our aim is to sensitize readers to the manifestations of this common co-morbidity and to highlight areas where further research is warranted. Because this monograph-style presentation represents the combined efforts of all of the authors, we have listed only the primary contributors to …
Correlation of AMPA Receptor Subunit Composition with Synaptic Input in the Mammalian Cochlear Nuclei

The composition of AMPA receptors in patches excised from somata and dendrites of six cell types in the mammalian cochlear nuclei was probed and compared electrophysiologically and pharmacologically with the rapid application of glutamate. Cells excited predominantly by auditory nerve fibers had AMPA receptors with exceptionally rapid gating (submillisecond deactivation and desensitization time constants). The nonlinear current–voltage relationship in the presence of spermine showed that few of these receptors had GluR2 subunits, and the insensitivity of desensitization to cyclothiazide indicated that they contained mostly flop splice variants. At synapses made by parallel fibers, AMPA receptors were slowly gating (time constants of deactivation and desensitization >1 msec) and contained higher levels of GluR2 and flip isoforms. However, receptors at auditory nerve synapses on cells that also receive parallel fiber input, the fusiform cells, had intermediate properties with respect to kinetics and contained GluR2 and flip isoforms. Given the diverse biophysical properties, patterns of innervation, patterns of electrical activity, and targets of each cell type in vivo, these data indicate that the kinetics and permeation properties of AMPA receptors are linked to factors associated with synaptic connectivity.
Litterfall production and fluvial export in headwater catchments of the southern Amazon

Resolving the carbon (C) balance in the Amazonian forest depends on an improved quantification of production and losses of particulate C from forested landscapes via stream export. The main goal of this work was to quantify litterfall, the lateral movement of litter, and the export of coarse organic particulate matter (>2 mm) in four small watersheds (1–2 ha) under native forest in southern Amazonia near Juruena, Mato Grosso, Brazil (10°25′S, 58°46′W). Mean litterfall production was 11.8 Mg ha−1 y−1 (5.7 Mg C ha−1 y−1). Litterfall showed strong seasonality, with the highest deposition in the driest months of the year. About two times more C per month was deposited on the forest floor during the 6-mo dry season (0.65 Mg C ha−1 mo−1) compared with the rainy season (0.3 Mg C ha−1 mo−1). The measured C concentration of the litterfall samples was significantly greater in the dry season than in the rainy season (49% vs. 46%). The lateral movement of litter increased from the plateau (upper landscape position) towards the riparian zone. However, the trend in C concentration of laterally transported litter samples was the opposite, being highest on the plateau (44%) and lowest in the riparian zone (42%). Stream-water exports of particulate C were positively correlated with streamflow, increasing in the rainiest months. The export of particulate C in streamflow was found to be very small (less than 1%) in relation to the amount of litterfall produced.
Homeless men : exploring the experience of shame

ing Core Ideas After the domain-categorized transcripts for each participant had been developed, the primary team members independently reviewed the raw data from three participants and abstracted or summarized them into core ideas within the respective domains. Core ideas are a summarization of participant data into concise and clear prose. Core ideas were summarized without reference to interpretation or inference. Instead, the summarizations were based on transcript evidence and the context of the given domain. The primary team members arrived at a consensus of the core ideas for the first three participant cases. As the core ideas for these three participants were reviewed and discussed, they were recategorized to different domains as the consensus determined it necessary. Once a common understanding of the core idea process was established, one team member reviewed the remaining domain categorized transcripts and identified core ideas. A second team member then reviewed the first team member’s core idea summarizations. The team then discussed and resolved all discrepancies, arriving at a final list of core ideas for each domain.
Reordering Metrics for MT

One of the major challenges facing statistical machine translation is how to model differences in word order between languages. Although a great deal of research has focussed on this problem, progress is hampered by the lack of reliable metrics. Most current metrics are based on matching lexical items in the translation and the reference, and their ability to measure the quality of word order has not been demonstrated. This paper presents a novel metric, the LRscore, which explicitly measures the quality of word order by using permutation distance metrics. We show that the metric is more consistent with human judgements than other metrics, including the Bleu score. We also show that the LRscore can successfully be used as the objective function when training translation model parameters. Training with the LRscore leads to output which is preferred by humans. Moreover, the translations incur no penalty in terms of Bleu scores.
The S-Ribonuclease Gene of Petunia hybrida Is Expressed in Nonstylar Tissue, Including Immature Anthers

To determine the ability of isolated S-locus promoter sequences to direct organ-specific gene expression, we used microprojectile bombardment to introduce chimeric S-allele/[beta]-glucuronidase genes into different tissues of Petunia hybrida for transient expression. Histochemical staining showed that S-locus/[beta]-glucuronidase fusions were expressed in pistil, ovary, and petal tissue. No expression of the chimeric genes was detected in leaves or in mature pollen, either by histochemical staining or by fluorescence assays. RNA blot hybridization confirmed that low levels of S-locus mRNA accumulate in petals and ovaries in vivo. Analysis of the expression pattern of S-locus promoter deletions showed that sequences in the immediate vicinity of the TATA box were sufficient to confer qualitatively correct organ-specific expression of [beta]-glucuronidase. To further investigate the potential for S-ribonuclease expression in pollen, we used the polymerase chain reaction to amplify RNA accumulated in developing anthers. These assays demonstrated that mRNA for the S-ribonuclease accumulates to low levels in developing anthers several days prior to corolla opening and pollen anthesis. We discuss these results in light of current models of self-incompatibility.
CO2-induced ocean acidification increases anxiety in Rockfish via alteration of GABAA receptor functioning

The average surface pH of the ocean is dropping at a rapid rate due to the dissolution of anthropogenic CO2, raising concerns for marine life. Additionally, some coastal areas periodically experience upwelling of CO2-enriched water with reduced pH. Previous research has demonstrated ocean acidification (OA)-induced changes in behavioural and sensory systems including olfaction, which is due to altered function of neural gamma-aminobutyric acid type A (GABAA) receptors. Here, we used a camera-based tracking software system to examine whether OA-dependent changes in GABAA receptors affect anxiety in juvenile Californian rockfish (Sebastes diploproa). Anxiety was estimated using behavioural tests that measure light/dark preference (scototaxis) and proximity to an object. After one week in OA conditions projected for the next century in the California shore (1125 ± 100 µatm, pH 7.75), anxiety was significantly increased relative to controls (483 ± 40 µatm CO2, pH 8.1). The GABAA-receptor agonist muscimol, but not the antagonist gabazine, caused a significant increase in anxiety consistent with altered Cl− flux in OA-exposed fish. OA-exposed fish remained more anxious even after 7 days back in control seawater; however, they resumed their normal behaviour by day 12. These results show that OA could severely alter rockfish behaviour; however, this effect is reversible.
Comparison of methods for prediction of prostate cancer in Turkish men with PSA levels of 0-10 ng/mL.

PURPOSE Several concepts to improve the diagnostic accuracy of prostate specific antigen (PSA) for prediction of prostate cancer have been studied. The aim of this study was to examine and compare the methods used for improving the diagnostic accuracy of PSA in a country with low incidence of prostate cancer. METHODS 997 patients with prostate biopsy were included into study. Predictive models using PSA, PSA density (PSAD), free PSA/total PSA (f/tPSA), binary logistic regression (LR) analysis, artificial neural networks (ANNs), and decision trees (DTs) have been developed. For LR, ANNs and DTs, a validation group consisting of 241 cases was reserved. RESULTS 193 (19%) biopsies out of 997 showed prostatic cancer. Median PSAD in patients with malignant and benign lesions were 0.21 and 0.16, respectively (p<0.001). According to 25% f/tPSA cut-off level, 18.4% of the patients with PSA<25% and 16.0% of the patients with PSA>25% had prostate cancer (p=0.423). Receiver operating characteristics (ROC) area under the curve (AUC) values for PSA, PSA density, f/tPSA, LR, ANNs, and DTs were 0.587, 0.625, 0.560, 0.678, 0.644, and 0.698, respectively. ROC AUCs in the validation group for LR, ANNs and DTs were 0.717, 0.516 and 0.629 respectively. CONCLUSIONS For cases with f/tPSA<25%, no increased probability for prostatic carcinoma was observed. Multivariate models have higher AUCs than PSA, PSAD or f/tPSA. LR, DTs and ANNs showed similar results, however application of ANNs to the validation group produced a significantly lower AUC, limiting the value of ANNs in this situation.
Applied bias slewing in transient Wigner function simulation of resonant tunneling diodes

The Wigner function formulation of quantum mechanics has shown much promise as a basis for accurately modeling quantum electronic devices, especially under transient conditions. In this work, we demonstrate the importance of using a finite applied bias slew rate (as opposed to instantaneous switching) to better approximate experimental device conditions, and thus to produce more accurate transient Wigner function simulation results. We show that the use of instantaneous (and thus unphysical) switching can significantly impact simulation results and lead to incorrect conclusions about device operation. We also find that slewed switching can reduce the high computational demands of transient simulations. The resonant tunneling diode (RTD) is used as a test device, and simulation results are produced with SQUADS (Stanford QUAntum Device Simulator).
Thrombolysis for Ischemic Stroke Associated With Infective Endocarditis: Results From the Nationwide Inpatient Sample

Background and Purpose— Cerebral ischemic events are highly prevalent and associated with high rates of death and disability in patients with infective endocarditis (IE). However, the role of thrombolysis in these patients remains unclear. We sought to determine the rates and outcomes of acute ischemic stroke patients with IE treated with intravenous thrombolysis (IVT). Methods— We determined the rates of post-thrombolytic intracerebral hemorrhage and favorable outcome among acute ischemic stroke patients with IE treated with IVT. Patients were identified using Nationwide Inpatient Sample data from 2002 to 2010. We compared the rates of various outcomes with ischemic stroke patients without IE treated with IVT. Results— There were 222 patients (mean age 59±18 years; 46% women) who were treated with IVT for acute ischemic stroke associated with IE and 134 048 patients (mean age 69±15 years; 49% women) who were treated for stroke without IE. The rate of post-thrombolytic intracerebral hemorrhage was significantly higher in patients with IE compared with those without IE (20% versus 6.5%; P=0.006). There was a significantly lower rate of favorable outcome in the IE group (10% versus 37%; P=0.01). Conclusions— High rates of post-thrombolytic intracerebral hemorrhage and low rates of favorable outcome mandate caution in using IVT in acute ischemic stroke patients with IE.
Predicting Fear of Crime using a Multilevel and Multi-Model Approach: A Study in Hillsborough County

vi Chapter 1: Introduction 1 “Roadmap” For the Dissertation 7 Chapter 2: Theoretical Framework & Literature Review 8 What is Fear of Crime ? 8 Theoretical Explanations of Fear 10 Social Integration 11 Informal social control hypothesis 13 Indirect victimization hypothesis 14 Which version of social integration? 15 The Disorder Model 16 What is disorder? 18 Research assessing the relationship between disorder and fear of crime 19 Research testing both the disorder and social integration models 20 Vulnerabilities Model 21 Types of vulnerabilities 22 Sociodemographic groups and vulnerability 23 Gender 23 Age 25 Racial/Ethnic minorities 27 Socioeconomic status 28 Prior victimization 29 Reciprocal Effects 31 Positive feedback loop 32 Negative feedback loop 34 Contextual Effects 36 The relationship between social integration and contextual effects 38 The relationship between disorder and contextual effects 40 The relationship between vulnerabilities and contextual effects 41 Current Study 42
Enamel hypoplasia in human teeth; an examination of its causes.

B e f o r e discussing the causes of hypo­ plasia of the enamel, I shall review briefly the process by which hypopla­ sia is produced. Calcification of the de­ ciduous dentition is largely an intra­ uterine process. According to the classic theory of tooth formation and calcifica­ tion, the first rods of enamel are formed after some dentin has been laid. Calci­ fication of the enamel then begins at the top of the follicle and gradually progresses until it reaches the base.
Why Sex? And Why Only in Pairs?

Understanding the purpose of sex remains one of the most important unresolved problems in evolutionary biology. The difficulty is not that there are too few theories of sex, the difficulty is that there are too many and none stand out. To distinguish between theories we suggest the following question: Why are there no triparental species in which an offspring is composed of the genetic material of three individuals? A successful theory should confer an advantage to biparental sex over asexual reproduction without conferring an even greater advantage to triparental sex. We pose our question in the context of two leading theories of sex, the (deterministic) mutational hypothesis that sex reduces the rate at which harmful mutations accumulate, and the red queen hypothesis that sex reduces the impact of parasitic attack by increasing genotypic variability. We show that the mutational hypothesis fails to provide an answer to the question because it implies that triparental sex dominates biparental sex, so the latter should never be observed. In contrast, we show that the red queen hypothesis is able to explain biparental sex without conferring an even greater advantage to triparental sex.
The Impact of Geophagia on the Iron Status of Black South African Women

Objectives: To determine the nutritional status and risk factors associated with women practicing geophagia in QwaQwa, South Africa. Materials and Methods: An observational epidemiological study design was adopted which included an exposed (geophagia) and nonexposed (control) group. A food frequency questionnaire, anthropometric measurements and blood sampling were applied to determine nutritional status of participants. Logistic regression analysis was performed in order to identify factors that were likely to be associated with the practice of geophagia. Results: The mean total energy intake for the geophagia group (G) and control group (C) were 10324.31 ± 2755.00 kJ and 10763.94 ± 2556.30 kJ respectively. Both groups fell within the overweight category according to the mean Body Mass Index (BMI) of each group (G= 25.59 kg/m; C= 25.14 kg/m). The mean serum iron levels of the geophagia group (6.929 μmol/l) were significantly lower than that of the control group (13.75 μmol/l) (p = 0.000). Serum transferrin (G=3.23g/l; C=2.7054g/l) and serum transferrin saturation (G=8.05%; C=18.74%) levels also differed significantly between groups (p=0.00). Factors that were associated with the practice of geophagia included haemoglobin (Odds ratio (OR):14.50), serumiron (OR: 9.80), serum-ferritin (OR: 3.75), serum-transferrin (OR: 6.92) and transferrin saturation (OR: 14.50). A significant negative association (p=0.014) was found between women who were wageearners and those who were not wage-earners and the practice of geophagia (OR: 0.143; CI: 0.027; 0.755). These findings seem to indicate that a permanent income may decrease the likelihood of practising geophagia. Key Findings: Geophagia was confirmed to be a risk factor for iron deficiency in this community. The significantly strong association between geophagia and iron deficiency emphasizes the importance of identifying the practice of geophagia in women, especially during their child bearing years. Keywords—Anaemia, anthropometry, dietary intake, geophagia, iron deficiency.