Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant Expression of Novel and Previously Described Cell Membrane Markers in Human Breast Cancer Cell Lines and Tumors

Purpose: In a previous gene expression array study, we identified some 300 genes that were differentially expressed in human epidermal growth factor receptor tyrosine kinase 2 (HER2)–positive versus HER2-negative breast cancer cells. We have now done validation experiments on a group of three cell membrane components that had previously not been implicated in breast cancer. We also studied the expression of three other cell membrane proteins known to play a role in mammary neoplasia. Experimental Design: By immunohistochemistry, we examined up to 130 archival breast carcinomas for Celsr2, E-cadherin, Kai1, and CD9 expression. The expression levels of NET-6 and TROP-2 were determined by quantitative reverse transcription-PCR in a subset of frozen tumors. We also studied fresh pellets and paraffin-embedded cell buttons of nine human breast cell lines. The relationship between the expression of all six membrane proteins and a variety of pathologic and biological variables, including estrogen receptor, HER2, and epidermal growth factor receptor status, was also examined. The NET-6 gene was transfected into a low-expressing cell line, and the effect on cellular morphology, growth, and invasion in vitro was recorded. Results: Celsr2 was down-regulated in one cell line and in 7% of breast cancers. E-cadherin, Kai1, and CD9 were down-regulated in 35%, 76%, and 79% of tumors, respectively, confirming the important role of these markers in human mammary neoplasia. In breast cancer cell lines and tissues, TROP-2 was generally expressed at low levels, although a few specimens showed relative overexpression. NET-6 levels were lower in HER2-negative breast carcinoma cells. In addition, NET-6 was markedly down-regulated in estrogen receptor–negative breast cancers, and expression was lowest in “basal-like” tumors. Ectopic expression of NET-6 in low-expressing MDA-MB-231 cells altered cellular morphology, inhibited growth in vitro, and decreased invasion in a Boyden chamber assay. Conclusions: We have confirmed the expression of three new membrane markers that had previously not been implicated in human breast cancer, and one of them (NET-6) was correlated with HER2 and estrogen receptor status. NET-6 levels were decreased in estrogen receptor–negative and high-grade tumors, and ectopic expression of this gene had an inhibitory effect on proliferation and invasion. Thus, NET-6 may represent a novel breast cancer suppressor gene.
Homicide and Social Disorganization on the Border: Implications for Latino and Immigrant Populations

type="main"> We advance social disorganization theory by examining homicides disaggregated by motive and gang relation and by using data from El Paso, Texas—a predominantly Latino city with high levels of immigration and poverty. We analyze homicide data from the El Paso Police Department's detective logs, 1985–1995, as well as data from the 1990 U.S. Decennial Census. Key measures of social disorganization tend to be associated with homicide but these relationships vary across type of homicide. Immigration and percent African American show no connection with any homicide measure, while percent Latino is only positively associated with gang-related homicides. Overall, social disorganization is useful in understanding homicide in El Paso, but race/ethnicity and immigration do not operate as predicted. These results add important knowledge to a growing literature regarding the neighborhood-level associations between immigration, Latinos, and crime.
Distributed Cooperative coverage Control of Sensor Networks

We present a distributed coverage control scheme for cooperating mobile sensor networks. The mission space is modeled using a density function representing the frequency of random events taking place, with mobile sensors operating over a limited range defined by a probabilistic model. A gradient-based algorithm is designed requiring local information at each sensor and maximizing the joint detection probabilities of random events. We also incorporate communication costs into the coverage control problem, viewing the sensor network as a multi-source, single-basestation data collection network. Communication cost is modeled as the power consumption needed to deliver collected data from sensor nodes, thus trading off sensing coverage and communication cost. The control Scheme is tested in a simulation environment to illustrate its adaptive, distributed, and asynchronous properties.
Synthesis and Characterization of Iodixanol

Iodixanol (Visipaque) is a new nonionic roentgen contrast medium intended for general use. Visipaque is a pharmaceutical formulation of iodixanol which is isotonic and iso-osmotic with blood. Two synthetic routes from 5-nitro-isophthalic acid to iodixanol are described. The chemical structure is confirmed by spectroscopical data (1H-NMR, 13C-NMR, FAB-MS, electrospray-MS, UV, IR and Raman). Chromatographic characteristics are related to the isomerism of iodixanol.
Reciprocal relations between self-critical perfectionism and depressive symptoms: Evidence from a short-term, four-wave longitudinal study

Is self-critical perfectionism an antecedent of depressive symptoms, a consequence of depressive symptoms, or both? In the present study, self-critical perfectionism (i.e., harsh criticism of one’s actions, negative reactions to perceived failures, and extreme concerns over others’ evaluations) and depressive symptoms were conceptualised as a unified, interlocking syndrome wherein self-critical perfectionism and depressive symptoms reciprocally influence each other over time. This reciprocal relations model was tested in 240 undergraduates studied using a four-wave, 4-week longitudinal design. As hypothesised, reciprocal relations were observed between self-critical perfectionism and depressive symptoms, with self-critical perfectionism predicting changes in depressive symptoms and vice versa. Results suggest persons high in self-critical perfectionism may find themselves entangled in an escalating pattern where self-critical perfectionism both leads to, and results from, depressive symptoms. Research focused exclusively on unidirectional relations between self-critical perfectionism and depressive symptoms may ignore information critical to accurately understanding self-critical perfectionism, depressive symptoms, and their interrelation. Instead of assuming unidirectional relations between self-critical perfectionism and depressive symptoms, researchers are encouraged to test for reciprocal relations between these two variables.
Deep machine learning provides state-of-the-art performance in image-based plant phenotyping

Deep learning is an emerging field that promises unparalleled results on many data analysis problems. We show the success offered by such techniques when applied to the challenging problem of image-based plant phenotyping, and demonstrate state-of-the-art results for root and shoot feature identification and localisation. We predict a paradigm shift in image-based phenotyping thanks to deep learning approaches.
Reinforcement of Linear Structure using Parametrized Relaxation Labeling

An approach for reinforcing underlying linear structure while suppressing unwanted noise, useful for analysis of medical images, has been presented. The method utilizes principles previously presented with regard to relaxation labeling processes, but differ in that the label set is now considered to be continuous and the distribution of label preference values for each object (pixel) parametrized by a single vector. Due to this parametrization, the total number of computations per pixel in the new method is now dependent only on the number of neighbors used in the computation, and not on the number of labels as well, as in previous methods. Thus, for a general reinforcement problem with m labels and n neighbors being considered for each pixel, the time complexity per object (pixel) per iteration goes as O (nm2) for the prototypical algorithm (e.g. (Zucker, et. al., 1977)) and is reduced by the approach presented here to O (n). The method uses a new approach for deciding local neighborhood influence and making a decision between reinforced linear structure with some magnitude and orientation and a no-structure condition based on the nonlinear (sigmoidal) thresholding of a linear vector sum. It should be noted that there is a similarity between this sigmoidal thresholding function and similar functions used in artificial neural networks (Hopfield, 1984). Ongoing work is being performed to further investigate such overlap. Also, it is planned to extend the approach in several ways. These include the ability to reinforce co-circularity, as well as to reinforce underlying planar structure by updating surface normals in true three-dimensional diagnostic imagery.
Memory-Savvy Distributed Interactive Ray Tracing

Interactive ray tracing in a cluster environment requires paying close attention to the constraints of a loosely coupled distributed system. To render large scenes interactively, memory limits and network latency must be addressed efficiently. In this paper, we improve previous systems by moving to a page-based distributed shared memory layer, resulting in faster and easier access to a shared memory space. The technique is designed to take advantage of the large virtual memory space provided by 64-bit machines. We also examine task reuse through decentralized load balancing and primitive reorganization to complement the shared memory system. These techniques improve memory coherence and are valuable when physical memory is limited.
Goal disengagement capacities and severity of disease across older adulthood

This study examined age-related associations between goal disengagement capacities, emotional distress, and disease severity across older adulthood. Given that an age-related increase in the experience of stressors might render important goals unattainable, it is expected that goal disengagement capacities would predict a decrease in the severity of experienced illness (i.e., the common cold) by preventing emotional distress (i.e., depressive symptoms), particularly so among individuals in advanced (as compared to early) old age. This hypothesis was tested in a 6-year longitudinal study of 131 older adults (age range = 64 to 90). Regression analyses showed that goal disengagement capacities buffered 6-year increases in older adults’ cold symptoms, and that this effect was significantly pronounced among older-old participants. Mediation analyses further indicated that changes in depressive symptoms exerted an indirect effect on the age-related association between goal disengagement and changes in cold symptoms. The study’s findings suggest that goal disengagement capacities become increasingly important for protecting emotional well-being and physical health as older adults advance in age.
Suboptimal gastroprotective coverage of NSAID use and the risk of upper gastrointestinal bleeding and ulcers: an observational study using three European databases

Background Gastro-protective agents (GPA) are co-prescribed with non-steroidal anti-inflammatory drugs (NSAID) to lower the risk of upper gastrointestinal (UGI) events. It is unknown to what extent the protective effect is influenced by therapy adherence. Aim To study the association between GPA adherence and UGI events among non-selective (ns) NSAID users. Methods The General Practice Research Database (UK 1998–2008), the Integrated Primary Care Information database (the Netherlands 1996–2007) and the Health Search/CSD Longitudinal Patient Database (Italy 2000–2007) were used. A nested case-control design was employed within a cohort of nsNSAID users aged ≥50 years, who also used a GPA. UGI event cases (UGI bleeding and/or symptomatic ulcer with/without obstruction/perforation) were matched to event-free members of the cohort for age, sex, database and calendar time. Adherence to GPA was calculated as the proportion of nsNSAID treatment days covered by a GPA prescription. Adjusted OR with 95% CI were calculated. Results The cohort consisted of 618 684 NSAID users, generating 1 107 266 nsNSAID episodes. Of these, 117 307 (10.6%) were (partly) covered by GPA, 4.9% of which with a GPA coverage <20% (non-adherence), and 68.1% with a GPA coverage >80% (full adherence). 339 patients experienced an event. Among non-adherers, the OR was 2.39 (95% CI 1.66 to 3.44) for all UGI events and 1.89 (95% CI 1.09 to 3.28) for UGI bleeding alone, compared to full adherers. Conclusions The risk of UGI events was significantly higher in nsNSAID users with GPA non-adherence. This underlines the importance of strategies to improve GPA adherence.
Meloidogyne aberrans sp. nov. (Nematoda: Meloidogynidae), a new root-knot nematode parasitizing kiwifruit in China

High infection rates of roots of wild kiwifruit (Actinidia chinensis Planch) and soil infestation by a root-knot nematode were found in Anshun, GuiZhou Province, China. Morphology, esterase phenotype and molecular analyses confirmed that this nematode was different from previously described root-knot nematodes. In this report, the species is described, illustrated and named Meloidogyne aberrans sp. nov. The new species has a unique combination of characters. A prominent posterior protuberance, round and faint perineal pattern and a medium-length stylet (13.6–15.5 μm) characterized the females. Second-stage juveniles (J2) were characterized by a smooth lip region with distinctly protruded medial lips and a depression in outline at the oral aperture, a relatively long stylet (15.9–16.8 μm), four incisures in the lateral field and a very short, even poorly defined, hyaline tail terminus (2.2–5.5 μm). More incisures (11–15) existed in the lateral field of males, and the stylet and spicules of males were 18.2–19.6 μm and 22.7–36.8 μm long respectively. Egg masses were typically produced within the roots of kiwifruit. The new species had a rare Est phenotype, S2. Phylogenetic trees inferred from SSU, LSU D2D3, ITS, and partial coxII-16S rRNA revealed that M. aberrans sp. nov. was within the Meloidogyne clade and was distinguished from all described root-knot nematodes. Moreover, from histopathological observations, M. aberrans sp. nov. induced the formation of multinucleate giant cells.
Computer–Based Graphic Organizers for Students with LD: A Systematic Review of Literature

This article presents a systematic review of the literature for studies that utilized computer–based graphic organizers for students with learning disabilities. A comprehensive search yielded 12 studies that were coded and analyzed. The authors investigated the effectiveness of the treatments on academic outcomes, and selected integral instructional and methodological features for evaluation in order to delineate practical implications and prioritize future research. Findings revealed high effect sizes on social studies measures and encouraging results for written expression, while comprehension results were less promising. This review found no evidence suggesting that these treatments were efficacious without the use of explicit instruction and guided practice.
Characterization of Mycobacterium tuberculosis Complex DNAs from Egyptian Mummies by Spoligotyping

ABSTRACT Bone and soft tissue samples from 85 ancient Egyptian mummies were analyzed for the presence of ancient Mycobacterium tuberculosis complex DNA (aDNA) and further characterized by spoligotyping. The specimens were obtained from individuals from different tomb complexes in Thebes West, Upper Egypt, which were used for upper social class burials between the Middle Kingdom (since ca. 2050 BC) and the Late Period (until ca. 500 BC). A total of 25 samples provided a specific positive signal for the amplification of a 123-bp fragment of the repetitive element IS6110, indicating the presence of M. tuberculosis DNA. Further PCR-based tests for the identification of subspecies failed due to lack of specific amplification products in the historic tissue samples. Of these 25 positive specimens, 12 could be successfully characterized by spoligotyping. The spoligotyping signatures were compared to those in an international database. They all show either an M. tuberculosis or an M. africanum pattern, but none revealed an M. bovis-specific pattern. The results from a Middle Kingdom tomb (used exclusively between ca. 2050 and 1650 BC) suggest that these samples bear an M. africanum-type specific spoligotyping signature. The samples from later periods provided patterns typical for M. tuberculosis. This study clearly demonstrates that spoligotyping can be applied to historic tissue samples. In addition, our results do not support the theory that M. tuberculosis originated from the M. bovis type but, rather, suggest that human M. tuberculosis may have originated from a precursor complex probably related to M. africanum.
The Effects of Job Characteristics on Citizenship Performance

Cavanaugh, Caitlin Maureen, M.S., Purdue University, December 2011. The Effects of Job Characteristics on Citizenship Performance. Major Professor: John T. Hazer. The study of job performance has been a high priority for organizational researchers and practitioners alike. Models of performance have acknowledged that it is affected by both individual differences and environmental factors and also that behaviors outside the job description, called citizenship performance, have value. Despite these acknowledgements, researchers have placed much more emphasis on understanding the influence of individual differences (rather than environmental characteristics) on citizenship performance. Counter to the emphasis on individual differences, the current study sought to evaluate the relationships between environmental characteristics and citizenship performance in the context of the Job Characteristics Model (JCM) and to determine whether the relationships could be both theoretically and empirically understood. Additionally, the relative importance of the environmental variables in the JCM were evaluated and compared to well-known individual difference predictors of citizenship performance. Finally, the current study sought to provide initial evidence for different patterns of relationships between the JCM variables and the three facets of citizenship performance. Undergraduate students employed for at least 20 hours per week were recruited for participation (n = 379) in a cross-sectional study, and data were
Executive Function and Personality in Adolescent and Adult Offenders vs. Non-Offenders

Abstract A comparison of young offenders, adult offenders and their respective reference groups was completed with a battery of psychometric tests to assess executive functioning and personality. Ancillary cognitive testing was performed to ascertain a baseline of functioning. These scores were included in statistical procedures to determine their significance in the presence of other variables. Four stepwise linear discriminant function analyses were run to differentiate the groups. Significant differences were found in executive functioning and personality, as offender groups demonstrated lower executive capacity andmaladaptive personality characteristics. More specifically, offender groups were significantly impaired in the domain of social competency, judgement, foresight and perspective taking while demonstrating higher levels of impulsivity, immaturity and aggression.
History of Reading Struggles Linked to Enhanced Learning in Low Spatial Frequency Scenes

People with dyslexia, who face lifelong struggles with reading, exhibit numerous associated low-level sensory deficits including deficits in focal attention. Countering this, studies have shown that struggling readers outperform typical readers in some visual tasks that integrate distributed information across an expanse. Though such abilities would be expected to facilitate scene memory, prior investigations using the contextual cueing paradigm failed to find corresponding advantages in dyslexia. We suggest that these studies were confounded by task-dependent effects exaggerating known focal attention deficits in dyslexia, and that, if natural scenes were used as the context, advantages would emerge. Here, we investigate this hypothesis by comparing college students with histories of severe lifelong reading difficulties (SR) and typical readers (TR) in contexts that vary attention load. We find no differences in contextual-cueing when spatial contexts are letter-like objects, or when contexts are natural scenes. However, the SR group significantly outperforms the TR group when contexts are low-pass filtered natural scenes [F(3, 39) = 3.15, p<. 05]. These findings suggest that perception or memory for low spatial frequency components in scenes is enhanced in dyslexia. These findings are important because they suggest strengths for spatial learning in a population otherwise impaired, carrying implications for the education and support of students who face challenges in school.
Mechanomyographic and electromyographic amplitude and frequency responses during fatiguing isokinetic muscle actions of the biceps brachii.

The purpose of this investigation was to examine the mechanomyographic (MMG) and electromyographic (EMG) amplitude and mean power frequency (MPF) patterns during fatiguing isokinetic muscle actions of the biceps brachii. Ten adults [three women (mean +/- SD age = 20 +/- 2 yrs) and seven men (mean +/- SD age = 23 +/- 3 yrs) ] volunteered to perform 50 consecutive maximal, concentric isokinetic muscle actions of the biceps brachii at 180 degrees x s(-1). The percent decline (mean +/- SD) in isokinetic peak torque (PT) was 70 +/- 17% and polynomial regression analyses indicated a cubic relationship (R2 = 0.994) between PT and repetition number. Both MMG amplitude and MMG MPF decreased linearly (r2 = 0. 774 and 0.238, respectively) across repetitions. The results for EMG amplitude demonstrated a cubic (R2 = 0.707) pattern across repetitions, where EMG amplitude increased during repetitions 1-20, remained stable during repetitions 20-40, and increased during repetitions 40-50. There was a quadratic (R2 = 0. 939) reduction in EMG MPF throughout the test. The decreases in MMG amplitude and MMG MPF may have been due to de-recruitment of fast fatiguing motor units, a reduction in muscular compliance, or the effects of "muscle wisdom. " The results for EMG amplitude may have reflected nonmaximal efforts by the subjects and/or peripheral fatigue. The factor(s) determining the decrease in EMG MPF are unclear, although a reduction in muscle fiber action potential conduction velocity may have been partially responsible.
1D inversion of multicomponent, multifrequency marine CSEM data: Methodology and synthetic studies for resolving thin resistive layers

Numerical methods for 1D forward modeling and inversion of marine controlled-source electromagnetic (CSEM) data are used to examine the inherent resolution of various acquisition configurations to thin resistive layers simulating offshore hydrocarbon reservoirs. Synthetic data studies indicate that jointly inverting frequencies of 0.1 and 1.0 Hz offers better resolution than inverting either frequency alone. Further increasing the bandwidth or density of frequencies does not produce a commensurate increase in resolution. An inline horizontal electric dipole is found to provide better resolution than either broadside or vertical electric dipoles. The horizontal electric and magnetic fields for any transmitter orientation have better resolution than vertical fields. Separate inversions of electric and magnetic fields perform equally well at recovering the reservoir, and there is no resolution improvement from jointly inverting both fields. Smooth inversion for a multiple resistive layer model detects the pr.