Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Quantitative Multiplex Tissue Immunoblotting for Biomarkers Predicts a Prostate Cancer Aggressive Phenotype

Background: Early prediction of disease progression in men with very low-risk (VLR) prostate cancer who selected active surveillance (AS) rather than immediate treatment could reduce morbidity associated with overtreatment. Methods: We evaluated the association of six biomarkers [Periostin, (−5, −7) proPSA, CACNA1D, HER2/neu, EZH2, and Ki-67] with different Gleason scores and biochemical recurrence (BCR) on prostate cancer TMAs of 80 radical prostatectomy (RP) cases. Multiplex tissue immunoblotting (MTI) was used to assess these biomarkers in cancer and adjacent benign areas of 5 μm sections. Multivariate logistic regression (MLR) was applied to model our results. Results: In the RP cases, CACNA1D, HER2/neu, and Periostin expression were significantly correlated with aggressive phenotype in cancer areas. An MLR model in the cancer area yielded a ROC-AUC = 0.98, whereas in cancer-adjacent benign areas, yielded a ROC-AUC = 0.94. CACNA1D and HER2/neu expression combined with Gleason score in a MLR model yielded a ROC-AUC = 0.79 for BCR prediction. In the small biopsies from an AS cohort of 61 VLR cases, an MLR model for prediction of progressors at diagnosis retained (−5, −7) proPSA and CACNA1D, yielding a ROC-AUC of 0.78, which was improved to 0.82 after adding tPSA into the model. Conclusions: The molecular profile of biomarkers is capable of accurately predicting aggressive prostate cancer on retrospective RP cases and identifying potential aggressive prostate cancer requiring immediate treatment on the AS diagnostic biopsy but limited in BCR prediction. Impact: Comprehensive profiling of biomarkers using MTI predicts prostate cancer aggressive phenotype in RP and AS biopsies. Cancer Epidemiol Biomarkers Prev; 24(12); 1864–72. ©2015 AACR.
Detecting collective anomalies from multiple spatio-temporal datasets across different domains

The collective anomaly denotes a collection of nearby locations that are anomalous during a few consecutive time intervals in terms of phenomena collectively witnessed by multiple datasets. The collective anomalies suggest there are underlying problems that may not be identified based on a single data source or in a single location. It also associates individual locations and time intervals, formulating a panoramic view of an event. To detect a collective anomaly is very challenging, however, as different datasets have different densities, distributions, and scales. Additionally, to find the spatio-temporal scope of a collective anomaly is time consuming as there are many ways to combine regions and time slots. Our method consists of three components: Multiple-Source Latent-Topic (MSLT) model, Spatio-Temporal Likelihood Ratio Test (ST_LRT) model, and a candidate generation algorithm. MSLT combines multiple datasets to infer the latent functions of a geographic region in the framework of a topic model. In turn, a region's latent functions help estimate the underlying distribution of a sparse dataset generated in the region. ST_LRT learns a proper underlying distribution for different datasets, and calculates an anomalous degree for each dataset based on a likelihood ratio test (LRT). It then aggregates the anomalous degrees of different datasets, using a skyline detection algorithm. We evaluate our method using five datasets related to New York City (NYC): 311 complaints, taxicab data, bike rental data, points of interest, and road network data, finding the anomalies that cannot be identified (or earlier than those detected) by a single dataset. Results show the advantages beyond six baseline methods.
Aurora-A Interacts with AP-2α and Down Regulates Its Transcription Activity

Aurora-A is a serine/threonine protein kinase and plays an important role in the control of mitotic progression. Dysregulated expression of Aurora-A impairs centrosome separation and maturation, which lead to disrupted cell cycle progression and tumorigenesis. However, the molecular mechanism by which Aurora-A causes cell malignant transformation remains to be further defined. In this report, using transcription factors array and mRNA expression profiling array, we found that overexpression of Aurora-A suppressed transcription activity of AP-2α, a tumor suppressor that is often downregulated in variety of tumors, and inhibited expression of AP-2α-regulated downstream genes. These array-based observations were further confirmed by microwell colorimetric TF assay and luciferase reporter assay. Downregulated transcription activity of AP-2α by Aurora-A was found to be associated with reduced AP-2α protein stability, which appeared to be mediated by Aurora-A enhanced ubiquitin-dependent proteasomal degradation of AP-2α protein. Interestingly, Aurora-A-mediated AP-2α degradation was likely dependent Aurora-A kinase activity since inhibition of Aurora-A kinase activity was able to rescue Aurora-A-induced degradation of AP-2α. Moreover, we defined a physical interaction between Aurora-A and AP-2α, and such interaction might bridge the suppressive effect of Aurora-A on AP-2α protein stability. These findings provide new insights into molecular mechanism by which Aurora-A acts as an oncogenic molecule in tumor occurrence and malignant development.
Friendship and Gender: Perspectives of Professional Men and Women

Same- and cross-sex friendships of 156 professional men and women were investigated using a self-report questionnaire consisting of rating scales and open-ended questions. Results indicated that while both sexes viewed the characteristics of an ideal friendship in similar ways, their actual experiences of friendships differed. Women's same-sex friendships were rated higher for overall quality, intimacy, enjoyment and nurturance. Men, on the other hand, rated their cross-sex friendships higher in these areas, with the exception of intimacy which was rated the same by men in both same- and cross-sex friendships. Cross-sex friendships provided both sexes with new understandings and perspectives of the opposite sex. Both sexes generally kept their friendships and sexual relationships separate though sexual feelings and tensions still existed in many cross-sex friendships. These results are similar to findings from studies with college students, indicating that women's participation in professional roles has not resulted in dramatic changes in friendship patterns. Gender differences in same- and cross-sex friendships remain strong, despite new career roles for women.
The relationship between job satisfaction and intention to leave at Mechanical Handling Engineering (MHE)-Demag Malaysia Sdn Bhd

The purpose of this research was to investigate the different aspects of job satisfaction mainly on intrinsic and extrinsic that impacts the MHE-Demag employees which eventually led to high turnover rate. In short, to determine and measure the factors that lead to job satisfaction and job dissatisfaction and to present findings and make recommendations to promote/improve job satisfaction in the mentioned organization. The data for this research was collected and administered by means of a structured questionnaire based on the Minnesota Job Satisfaction Questionnaire (MSQ). It was discovered that most of the employees drew a lower job satisfaction from the absence of career development, interpersonal relationship and decision making compared to other aspects of job satisfaction such as remuneration and the benefit that they receive, general working environment, the ability to work independently and etc. in overall. Hence, it was found that employees were generally dissatisfied with their jobs in this relevant organization with the high possibility of either to leave or quit in long term, in other words
Local reasoning, separation and aliasing

Structures built by pointer aliasing, such as DAGs and graphs, are notoriously tricky to deal with. The mechanisms of separation logic can deal with these structures, but so far this has been done by the maintenance of a global invariant. Specifications and proofs which use local reasoning, and which may point the way to a structured programming for pointers, are discussed. An idiom for inclusion sharing, where one structure is included in another, is presented. A notion of ‘partial graphs’ – graphs with dangling pointers – is used to facilitate proof.
Impact of admission hyperglycemia on hospital mortality in various intensive care unit populations*

Objective:Hyperglycemia in intensive care unit patients has been associated with an increased mortality rate, and institutions have already begun tight glucose control programs based on a limited number of clinical trials in restricted populations. This study aimed to assess the generalizability of the association between hyperglycemia and in-hospital mortality in different intensive care unit types adjusting for illness severity and diabetic history. Design:Retrospective cohort study. Setting:The medical, cardiothoracic surgery, cardiac, general surgical, and neurosurgical intensive care units of the University of Maryland Medical Center. Patients:Patients admitted between July 1996 and January 1998 with length of stay ≥24 hrs (n = 2713). Interventions:On intensive care unit admission, blood glucose and other physiologic variables were evaluated. Regular measurements were taken for calculation of Acute Physiology and Chronic Health Evaluation III scoring. Patients were followed through hospital discharge. Admission blood glucose was used to classify patients as hyperglycemic (>200 mg/dL) or normoglycemic (60–200 mg/dL). The contribution of hyperglycemia to in-hospital mortality stratified by intensive care unit type and diabetes history while controlling for illness severity was estimated by logistic regression. Measurements and Main Results:The adjusted odds ratios for death comparing all patients with hyperglycemia to those without were 0.81 (95% confidence interval, 0.37, 1.77) and 1.76 (95% confidence interval, 1.23, 2.53) for those with and without diabetic history, respectively. Higher mortality was seen in hyperglycemic patients without diabetic history in the cardiothoracic, (adjusted odds ratio, 2.84 [1.21, 6.63]), cardiac (adjusted odds ratio, 2.64 [1.14, 6.10]), and neurosurgical units (adjusted odds ratio, 2.96 [1.51, 5.77]) but not the medical or surgical intensive care units or in patients with diabetic history. Conclusions:The association between hyperglycemia on intensive care unit admission and in-hospital mortality was not uniform in the study population; hyperglycemia was an independent risk factor only in patients without diabetic history in the cardiac, cardiothoracic, and neurosurgical intensive care units.
Cdk5-Mediated Phosphorylation of δ-Catenin Regulates Its Localization and GluR2-Mediated Synaptic Activity

Cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation plays an important role in proper synaptic function and transmission. Loss of Cdk5 activity results in abnormal development of the nervous system accompanied by massive disruptions in cortical migration and lamination, therefore impacting synaptic activity. The Cdk5 activator p35 associates with δ-catenin, the synaptic adherens junction protein that serves as part of the anchorage complex of AMPA receptor at the postsynaptic membrane. However, the implications of Cdk5-mediated phosphorylation of δ-catenin have not been fully elucidated. Here we show that Cdk5-mediated phosphorylation of δ-catenin regulates its subcellular localization accompanied by changes in dendritic morphogenesis and synaptic activity. We identified two Cdk5 phosphorylation sites in mouse δ-catenin, serines 300 and 357, and report that loss of Cdk5 phosphorylation of δ-catenin increased its localization to the membrane. Furthermore, mutations of the serines 300 and 357 to alanines to mimic nonphosphorylated δ-catenin resulted in increased dendritic protrusions accompanied by increased AMPA receptor subunit GluR2 localization at the membrane. Consistent with these observations, loss of Cdk5 phosphorylation of δ-catenin increased the AMPA/NMDA ratio. This study reveals how Cdk5 phosphorylation of the synaptic mediator protein δ-catenin can alter its localization at the synapse to impact neuronal synaptic activity.
Inactivation of Glyceraldehyde-3-Phosphate Dehydrogenase by Fumarate in Diabetes

OBJECTIVE—S-(2-succinyl)cysteine (2SC) is formed by a Michael addition reaction of the Krebs cycle intermediate, fumarate, with cysteine residues in protein. We investigated the role of fumarate in chemical modification and inhibition of the sulfhydryl enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), in vitro and in tissues of diabetic rats. RESEARCH DESIGN AND METHODS—GAPDH was incubated with fumarate in PBS to assess effects of fumarate on enzyme activity in vitro. Sites of 2SC formation were determined by analysis of tryptic peptides by high-performance liquid chromatography–quadrupole/time-of-flight mass spectrometry. 2SC and fumarate in gastrocnemius muscle of control and streptozotocin-induced diabetic rats were measured by liquid chromatography/tandem mass spectrometry and by gas chromatography/mass spectrometry, respectively. GAPDH was isolated from muscle by immunoprecipitation, and sites of modification of GAPDH were determined by mass spectrometry analysis. RESULTS—2SC was found, both in vitro and in vivo, about equally at active-site Cys-149 and nucleophilic Cys-244. Inactivation of GAPDH by fumarate in vitro correlated with formation of 2SC. In diabetic compared with control rats, fumarate and 2SC concentration increased approximately fivefold, accompanied by an ∼25% decrease in GAPDH specific activity. The fractional modification of GAPDH by 2SC was significantly increased in diabetic versus control animals, consistent with the decreased specific activity of GAPDH in muscle of diabetic animals. CONCLUSIONS—Fumarate contributes to inactivation of GAPDH in diabetes. 2SC may be a useful biomarker of mitochondrial stress in diabetes. Modification of GAPDH and other enzymes and proteins by fumarate may contribute to the metabolic changes underlying the development of diabetes complications.
Image Registration with Sparse Approximations in Parametric Dictionaries

We examine in this paper the problem of image registration from the new perspective where images are given by sparse approximations in parametric dictionaries of geometric functions. We propose a registration algorithm that looks for an estimate of the global transformation between sparse images by examining the set of relative geometrical transformations between the respective features. We propose a theoretical analysis of our registration algorithm, and we derive performance guarantees based on two novel important properties of redundant dictionaries, namely the robust linear inde- pendence and the transformation inconsistency. We propose several illustrations and insights about the importance of these dictionary properties and show that common properties such as coherence or the restricted isometry property fail to provide sufficient information in registration problems. We finally show with illustrative experiments on simple visual objects and handwritten digit images that our algorithm outperforms baseline competing methods in terms of transformation-invariant distance computation and classification.
THE EVOLUTIONARY SIGNIFICANCE OF BACTERIA ASSOCIATED WITH RHAGOLETIS

All Rhagoletis reportedly establish associations with one or more bacterial species, but the bases for these interactions and their implications for host race formation and speciation are poorly understood. Here we present the results of four studies designed to increase our understanding of these relationships. In the first study, we identify the bacteria associated with seven Rhagoletis taxa by surveying the inhabitants of the esophageal bulb, an organ whose major function appears to be the housing of microorganisms. The results suggest that no bacterium has entered into an obligate symbiotic relationship with any of the Rhagoletis taxa surveyed, although one bacterium, Klebsiella oxytoca, is a very common associate of six of the seven. In the second study we use horizontal starch gel electrophoresis to determine the genetic similarity of K. oxytoca clones isolated from different Rhagoletis populations. This analysis provides a rare look into the genetic structure of natural populations of an enteric bacterium and permits the construction of a dendrogram for the clones—a dendrogram which indicates that there is no clear‐cut pattern to the distribution of K. oxytoca genotypes among Rhagoletis. Taken together, the above studies provide indirect evidence that the bacteria associated with Rhagoletis are not important determinants of host plant specificity. The third and fourth studies assess two possible functions associated bacteria may perform for Rhagoletis: pectic substances degradation and nitrogen fixation. Our results do not lend support to either function.
A novel interdigital capacitor with accurate model for left-handed metamaterials

This paper presents a novel interdigital capacitor (IDC) structure with accurate lumped-element circuit model. The IDC employs slotted ground structures and via holes. The proposed structure is able to eliminate the spurious spikes of conventional IDCs. A novel circuit model for the proposed interdigital capacitor is constructed to predict the characteristics of the left-handed metamaterial (LHM) unit cell integrating the proposed IDC. Simulation and measurement show that the spurious spikes are suppressed and the left-handed (LH) characteristics are well predicted by the proposed circuit model.
Glass-Box Program Synthesis: A Machine Learning Approach

Recently proposed models which learn to write computer programs from data use either input/output examples or rich execution traces. Instead, we argue that a novel alternative is to use a glass-box scoring function, given as a program itself that can be directly inspected. Glass-box optimization covers a wide range of problems, from computing the greatest common divisor of two integers, to learning-to-learn problems. In this paper, we present an intelligent search system which learns, given the partial program and the glass-box problem, the probabilities over the space of programs. We empirically demonstrate that our informed search procedure leads to significant improvements compared to brute-force program search, both in terms of accuracy and time. For our experiments we use rich context free grammars inspired by number theory, text processing, and algebra. Our results show that (i) running our framework iteratively can considerably increase the number of problems solved, (ii) our framework can improve itself even in domain agnostic scenarios, and (iii) it can solve problems that would be otherwise too slow to solve with brute-force search.
A Study on Using the History of Industrial Melanism to Teach the Nature of Science

Rudge (2004) presented an innovative approach to using the history of research on industrial melanism to help students learn issues associated with the nature of science (NOS). The phenomenon of industrial melanism is presented to students as a "mystery phenomenon" in which they are provided with examples of observations that led past investigators to discover the phenomenon. Students are asked to consider why the phenomenon is occurring and predictably develop explanations that represent well-known alternative conceptions of evolutionary phenomena once proposed by past scientists. Students are then challenged to think through how they might test among these alternatives, with their predictable responses being used to motivate discussions of the results of similar experiments by past scientists. Throughout the three day unit, issues associated with the nature of science are addressed using an explicit and reflective approach (c.f. Abd-El-Khalick & Lederman 2000). Rudge et. al. (2007) presented the results of a pilot study (19 participants) aimed at evaluating the efficacy of this unit with reference to a targeted set of NOS issues including the nature of theories and experiments, theory change, how the results of experiments are interpreted, and what role imagination and creativity play in science. In the present paper we present the results of a more extensive study involving a total of 130 participants. The efficacy of the unit is once more assessed by means of open-ended surveys (VNOS) (Lederman Abd-El-Khalick, Bell & Schwartz 2002) and follow-up interviews. A collective comparison of pre- and post- responses of students to survey questions and interviews with 17 participants provides some evidence of improvement. The essay concludes with a discussion of several lessons learned regarding the usefulness of the VNOS instrument as a measure of students' understandings of issues associated with the nature of science.
Who's in Control?: Categorizing Nuanced Patterns of Behaviors within a Game-Based Intelligent Tutoring System

The authors use dynamical analyses to investigate the relation between students’ patterns of interactions with various types of game-based features and their daily performance. High school students (n=40) interacted with a game-based intelligent tutoring system across eight sessions. Hurst exponents were calculated based on students’ choice of interactions with four types of gamebased features: generative practice, identification mini-games, personalizable features, and achievement screens. These exponents indicate the extent to which students’ interaction patterns with game-based features are random or deterministic (i.e., controlled). Results revealed a positive relation between deterministic behavior patterns and daily performance measures. Further analyses indicated that students’ propensity to interact in a controlled manner varied as a function of their commitment to learning. Overall, these results provide insight into the potential relations between students’ pattern of choices, individual differences in learning commitment, and daily performance in a learning environment.
Where Should We Intervene?

Effective intervention with sexual offenders requires the targeting of appropriate risk factors. In this study, information on dynamic (changeable) risk factors was collected through interviews with community supervision officers and file reviews of 208 sexual offense recidivists and 201 nonrecidivists. The recidivists were generally considered to have poor social supports, attitudes tolerant of sexual assault, antisocial lifestyles, poor self-management strategies, and difficulties cooperating with supervision. The overall mood of the recidivists and nonrecidivists was similar, but the recidivists showed increased anger and subjective distress just before reoffending. The dynamic risk factors reported by the officers continued to be strongly associated with recidivism, even after controlling for preexisting differences in static risk factors. The factors identified in the interview data were reflected (to a lesser extent) in the officers' contemporaneous case notes, which suggests that the interview findings cannot be completely attributed to retrospective recall bias.