Miracle-dz/UniFAR-FTUs huggingface dataset:
Substitutional Reality: Using the Physical Environment to Design Virtual Reality Experiences

Experiencing Virtual Reality in domestic and other uncontrolled settings is challenging due to the presence of physical objects and furniture that are not usually defined in the Virtual Environment. To address this challenge, we explore the concept of Substitutional Reality in the context of Virtual Reality: a class of Virtual Environments where every physical object surrounding a user is paired, with some degree of discrepancy, to a virtual counterpart. We present a model of potential substitutions and validate it in two user studies. In the first study we investigated factors that affect participants' suspension of disbelief and ease of use. We systematically altered the virtual representation of a physical object and recorded responses from 20 participants. The second study investigated users' levels of engagement as the physical proxy for a virtual object varied. From the results, we derive a set of guidelines for the design of future Substitutional Reality experiences.
Assessment of Thin-Layer Breast Aspirates for Immunocytochemical Evaluation of HER2 Status

OBJECTIVE To determine whether immunocytochemistry (ICC) for HER2 on ThinPrep (TP)-processed breast fine needle aspiration biopsies (Cytyc Corp., Boxborough, Massachusetts, U.S.A.) is comparable to the findings of immunohistochemistry on corresponding surgically removed tissue. STUDY DESIGN Immunostaining was performed on 63 malignant breast fine needle aspirates and compared to immunostaining on paraffin sections (PSs) from the subsequent biopsies. The HercepTest (Dako, Carpinteria, California, U.S.A.) and TAB250 antibodies were utilized. Cases in which the TP and paraffin HER2 results did not correlate were further assessed for gene amplification by differential polymerase chain reaction (dPCR). RESULTS HER2 overexpression was found in 9 of the 63 cases (14%). TAB250 had higher specificity on PS versus TP (P = .008), and TAB250 had higher specificity on PS versus the HercepTest on PS and TP (P = .004 and .0001, respectively). CONCLUSION HER2 immunostaining with both the HercepTest and TAB250 on TP is unreliable due to low specificity (72% and 83% for HercepTest and TAB250, respectively). However, both antibodies have high sensitivity (89% and 100%, respectively); suggesting that this method may have some utility as a preliminary screening test for HER2 status. Negative HER2 staining by ICC is highly predictive of the absence of HER2 overexpression, whereas positive HER2 staining on TP would require further validation by either dPCR of fluorescence in situ hybridization.
Evaluation of Spliced Open-end Yarn Performances Using Fuzzy Method

This work explored a prediction of spliced open-end spun-yarn appearance, strength, and twist using the fuzzy method. To determine the most relevant input variables, affecting the spliced open-end spun yarns, and output properties, defining the splice performance, a principal component analysis was used. Therefore, the selected parameters (recalling yarn code, duration of tearing, and delivered quantity of fibers code) were used to predict the splice performance using the fuzzy logic technique. Compared with the experimental method, the fuzzy technique gives more accurate results that help in the splice properties prediction as function of selected input parameters.
Metalloproteinase-2, -7 and -9 and tissue inhibitor of metalloproteinase-1 and -2 expression in normal, hyperplastic and neoplastic endometrium: a clinical-pathological correlation study.

BACKGROUND Matrix metalloproteinases (MMPs) and their inhibitors are key-players in extracellular matrix and basement membrane degradation, and are involved in both physiological and malignant processes. The aim of this study was to examine MMP-2, -7 and -9 and TIMP-1 and -2 expression in normal, hyperplastic and malignant endometrium, and their relation to clinical and histological prognostic factors. MATERIALS AND METHODS We performed qualitative and semi-quantitative immunohistochemical analysis of 20 samples of normal endometrium (10 in the proliferative phase, 10 in the secretory phase), 39 samples of hyperplastic endometrium (17 without atypia and 22 with atypia) and 38 samples of endometrioid carcinoma, by using specific monoclonal antibodies. RESULTS In normal endometrium, epithelial expression of MMP-2 (P = 0.0007), MMP-7 (P = 0.0002) and TIMP-2 (P = 0.0004) was increased during the proliferative phase of the menstrual cycle. MMP-2 expression correlated negatively with TIMP-2 expression (P = 0.001, rho = 0.702). Endometrial stromal cells in the secretory phase showed strong MMP-2 expression (P = 0.004) and weak MMP-7 (P = 0.001) and TIMP-1 expression (P = 0.01). In hyperplastic endometrium, the presence of atypia was associated with lower TIMP-2 expression (P = 0.005) and was also associated with a trend towards higher MMP-2 expression. Endometrial stromal cell expression of MMP-2, -7 and -9 and TIMP-1 and -2 did not differ between hyperplastic endometrium with and without atypia. A gradient of MMP-2 and -9 expression was observed from hyperplastic endometrium to endometrial carcinomas. In endometrial carcinomas, MMP-2 expression increased (P = 0.0004) and TIMP-2 expression decreased (P = 0.0005) with the histological grade. TIMP-2 expression correlated with myometrial invasion (P = 0.005), lymphovascular space involvement (P = 0.008) and lymph node involvement (P = 0.007). CONCLUSION These results support the involvement of MMPs and TIMPs in endometrial carcinogenesis. Strong MMP-2 and weak TIMP-2 expression were the most potent markers of endometrial malignancies with a high risk of local and distant spread.
Assessing the Utility of Automatic Cancer Registry Notifications Data Extraction from Free-Text Pathology Reports

Cancer Registries record cancer data by reading and interpreting pathology cancer specimen reports. For some Registries this can be a manual process, which is labour and time intensive and subject to errors. A system for automatic extraction of cancer data from HL7 electronic free-text pathology reports has been proposed to improve the workflow efficiency of the Cancer Registry. The system is currently processing an incoming trickle feed of HL7 electronic pathology reports from across the state of Queensland in Australia to produce an electronic cancer notification. Natural language processing and symbolic reasoning using SNOMED CT were adopted in the system; Queensland Cancer Registry business rules were also incorporated. A set of 220 unseen pathology reports selected from patients with a range of cancers was used to evaluate the performance of the system. The system achieved overall recall of 0.78, precision of 0.83 and F-measure of 0.80 over seven categories, namely, basis of diagnosis (3 classes), primary site (66 classes), laterality (5 classes), histological type (94 classes), histological grade (7 classes), metastasis site (19 classes) and metastatic status (2 classes). These results are encouraging given the large cross-section of cancers. The system allows for the provision of clinical coding support as well as indicative statistics on the current state of cancer, which is not otherwise available.
Benign cellular changes in Pap smears. Causes and significance.

OBJECTIVE We reviewed consecutive cases classified as benign cellular changes (BCC) over a four-month period. STUDY DESIGN Cases classified as BCC were retrieved from the cytology files. A search was carried out to identify the previous Pap smears and concomitant cervical biopsies. RESULTS One thousand one hundred three cases (23% of our gynecologic smears) were classified as BCC. Ninety-two patients (8.3%) underwent concurrent cervical biopsies. Specific infections accounted for 8% of BCC cases; reactive changes accounted for 92%. Of the biopsy specimens, 8.3% had no significant pathologic change. The most common biopsy diagnoses were cervicitis (31.5%), immature squamous metaplasia (16.3%) and reserve cell hyperplasia (10.8%). Miscellaneous benign diagnoses accounted for 21.7%. Cervical intraepithelial neoplasia (CIN) 1/human papillomavirus (HPV) was present in 14% of cases. All patients with biopsy diagnoses of CIN 1 had at least two previous abnormal Pap smears. Previous biopsy reports were available for review in 127 (12%) of the 1,103 patients. Of these 127 cases, 53.5% had a previous diagnosis of CIN/HPV; 9.4% had invasive carcinoma. A benign diagnosis was reported in 36.5%. CONCLUSION The majority of BCC cases are due to reactive and inflammatory processes. In patients with a previous history of CIN, BCC may be of some significance. In patients with no significant prior cervical abnormalities, a Pap smear classified as BCC represents a reactive process.
On the use of instantaneous and transitional spectral information in speaker recognition

The use of instantaneous and transitional spectral representations of spoken utterances for speaker recognition is investigated. LPC derived-cepstral coefficients are used to represent instantaneous spectral information and best linear fits of each cepstral coefficient over a specified time window are used to represent transitional information. An evaluation has been carried out using a data base of isolated digit utterances over dialed-up telephone lines by 10 talkers. Two vector quantization (VQ) codebooks, instantaneous and transitional, are constructed from training utterances for each speaker. The experimental results show that the instantaneous and transitional representations are relatively uncorrelated thus providing complementary information for speaker recognition. A rectangular window of approximately 100-150 ms duration provides an effective estimate of spectral transitions for speaker recognition. Also, simple transmission channel variations are shown to affect the instantaneous spectral representations and the corresponding recognition performance significantly, while the transitional representations and performance are relatively resistant.
The Serotonin Transporter Gene Length Polymorphism (5-HTTLPR) and Life Events: No Evidence for an Interaction Effect on Neuroticism and Anxious Depressive Symptoms

The finding of a significant gene by environment interaction effect on depression of the serotonin transporter length polymorphism (5-HTTLPR) and the Number of experienced Life Events (NLE) was not replicated in two large meta-analyses (Munafo et al., 2009; Risch et al., 2009). These meta-analyses have been criticized on the grounds that large studies that get most weight in meta-analyses have the poorest measurement quality of life events and, as a consequence, do not find an effect. Another issue is the time frame across which the NLE are measured. Proximal life events appear to be better predictors of depression than more distal events. We present the results of analyses of the 5-HTTLPR × NLE effect on anxious depression and neuroticism scores in a sample of 1,155 twins and their parents and siblings from 438 families. The interaction effect was tested separately for NLE experienced across the life span and NLE experienced in the past year. There was a significant main effect of NLE on anxious depression and neuroticism, especially when these were experienced in the past year. No interaction with 5-HTTLPR was found for NLE either experienced across the life span or across the past year. Our results support the two recent meta-analyses. Given recent insights from genome wide association studies, it seems more useful to focus on the joint effect of several genes, that are, for example, part of the same biological pathway, in interaction with the environment, than on one candidate gene.
Prognostic significance of epidermal growth factor receptor expression in glioma patients

Purpose There is a great controversy regarding the prognostic significance of epidermal growth factor receptor (EGFR) in glioma patients. The current meta-analysis was conducted to evaluate the effect of abnormal EGFR expression on overall survival in glioma patients. Materials and methods A comprehensive literature search of PubMed, EMBASE, Google Scholar, Web of Science, and Cochrane Library was conducted. The combined hazard ratio (HR) and its 95% confidence intervals (CIs) were used to evaluate the association between EGFR expression and survival in glioma. Results A total of 476 articles were screened, and 17 articles containing 1,458 patients were selected. The quality assessment of the included studies was performed by the Newcastle–Ottawa Scale. Overexpression of EGFR was found to be an indicator of poor prognosis in overall survival in glioma patients (HR =1.72, 95% CI 1.32–2.25, P=0.000, random effect) and glioblastoma multiforme patients (HR =1.57, 95% CI 1.15–2.14, P=0.004, random effect). Subgroup analysis was conducted to explore the source of high heterogeneity. Conclusion This meta-analysis indicated that high expression of EGFR may serve as a biomarker for poor prognosis in glioma patients.
Subtype-Specific Radiation Response and Therapeutic Effect of FAS Death Receptor Modulation in Human Breast Cancer

Breast cancer is the most common malignancy diagnosed among women and represents a heterogeneous group of subtypes. Radiation therapy is a critical component of treatment for breast cancer patients. However, little is known about radiation response among these intrinsic subtypes. In previous studies, we identified a significant induction of FAS after irradiation in biologically favorable breast cancer patients and breast cancer cell lines. Here, we expanded our study and investigated radiation response in a mouse model of breast cancer. MCF7 (luminal), HCC1954 (HER2+) or SUM159 (basal) cells were implanted orthotopically into the dorsal mammary fat pad of nude mice. These mice were then treated with different doses of radiation to assess tumor growth control. We further investigated the therapeutic effect of FAS modulation by silencing FAS in radiation-responsive tumors and injecting FAS agonist antibody into radiation-resistant tumors. Exposure to radiation inhibited MCF7, and to a lesser extent HCC1954 tumor growth in a dose-dependent manner. In contrast, SUM159 tumors were resistant to radiation. The estimated TCD50 values were 19.3 Gy for MCF7 and 44.9 Gy for SUM159. Radiation induced FAS expression in MCF7 tumors, but not SUM159 tumors. We found that silencing of FAS did not negatively impact radiation response in MCF7 tumors, possibly due to compensation by other apoptotic pathways. On the other hand, FAS activating antibody in combination with radiation treatment delayed SUM159 and HCC1954 tumor growth. However, it did not reach statistical significance compared to radiation treatment alone. Our results suggest that there is intrinsic variation in radiation response among breast cancer subtypes. FAS activation concurrent with radiation slows tumor growth in the radiation-resistant subtypes, but the effect was not significant. Alternative subtype-specific modulators of radiation response are under investigation.
Turkish Nurses' Attitudes and Practices Regarding Oral Care.

PURPOSE This study was conducted to determine the attitudes and practices of nurses working in intensive care units of four different hospitals regarding oral care. METHODS One hundred eighty-five nurses who worked in adult intensive care units comprised the sample of this cross-sectional descriptive study. CONCLUSION It can be said that intensive care nurses perform oral care without an oral care protocol and assessment guideline, and that the methods and frequency of oral care and solutions and tools used for oral care differ from one institution to another. IMPLICATIONS FOR NURSING PRACTICE The results emphasized the need for continuing training in this area.
Computational impact responses of reinforced concrete slabs

The responses of reinforced concrete slabs subject to an impact loading near the ultimate load range are explored. The analysis is carried out on a simply supported rectangular reinforced concrete slab using a nonlinear explicit dynamic procedure and considering three material models: Drucker-Prager, modified Drucker-Prager, and concrete damaged plasticity, available in the commercial finite element software, ABAQUS/Explicit. For comparison purposes, the impact forcetime response, steel reinforcement failure, and concrete perforation pattern are verified against the existing experimental results. Also, the effectiveness of mesh density and damage wave propagation are studied independently. It is shown that the presently adopted finite element procedure is able to simulate and predict fairly accurate the behavior of reinforced concrete slab under impact load. More detailed investigations are however demanded for the justification of effects coming from an imperfect projectile orientation as well as the load and structural surface conditions, including the impulsive contacted state, which are inevitable in an actual impact environment.
Investigation for the Reduction of In-plane Compressive Strength in Preconditioned Thin Composite Panels

This paper investigates the effects of precondition characteristics on the residual compressive strength (RCS) of 16-ply carbon/epoxy panels through the establishment of their compressive and buckling response characteristics. The preconditions of varying sizes include impact damage and embedded artificial delaminations of both circular and elliptical shapes. A sequence of prebuckling, local and global buckling, and postbuckling is found in both the longitudinal and transverse directions. The possibility of delamination propagation is examined using the response characteristics on the basis of the sequences. A damage threshold is found at the 25% panel width or 455mm 2damage area. Both the global buckling loads and the RCSs suffer substantial degradation but in a different manner, depending on the threshold. For small damages, the global buckling loads are unaffected but the RCSs suffer substantial degradation, though there is little evidence for the delamination propagation. For large damages, while the global buckling loads are reduced moderately with an increase of the damages due likely to the unstable global buckling-to-postbuckling transition, the RCSs do not suffer further reduction, though evidence is found for the delamination propagation. These panels fail soon after the unstable global bucklingtopostbuckling transition. Panels with multiple delaminations suffer a greater reduction in RCS than the impact-damaged panels. A combination of the delamination size and number is shown to have the most dominant effect on the RCSs. It is demonstrated that the present method of embedding artificial delaminations proves to be very useful for studying the RCS of impact-damaged panels via the establishment of response characteristics and their links to the effects of the preconditions on them.
A dynamic large-update primal‐dual interior-point method for linear optimization

Primal-dual interior-point methods (IPMs) have shown their power in solving large classes of optimization problems. However, at present there is still a gap between the practical behavior of these algorithms and their theoretical worst-case complexity results, with respect to the strategies of updating the duality gap parameter in the algorithm. The so-called small-update IPMs enjoy the best known theoretical worst-case iteration bound but work very poorly in practice, while the so-called large-update IPMs have superior practical performance but with relatively weaker theoretical results. In this article, by restricting us to linear optimization (LO), we first exploit some interesting properties of a self-regular proximity function, proposed recently by the authors of this work and Roos, and use it to define a neighborhood of the central path. These simple but interesting properties of the proximity function indicate that, when the current iterate is in a large neighborhood of the central path, then the large-update IPM emerges to be the only natural choice. Then, we apply these results to design a specific self-regularity based IPM. Among others, we show that this self-regularity based IPM can also predict precisely the change of the duality gap as the standard IPM does. Therefore, we can directly apply the modified IPM to the simplified self-dual homogeneous model for LO. This provides a remedy for an implementation issue of the new self-regular IPMs. A dynamic large-update IPM in large neighborhood is proposed. Different from traditional large-update IPMs, the new dynamic IPM always takes large-updates and does not utilize any inner iteration to get centered. An worst-case iteration bound of the algorithm is established.
Lifestyle Factors and Indices of Kidney Function in the Framingham Heart Study

Background and Objectives: Lifestyle characteristics are modifiable factors that could be targeted as part of chronic kidney disease (CKD) prevention. We sought to determine the association of lifestyle characteristics with incident estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m2 and rapid eGFR decline in older adults in the United States. Methods: Prospective cohort study of Framingham Offspring participants with baseline eGFR <60 ml/min/1.73 m2 (n = 1,802) who attended the seventh (1998-2001; baseline) and eighth (2005-2008; follow-up) examinations (mean age = 59 years, 54.8% women). Predictors included measures of diet quality, physical activity, alcohol intake, and current smoking status assessed during baseline. Outcomes were based on creatinine-based eGFR at baseline and follow-up and included incident eGFR <60 ml/min/1.73 m2 (at follow-up) and rapid eGFR decline (annual eGFR decrease ≥3 ml/min/1.73 m2). Results: Over an average follow-up of 6.6 years, 9.5% (n = 171) of participants developed incident eGFR <60. A trend was observed across quartiles of diet quality, with higher levels of diet quality associated with a decreased odds ratio (OR) of incident eGFR <60 (p trend = 0.045). Higher diet quality was associated with decreased odds of rapid eGFR decline (p trend = 0.03) and was attenuated with additional adjustment (p trend = 0.07). In sensitivity analysis for rapid eGFR decline using a secondary definition (annual eGFR decrease ≥3 and incident eGFR <60), diet associations remained significant with additional adjustment (p trend = 0.04). No associations were observed with physical activity, smoking status, or alcohol intake with incident eGFR <60 or rapid eGFR decline (all p > 0.19). Conclusions: Higher diet quality may be associated with a decreased risk of incident eGFR <60 ml/min/1.73 m2, and rapid eGFR decline. Whether adherence to a healthy diet can prevent reduction in kidney function warrants further study.
A quantitative philology of introspection

The cultural evolution of introspective thought has been recognized to undergo a drastic change during the middle of the first millennium BC. This period, known as the “Axial Age,” saw the birth of religions and philosophies still alive in modern culture, as well as the transition from orality to literacy—which led to the hypothesis of a link between introspection and literacy. Here we set out to examine the evolution of introspection in the Axial Age, studying the cultural record of the Greco-Roman and Judeo-Christian literary traditions. Using a statistical measure of semantic similarity, we identify a single “arrow of time” in the Old and New Testaments of the Bible, and a more complex non-monotonic dynamics in the Greco-Roman tradition reflecting the rise and fall of the respective societies. A comparable analysis of the twentieth century cultural record shows a steady increase in the incidence of introspective topics, punctuated by abrupt declines during and preceding the First and Second World Wars. Our results show that (a) it is possible to devise a consistent metric to quantify the history of a high-level concept such as introspection, cementing the path for a new quantitative philology and (b) to the extent that it is captured in the cultural record, the increased ability of human thought for self-reflection that the Axial Age brought about is still heavily determined by societal contingencies beyond the orality-literacy nexus.