Miracle-dz/UniFAR-FTUs huggingface dataset:
Semaphorin Signaling in Vertebrate Neural Circuit Assembly

Neural circuit formation requires the coordination of many complex developmental processes. First, neurons project axons over long distances to find their final targets and then establish appropriate connectivity essential for the formation of neuronal circuitry. Growth cones, the leading edges of axons, navigate by interacting with a variety of attractive and repulsive axon guidance cues along their trajectories and at final target regions. In addition to guidance of axons, neuronal polarization, neuronal migration, and dendrite development must be precisely regulated during development to establish proper neural circuitry. Semaphorins consist of a large protein family, which includes secreted and cell surface proteins, and they play important roles in many steps of neural circuit formation. The major semaphorin receptors are plexins and neuropilins, however other receptors and co-receptors also mediate signaling by semaphorins. Upon semaphorin binding to their receptors, downstream signaling molecules transduce this event within cells to mediate further events, including alteration of microtubule and actin cytoskeletal dynamics. Here, I review recent studies on semaphorin signaling in vertebrate neural circuit assembly, with the goal of highlighting how this diverse family of cues and receptors imparts exquisite specificity to neural complex connectivity.
A roadmap for the genetic analysis of renal aging

Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age‐related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age‐associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high‐resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression.
Endothelin and endothelin converting enzyme-1 in the fish gill: evolutionary and physiological perspectives

SUMMARY In euryhaline fishes like the killifish (Fundulus heteroclitus) that experience daily fluctuations in environmental salinity, endothelin 1 (EDN1) may be an important regulator molecule necessary to maintain ion homeostasis. The purpose of this study was to determine if EDN1 and the endothelin converting enzyme (ECE1; the enzyme necessary for cleaving the precursor proendothelin-1 to EDN1) are present in the killifish, to determine if environmental salinity regulates their expression, and to examine the phylogenetic relationships among the EDNs and among the ECEs. We sequenced killifish gill cDNA for two EDN1 orthologues, EDN1A and EDN1B, and also sequenced a portion of ECE1 cDNA. EDN1A and ECE1 mRNA are expressed ubiquitously in the killifish while EDN1B mRNA has little expression in the killifish opercular epithelium or gill. Using in situ hybridization and immunohistochemistry, EDN1 was localized to large round cells adjacent to the mitochondrion-rich cells of the killifish gill, and to lamellar pillar cells. In the gill, EDN1A and EDN1B mRNA levels did not differ with acute (<24 h) or chronic (30 days) acclimation to seawater (SW); however, EDN1B levels increased threefold post SW to freshwater (FW) transfer, and ECE1 mRNA levels significantly increased twofold over this period. ECE1 mRNA levels also increased sixfold over 24 h post FW to SW transfer. Chronic exposure to SW or FW had little effect on ECE1 mRNA levels. Based upon our cellular localization studies, we modeled EDN1 expression in the fish gill and conclude that it is positioned to act as a paracrine regulator of gill functions in euryhaline fishes. It also may function as an autocrine on pillar cells, where it is hypothesized to regulate local blood flow in the lamellae. From our phylogenetic analyses, ECE is predicted to have an ancient origin and may be a generalist endoprotease in non-vertebrate organisms, while EDNs are vertebrate-specific peptides and may be key characters in vertebrate evolution.
Responding to the Challenges of a Contemplative Curriculum

The undergraduate Psychology program at John F. Kennedy University in Pleasant Hill, California, is one of a small number of undergraduate programs that offer a holistic, transformative, and integrative approach to psychology. One important dimension of the program’s educational approach is the use of contemplative practices in the classroom. Drawing on the teaching experiences of four experienced faculty members, the author discusses the multiple educational purposes that contemplative pedagogies serve as well as the various strategies used to introduce and integrate these transformational pedagogies into the classroom. The author also discusses ways to maintain students’ psychological safety, ensure instructors’ contemplative competence, and maintain the separation of church and state.
Shared Genomics: High Performance Computing for distributed insights in genomic medical research

The study of the genetics of diseases is entering a new era. Increasingly, genome-wide association studies are being used to identify positions within the human genome that have a link with a disease condition. The number of genomic locations studied means that High Performance Computing (HPC) solutions will have to increasingly be used in the statistical analysis of these data sets. Understanding the biomedical implications of the statistical analysis will also require heavy use of bioinformatics annotation tools. In this paper we report the outcome of developing HPC statistical genetics analysis codes for use by clinical researchers. Statistical results are automatically annotated with relevant biological information by calling multiple web-services orchestrated via pre-existing scientific workflows. Access to the HPC codes and bioinformatics annotation processes is via a client Workbench which hides as much as possible from the user the HPC infrastructure and bioinformatics annotation processes, whilst aiding the exchange of ideas and results between stakeholders.
Enhanced photocoagulation with catheter-based diffusing optical device

Abstract. A novel balloon catheter-based diffusing optical device was designed and evaluated to assist in treating excessive menstrual bleeding. A synthetic fused-silica fiber was micro-machined precisely to create scattering segments on a 25 mm long fiber tip for uniform light distribution. A visible wavelength (λ=532 nm) was used to specifically target the endometrium due to the high vascularity of the uterine wall. Optical simulation presented 30% wider distribution of photons along with approximately 40% higher irradiance induced by addition of a glass cap to the diffuser tip. Incorporation of the optical diffuser with a polyurethane balloon catheter considerably enhanced coagulation depth and area (i.e., 3.5 mm and 18.9 cm2 at 1 min irradiation) in tissue in vitro. The prototype device demonstrated the coagulation necrosis of 2.8±1.2 mm (n=18) and no thermal damage to myometrium in in vivo caprine models. A prototype 5 cm long balloon catheter-assisted optical diffuser was also evaluated with a cadaveric human uterus to confirm the coagulative response of the uterine tissue as well as to identify the further design improvement and clinical applicability. The proposed catheter-based diffusing optical device can be a feasible therapeutic tool to photocoagulate endometrial cell layers in an efficient and safe manner.
Rudimentary pedal grasping in mice and implications for terminal branch arboreal quadrupedalism

We use an outbred laboratory mouse strain (ICR/CD‐1, Charles River Laboratories, Inc.) to model a type of preprimate locomotion associated with rudimentary pedal grasping. Ten male mice were assigned to either control or climbing groups (n = 5 per group). Climbing mice lived within a specialized terrarium that included ∼7.5 m of thin branches (5 and 10 cm long) with a thickness of 3.3mm, arranged in a reticulated canopy. Food, water, and a nest site were placed among the branches. To discourage mice from palmigrade or digitigrade locomotion, the floor of the terrarium was flooded with a few centimeters of water. Climbing mice were placed in this setting upon weaning and reared for 3 months until they were mature in size. Litter, and age‐matched controls were also maintained for comparison with climbers. Climbing mice quickly acclimated to the requirements of the fine‐branch model using the foot and tail for grasping and balance. At maturity, climbing and control mice exhibited minor, but significant, morphological plasticity. For climbers, this includes a greater angle of the femoral neck, larger patellar groove index, relatively shorter talar neck length, and more circular talar head aspect ratio (P < 0.10). Climbers also exhibit increased curvature of the distal third metacarpal, decreased talar head angle, and relatively longer caudal vertebrae transverse processes (P < 0.05). These results in a small‐bodied eutherian mammal suggest that facultative hallucial opposability and coordinated tail use enable a kind of grasping active arboreal quadrupedality relevant to the latest stages of pre‐euarchontan evolution. In light of these data, we hypothesize that a unique advantage of mouse‐sized mammals is that they exhibit a highly flexible body plan allowing them to engage in a diverse array of anatomical positions without requiring specific limb morphologies. J. Morphol. ,2011. © 2010 Wiley‐Liss, Inc.
The Effects of Metacognitive Writing on Student Achievement in Advanced Placement(RTM) Calculus

The Effects of Metacognitive Writing on Student Achievement in Advanced Placement Calculus by Lindsay M. O’Neal Chairperson of the Dissertation Committee: Dr. Andrew Lumpe, School of Education Grounded in metacognitive theory (Flavell, 1976) and historical foundations that reach back as far as the writings of Plato (1973), the last few decades have seen an increase in research regarding the impact of metacognitive practice on student learning, often through the use of reflective writing. Studies have focused on a range of aspects, from how to measure metacognition to the effect metacognitive practice has on the academic achievement of students in a variety of subject areas. Specifically with regard to mathematics, researchers have studied the impact of reflective strategies on primary, secondary, and university level students. The purpose of this study was to explore the impact of reflective writing practice on the achievement of Advanced Placement (AP) Calculus students in a comprehensive high school setting. This quasi-experimental study utilized a pretest-posttest control group design, with nonrandom assignment of students to the control and experimental groups. The independent variable was the use of reflective writing prompts, completed only by the experimental group. The non-calculator multiple choice portion of released AP Calculus AB examinations served as the dependent variable. Descriptive statistics were evaluated to determine if the data met the requirements for parametric analyses. Analysis of covariance was completed to analyze the data for statistically significant differences between the groups. In addition, theme extraction was carried out using Semantria® text analysis software to examine common themes within the reflective student writings as well as Sentiment values for those themes. Finally, Pearson’s r correlation coefficient was calculated to determine any correlation between number of extracted themes and posttest score. The ANCOVA revealed a statistically significant difference between the groups, but with the control group maintaining a higher mean than that of the experimental group. Common themes in the reflective writing included a variety of calculus concepts addressed during the timeframe of the study. A statistically significant correlation was found between the number of extracted themes and student’s score on the posttest.
A Multiple Rule Engine-Based Agent Control Architecture

This paper introduces a multiple rule engine agent architecture intended for prototyping heterogeneous agents. It also briefly describes how this same architecture might be used for concurrent and hierarchical goal processing. The proposed framework has an embedded main rule engine supporting goal processing as well as providing high level decision and control for the agent. It also possesses a mechanism for dynamically spawning rule engine-based agent behaviours (using separate rule engines) to process subgoals, and it maintains information/status communication channels between the main rule engine and the rule-based agent behaviours. The agent together with its agent behaviours are all realized in a similar manner. Each embedded rule engine has the ability to configure multiple agent behaviours either in parallel or hierarchically. In addition, this approach allows the construction of reuseable, rule-based agent capabilities that can easily be composed and layered to achieve a specific, application-oriented composite capability.
Statuses, Roles, and the Sense of Mattering

Individuals with a sense of mattering perceive they are acknowledged and relevant in the lives of other people. Using data from a representative sample of adults age eighteen to fifty-five from Toronto, Canada, who are employed in the paid labor force, we examine the effects of statuses, roles, and occupational conditions on mattering. Being female, having children, and holding jobs with more autonomy, complexity, fulfillment, and supervision duties enriches the conviction of mattering. Relationship and parental strains are related negatively to mattering, which conceals the positive effects of spousal-partner and parental roles. Results show gender-contingent effects: women in our sample derive greater benefits for mattering from education, but they also are affected more negatively by work-to-home conflict. Conversely, in our findings, men gain more from having children and being involved in a relationship, but they are also affected more negatively by relationship strains. Other results show that the positive relationship of age with job autonomy and complexity suppresses its negative association with mattering. Collectively, these results add to knowledge about the social-structural influences on the self-concept.
A generic framework for machine transliteration

Machine Transliteration deals with the conversion of text strings from one orthography to another, while preserving the phonetics of the strings in the two languages. Transliteration is an important problem in machine translation or crosslingual information retrieval, as most proper names and generic iconic terms are out-of-vocabulary words, and therefore need to be transliterated. There are numerous methods explored in the literature for machine transliteration, ranging from rule-based techniques to statistical learning techniques. Here we focus our attention on language-independent techniques that potentially can scale well with a large number of languages. In this paper, we present a modular, statistical learning framework that lends itself for easy experimentation with transliteration tasks between a variety of different languages, in a language-independent manner. The workbench includes a variety of components – algorithms, data-sets and transliterations scripts – for a quick assembly of an effective transliteration system across langauges. We believe that such workbenches would be important in an increasingly multilingual world, for building systems that span a number of languages, quickly and effectively.
School Counselors' Constructions of Student Confidentiality.

Confidentiality in counseling relationships helps ensure trust between clients and counselors. Yet, defining and understanding the boundaries of confidentiality in school settings is often difficult, as school counselors are engaged in multiple relationships with various stakeholders. This qualitative phenomenological study explores the experiences of nine practicing school counselors to answer the following two research questions: 1) how do professional school counselors respond to ethical issues related to student confidentiality as they perform their responsibilities within the school community? And, 2) how do school counselors believe members of the school community perceive student confidentiality? Upon analysis, two main themes emerged from participants’ narratives: relationships and training. Subthemes were also present for each of the two main themes. Under relationships, subthemes include trust, school culture, teamwork and consultation. Under training, subthemes of graduate training, professional development, and experience emerged. Implications for counselor educators and school counseling graduate programs are discussed.
Topical Polyethylene Glycol as a Novel Chemopreventive Agent for Oral Cancer via Targeting of Epidermal Growth Factor Response

Head and neck squamous cell carcinoma (HNSCC) is a major cause of morbidity and mortality underscoring the need for safe and effective chemopreventive strategies. Targeting epidermal growth factor receptor (EGFR) is attractive in that it is an early critical event in HNSCC pathogenesis. However, current agents lack efficacy or have unacceptable toxicity. Several groups have demonstrated that the over-the-counter medication, polyethylene glycol (PEG) has remarkable chemopreventive efficacy against colon carcinogenesis. Importantly, we reported that this effect is mediated through EGFR internalization/degradation. In the current study, we investigated the chemopreventive efficacy of this agent against HNSCC, using both the well validated animal model 4-NQO (4-nitroquinoline 1-oxide) rat model and cell culture with the human HNSCC cell line SCC-25. We demonstrated that daily topical application of 10% PEG-8000 in the oral cavity (tongue and cavity wall) post 4NQO initiation resulted in a significant reduction in tumor burden (both, tumor size and tumors/tumor bearing rat) without any evidence of toxicity. Immunohistochemical studies depicted decreased proliferation (number of Ki67-positive cells) and reduced expression of EGFR and its downstream effectors cyclin D1 in the tongue mucosa of 4NQO-rats treated with PEG. We showed that EGFR was also markedly downregulated in SCC-25 cells by PEG-8000 with a concomitant induction of G1-S phase cell-cycle arrest, which was potentially mediated through upregulated p21cip1/waf1. In conclusion, we demonstrate, for the first time, that PEG has promising efficacy and safety as a chemopreventive efficacy against oral carcinogenesis.
power, resistance, and the cult of Muslim saints in a northern Egyptian town

Practice theory is employed to analyze the cult of Muslim saints. Unlike much of the previous work by anthropologists on this topic, the present study has an urban, rather than rural and tribal, ethnographic locus. A major finding is that privileged as well as nonprivileged individuals use the cult for ideological discourse and dramaturgy. This has seminal implications for understanding the relation of power to resistance. An unobtrusive form of power that does not inspire resistance appears to match Bourdieu's concept of “symbolic power. ” In contrast with the Weberian and Marxist zero-sum views of power, symbolic power appears to be a positive-sum phenomenon. [power, resistance, discourse, practice theory, Muslim saint cult, urban Egypt]
Co-Scheduling Algorithms for Cache-Partitioned Systems

Cache-partitioned architectures allow subsections of the shared last-level cache (LLC) to be exclusively reserved for some applications. This technique dramatically limits interactions between applications that are concurrently executing on a multicore machine. Consider n applications that execute concurrently, with the objective to minimize the makespan, defined as the maximum completion time of the n applications. Key scheduling questions are: (i) which proportion of cache and (ii) how many processors should be given to each application? Here, we assign rational numbers of processors to each application, since they can be shared across applications through multi-threading. In this paper, we provide answers to (i) and (ii) for perfectly parallel applications. Even though the problem is shown to be NP-complete, we give key elements to determine the subset of applications that should share the LLC (while remaining ones only use their smaller private cache). Building upon these results, we design efficient heuristics for general applications. Extensive simulations demonstrate the usefulness of co-scheduling when our efficient cache partitioning strategies are deployed.
The changing significance of different stressors after the announcement of bankruptcy: A longitudinal investigation with special emphasis on job insecurity.

The author investigates the effect of job insecurity and other job stressors on the mental health of steel workers. Levels of job stress and mental health were measured seven years before and seven months after the company at which they worked had gone into receivership, a method that can be described as a quasi-experimental field study with a sample of blue-collar non-supervisory male workers. Two out of four job stressors were found to be at a lower level when the second wave of research took place. Regression analyses showed that the correlation between these job stressors and psychosomatic complaints is now lower than during the first wave but that they reach the former level when job insecurity is added. Job insecurity was mainly connected to an increase in psychosomatic complaints and in anxiety. Self-esteem, depression, and irascibility showed no important relationship to job insecurity when the variables were controlled for mental health status before the onset of job insecurity. Social support, opportunities in the labor market, and duration of contract in the company are identified as moderating the relation between mental health and job insecurity. One conclusion is that positive health effects due to reduction in the stress level may be offset by acute job insecurity. Copyright © 2000 John Wiley & Sons, Ltd.