Miracle-dz/UniFAR-FTUs huggingface dataset:
FMRFamide-like peptides expand the behavioral repertoire of a densely connected nervous system

Significance Under environmental stress, animals can adopt different forms and behaviors through phenotypic plasticity. The roundworm Caenorhabditis elegans can exit reproductive growth and enter the stress-resistant dauer larval stage. We investigated phenotypic plasticity in a whole organism by comparing gene expression during dauer and reproductive development using RNA sequencing. As animals entered dauer, we observed striking up-regulation of neuronal signaling peptides, which promote the dauer-entry decision instead of reproductive growth. These neuropeptides also enable new behaviors in dauers for exploiting carrier animals for dispersal. Neuropeptides are similarly up-regulated in the infective, dauer-like stages of parasitic roundworms, indicating dauer as a strong model for studying parasitic behaviors. Our investigation reveals that neuropeptides can alter developmental decision-making and behavior in stressed C. elegans. Animals, including humans, can adapt to environmental stress through phenotypic plasticity. The free-living nematode Caenorhabditis elegans can adapt to harsh environments by undergoing a whole-animal change, involving exiting reproductive development and entering the stress-resistant dauer larval stage. The dauer is a dispersal stage with dauer-specific behaviors for finding and stowing onto carrier animals, but how dauers acquire these behaviors, despite having a physically limited nervous system of 302 neurons, is poorly understood. We compared dauer and reproductive development using whole-animal RNA sequencing at fine time points and at sufficient depth to measure transcriptional changes within single cells. We detected 8,042 genes differentially expressed during dauer and reproductive development and observed striking up-regulation of neuropeptide genes during dauer entry. We knocked down neuropeptide processing using sbt-1 mutants and demonstrate that neuropeptide signaling promotes the decision to enter dauer rather than reproductive development. We also demonstrate that during dauer neuropeptides modulate the dauer-specific nictation behavior (carrier animal-hitchhiking) and are necessary for switching from repulsion to CO2 (a carrier animal cue) in nondauers to CO2 attraction in dauers. We tested individual neuropeptides using CRISPR knockouts and existing strains and demonstrate that the combined effects of flp-10 and flp-17 mimic the effects of sbt-1 on nictation and CO2 attraction. Through meta-analysis, we discovered similar up-regulation of neuropeptides in the dauer-like infective juveniles of diverse parasitic nematodes, suggesting the antiparasitic target potential of SBT-1. Our findings reveal that, under stress, increased neuropeptide signaling in C. elegans enhances their decision-making accuracy and expands their behavioral repertoire.
P62/Ubiquitin IHC Expression Correlated with Clinicopathologic Parameters and Outcome in Gastrointestinal Carcinomas

P62 and ubiquitin are small regulatory proteins demonstrated to have implications in the prognosis and survival of various malignancies including: hepatocellular, breast, ovarian, and some gastrointestinal carcinomas. Several trials studied the link of their activity to the extrinsic apoptosis pathway and showed that their autophagy modification has a critical stand point in tumorigenesis. These findings explain their vital role in controlling the process of cell death and survival. It has been shown recently that p62 and ubiquitin overexpression in different types of cancers, such as triple negative breast and ovarian cancers, have directly correlated with incidence of distant metastases. We aim to evaluate p62/ubiquitin expression in gastrointestinal carcinomas of gastric, colonic, and pancreatic origin, and correlate with annotated clinicopathologic data. In gastric carcinoma (61), positive p62 nuclear expression was noted in 57% and cytoplasmic in 61%, while positive ubiquitin was nuclear expressed in 68.8%, and cytoplasmic in 29.5%. In colon carcinoma (45), positive p62 nuclear expression was noted in 29% and cytoplasmic in 71%, while positive ubiquitin was nuclear in 58% and cytoplasmic in 44%. In pancreatic cancer (18), positive p62 nuclear expression was noted in 78% and cytoplasmic in 56%, while positive ubiquitin was nuclear in 83% and cytoplasmic in 72%. Normal gastric (6), colon (4), and pancreatic (4) tissues were negative for both P62 and ubiquitin (nuclear and cytoplasmic staining <20%). Ubiquitin high expression was associated with more lymph node metastases in colon (4.14 vs 1.70, P = 0.04), and pancreatic adenocarcinomas (3.07 vs 0.33, P = 0.03). Also, ubiquitin high expression was associated with worse pancreatic adenocarcinoma overall survival (1.37 vs 2.26 mos, P = 0.04). In addition, gastric cancer patients with high p62 expression tend to have more poorly differentiated grade when compared to those with low expression (21 vs 17, P = 0.04) but less lymph node metastases (2.77 vs 5.73, P = 0.01). P62 and ubiquitin expression did not correlate with other clinicopathologic parameters in gastric, colon or pancreatic denocarcinomas. The results suggest that p62 and ubiquitin are highly expressed in gastric, colonic, and pancreatic carcinomas. High ubiquitin expression was noted to have an impact on number of lymph node metastases in patients with colon and pancreatic adenocarcinomas, but on overall survival only in patients with pancreatic adenocarcinoma. Also, P62 high expression is correlated with poor differentiation, but less lymph node metastases, in gastric carcinoma.
INTEGRATIVE TESTING OF HOW ENVIRONMENTS FROM THE PAST TO THE PRESENT SHAPE GENETIC STRUCTURE ACROSS LANDSCAPES

Tests of the genetic structure of empirical populations typically focus on the correlative relationships between population connectivity and geographic and/or environmental factors in landscape genetics. However, such tests may overlook or misidentify the impact of candidate factors on genetic structure, especially when connectivity patterns differ between past and present populations because of shifting environmental conditions over time. Here we account for the underlying demographic component of population connectivity associated with a temporarily dynamic landscape in tests of the factors structuring population genetic variation in an Australian lizard, Lerista lineopunctulata, from 24 nuclear loci. Correlative tests did not support significant effect from factors associated with a static contemporary landscape. However, spatially explicit demographic modeling of genetic differentiation shows that changes in environmental conditions (as estimated from paleoclimatic data) and corresponding distributional shifts from the past to present landscape significantly structures genetic variation. Results from model‐based inference (i.e., from an integrative modeling approach that generates spatially explicit expectations that are tested with approximate Bayesian computation) contrasts with those from correlative analyses, highlighting the importance of expanding the landscape genetic perspective to tests the links between pattern and process, revealing how factors shape patterns of genetic variation within species.
Low dose CT in early lung cancer diagnosis: Prevalence data.

PURPOSE Lung cancer has a high mortality rate and its prognosis largely depends on early detection. We report the prevalence data of the study on early detection of lung cancer with low-dose spiral CT underway at our hospital. MATERIALS AND METHODS Since the beginning of 2001, 519 asymptomatic volunteers have undergone annual blood tests, sputum tests, urinalyses and low-dose spiral CT. The inclusion criteria were age (=/> 55 years old), a history of cigarette smoking and a negative history for previous neoplastic disease. The diagnostic workup varied depending on the size and CT features of the nodules detected. RESULTS At baseline, the CT scan detected nodules > 5 mm in 22% of subjects; the nodules were single in 42 and multiple in 71. In 53% of cases the findings were completely negative, while in 122 (23.4%) nodules with a diameter < 5 mm were detected. Six cases of lung cancer were identified, of which four were stage I, one stage was IIIB and one was stage IV with adrenal metastases. CONCLUSIONS Our preliminary data on spiral CT as a potential new diagnostic tool for lung cancer screening, although less promising than the Japanese and ELCAP results, confirm the feasibility of the technique. Additional validation is, however, required.
Regular categories, oligomorphic monoids, and tensor categories

Knop constructed a tensor category associated to a finitely-powered regular category equipped with a degree function. In recent work with Harman, we constructed a tensor category associated to an oligomorphic group equipped with a measure. In this paper, we explain how Knop's approach fits into our theory. The first, and most important, step describes finitely-powered regular categories in terms of oligomorphic monoids; this may be of independent interest. We go on to examine some aspects of this construction when the regular category one starts with is the category of $G$-sets for an oligomorphic group $G$, which yields some interesting examples.
Students’ perceptions of foundation degrees

In 2008 there were 87,339 people enrolled on foundation degrees (FDs) in the UK (Foundation Degree Forward, 2009), and educational institutions in the UK offered 1700 different foundation degrees in over 25 subjects, with nearly 900 more in development (Action on Access, 2010). In addition, student views are seen to be of importance, as demonstrated by the National Student Survey and the notion of the student as consumer. This paper reports on a study of the views of students undertaking FDs in one university. A mixed-methods evaluation approach was used. Data were collected from students through questionnaires, interviews and focus groups. This was an ambitious project that yielded a vast amount and range of qualitative and quantitative data across multiple cohorts of seven different foundation degrees. Overall, students’ perceptions are positive, although some findings vary from one foundation degree to another. Across all subjects, students were agreed on their positive rating on five of the key elements of FDs. There was also agreement that employers did not, on the whole, value the foundation degree qualification. This paper presents the findings of this study and conclusions are drawn that add to the literature about FDs that will be of relevance to those involved in the development and delivery of FDs.
Reduced mirror neuron activity in schizophrenia and its association with theory of mind deficits: evidence from a transcranial magnetic stimulation study.

BACKGROUND The "mirror-neuron system" has been proposed to be a neurophysiological substrate for social cognition (SC) ability. We used transcranial magnetic stimulation (TMS) paradigms to compare putative mirror neuron activity (MNA) in 3 groups: antipsychotic-naive, medicated schizophrenia patients, and healthy comparison subjects. We also explored the association between MNA and SC ability in patients. METHODS Fifty-four consenting right-handed schizophrenia patients (33 antipsychotic naive) and 45 matched healthy comparison subjects completed a TMS experiment to assess putative premotor MNA. We used 4 TMS paradigms of eliciting motor-evoked potentials (MEP) in the right first dorsal interosseous (FDI) muscle. These were applied while the subjects observed a goal-directed action involving the FDI (actual action and its video) and a static image. The difference in the amplitude of the MEP while they observed the static image and the action provided a measure of MNA. Subjects also underwent SC assessments (theory of mind [ToM], emotion processing, and social perception). RESULTS Two-way repeated measures ANOVA revealed significant group × occasion interaction effect in 3 TMS paradigms, indicating deficient motor facilitation during action observation relative to rest state in antipsychotic-naive schizophrenia patients as compared with the other two groups. Among patients, there were significant direct correlations between measures of MNA and ToM performance. CONCLUSIONS Antipsychotic-naive schizophrenia patients have poorer MNA than medicated patients and healthy controls. Measures of putative MNA had significant and consistent associations with ToM abilities. These findings suggest a possibility of deficient mirror neuron system underlying SC deficits in schizophrenia.
Human Postcranial Variation in the Ukrainian Mesolithic-Neolithic

MEDINA LARA, F. , C. BARROSO RUIZ, J. L. SANCHIDRIAN TORTI, AND A. RUIZ BUSTOS. I987. "Avance al estudio de los niveles musterienses de la cueva del Boquete de Zafarraya, Alcaucin, Malaga (Excavaciones de I98I-83)," in Homenaje a L. Siret, pp. 94-105. Sevilla: Consejeria de Cultura. MORLAN, R. E. I984. Toward the definition of criteria for recognition of artificial bone alterations. Quaternary Research 22: I60-71. OBERMAIER, H. 1925. El hombre f6sil. Madrid: C.I. P.P. OLSEN, L. S. I988. On distinguishing natural from cultural damage on archaeological antler. Journal of Archaeological Science I6:125-35. OLSEN, L. S. , AND P. SHIPMAN. I988. Surface modification on bone: Trampling versus butchery. Journal of Archaeological Science 15:535-53. ORDIDGE, R. M. I985. The equine metacarpus. 2. The cannon bone. Veterinary Annual 25:192-200. PEI, W. C. 1938. Le r6le des animaux et des causes naturelles dans la cassure des os. Palaeontologia Sinica, n.s. , 7:I-I6. RUIZ BUSTOS, A. I984. El yacimento paleontol6gico de CullarBaza I. Investigaci6n y Ciencia 91:20-30. SADDEK-KOOROS, H. 1975. "Intentional fracturing of bone: Description of criteria," in Archaeozoological studies. Edited by A. T. Clason, pp. 139-50. Amsterdam: North Holland Publishing. SAENZ DE BURUAGA, A. S. I99I. Elpaleolitico superior de la cueva de Gatzarria. Zuberoa, Pais Vasco. Velea, Serie Mayor, 6. SHIPMAN, P. I98I. Applications of scanning electron microscopy to taphonomic problems. Annals of the New York Academy of Sciences 376:357-86. I988. "Actualistic studies of animal resources and hominid activities," in Scanning electron microscopy in archaeology. Edited by S. L. Olsen, pp. 26i-85. British Archaeological Reports International Series 452.
Fault Rupture Propagation through Sand: Finite-Element Analysis and Validation through Centrifuge Experiments

The three notorious earthquakes of 1999 in Turkey (Kocaeli and Duzce) and Taiwan (Chi-Chi), having offered numerous examples of surface fault rupturing underneath civil engineering structures, prompted increased interest in the subject. This paper develops a nonlinear finite-element methodology to study dip–slip (“normal” and “reverse”) fault rupture propagation through sand. The procedure is verified through successful Class A predictions of four centrifuge model tests. The validated methodology is then utilized in a parametric study of fault rupture propagation through sand. Emphasis is given to results of engineering significance, such as: (1) the location of fault outcropping; (2) the vertical displacement profile of the ground surface; and (3) the minimum fault offset at bedrock necessary for the rupture to reach the ground surface. The analysis shows that dip–slip faults refract at the soil–rock interface, initially increasing in dip. Normal faults may keep increasing their dip as they approach the .
Operationalising self-evaluation in schools: experiences from Ireland and Iceland

School inspection, school self-evaluation and the relationship between them are important themes in current educational policy debates. Many education systems are seeking to find a balance between the, at times, conflicting demands for a robust, transparent and effective system of school evaluation that at the same time allows for professional growth and development within schools. These tensions play out in different ways across different systems and this paper seeks to explore points of commonality and contrast between the Irish and Icelandic experience. The paper begins by reporting research in Ireland which demonstrates that while self-evaluation is theoretically a key component of the national system of school evaluation, in reality there is little sign of it emerging in any significant way in practice in schools. In contrast, research from Iceland is reported which shows that, after a slow beginning, self-evaluation in schools is now bearing fruit in a variety of ways. From these diverse experiences, some conclusions are drawn concerning the conditions under which self-evaluation can become embedded in education systems.
Evidence for morphological composition at the form level in speech production

We investigated in two picture–word-interference experiments whether there is evidence for composition during compound production (Experiment 1). In Experiment 2, we tried to determine the level at which composition takes place. In Experiment 1, shared morphemes between distractor and target (HANDTASCHE, handbag) sped up naming regardless of category membership: semantically opaque (Plaudertasche, chatterbox) and semantically transparent distractors (Reisetasche, travelling bag) facilitated picture naming to a comparable degree. In Experiment 2, targets (BROTMESSER, bread knife) were combined with a simple word distractor (Kuchen, cake) categorically related to a target compound constituent but not related to the compound as a whole. This target was further paired with a categorically related compound distractor (Kochlöffel, wooden spoon). The simple word distractor was also paired with a categorically related compound constituent (BROT, bread). Whenever distractor (e.g., Kochlöffel, Kuchen) and target (BROTMESSER, BROT, respectively) were categorically related, semantic inhibition was observed. Distractors (e.g., Kuchen) related to only one compound constituent did not affect compound production. Taken together, our results indicate that during compound production a single lemma node is activated and that morphological composition takes place at the form level of representation. Current lexical selection mechanisms in language production models are not supported by these data.
What is Happening to Satisfaction and Quality of Relationships Between Step/Grandparents and Step/Grandchildren?

Abstract The purpose of this study was twofold: (1) to explore factors regarding quality of relationships and satisfaction, across generations, in terms of gender and age; and (2) to understand the perspectives of both step/grandparents and step/grandchildren. In this study, young adult college students and their identified grandparents or stepgrandparents described their relationship in terms of satisfaction, companionship, instrumental aid, intimacy, nurturance, affection, admiration, reliable alliance, conflict, and antagonism. Within- and between-group comparisons were made regarding each of these relationship factors by gender and age. Grandparents reported having more satisfaction with cross-generational relationships than stepgrandparents or stepgrandchildren. Grandmothers reported receiving higher instrumental aid from grandchildren. Older grandparents and grandfathers reported having higher conflict with grandchildren. Emerging trends and areas of need for future research in grandparent-grandchild and stepgrandparent-stepgrandchild relationships were discussed.
Illness experience and occupations of people with chronic fatigue syndrome

Chronic fatigue syndrome affects people's physical and cognitive capacities for participation in their occupations, but has received limited consideration by occupational therapists. This qualitative study explores the illness experiences and occupations of five people living with chronic fatigue syndrome. Narrative data were collected using the Occupational Performance History Interview-II (OPHI-II). Key aspects of participants’ illness experiences, identified through thematic analysis, were: (i) experiencing and understanding chronic fatigue syndrome; (ii) experiencing different types of fatigue; (iii) ‘an ending and a beginning’; (iv) experiencing doing activities; and (v) doing something towards getting well. These findings reveal participants’ life stories, identities, relationships, and occupations had been dramatically altered. Their implication is that people living with this condition face issues, for which occupational therapy can be of assistance. The efficacy of interventions to enable them to adapt their occupations and rebuild their lives merits further research. The potential usefulness of OPHI-II for learning about how clients’ occupations are altered by chronic illness in research and practice is illustrated.
Multi-Agent Learning with Policy Prediction

Due to the non-stationary environment, learning in multi-agent systems is a challenging problem. This paper first introduces a new gradient-based learning algorithm, augmenting the basic gradient ascent approach with policy prediction. We prove that this augmentation results in a stronger notion of convergence than the basic gradient ascent, that is, strategies converge to a Nash equilibrium within a restricted class of iterated games. Motivated by this augmentation, we then propose a new practical multi-agent reinforcement learning (MARL) algorithm exploiting approximate policy prediction. Empirical results show that it converges faster and in a wider variety of situations than state-of-the-art MARL algorithms.
An Aesthetic (Deweyan) Perspective on Science Learning: Case Studies of Three Fourth Graders

After a critique of 2 popular and current perspectives on the nature of understanding in science education (learning as change in conceptual understanding and learning as change in discourse and participation with others), we offer our own competing perspective drawing from Dewey, aesthetics, and aesthetic experience. We believe complex learning is best viewed as a dialogic process between person, world, and socio-cultural context that ends in a rich network of knowledge combined with a deep appreciation for the beauty and power of subject matter that transform one's perceptions of the world and of her/himself as knower. We use our perspective, that of aesthetic understanding, as an analytic lens to critique and illuminate the learning of 3 students studying geology in a fourth-grade classroom.
Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities

The phytoplankton of the world's oceans play an integral part in global carbon cycling and food webs by conversion of carbon dioxide into organic carbon. They accomplish this task through the action of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Here we have investigated the phylogenetic diversity in the form I rbcL locus in natural phytoplankton communities of the open ocean and representative clones of marine autotrophic picoplankton by mRNA or DNA amplification and sequencing of a 480 to 483 bp internal fragment of this gene. Five gene sequences were recovered from nucleic acids of natural phytoplankton communities of the Gulf of Mexico. The rbcL genes of two Prochlorococcus isolates and one Synechococcus strain (WH8007) were also sequenced. Sequences were aligned with the database of rbcL genes and subjected to both neighbor-joining and parsimony analyses. The five sequences from the natural phytoplankton community spanned nearly the entire diversity of characterized form I rbcL genes, with some sequences closely related to isolates such as Synechococcus and Prochlorococcus (forms IA and I) and prymnesiophyte algae (form ID), while other sequences were deeply rooted. Unexpectedly, the deep euphotic zone contained an organism that possesses a transcriptionally active rbcL gene closely related to that of a recently characterized manganese-oxidizing bacterium, suggesting that such chemoautotrophs may contribute to the diversity of carbon-fixing organisms in the marine euphotic zone.