Miracle-dz/UniFAR-FTUs huggingface dataset:
Segmentation of Overlapping Chromosome Images Using Computational Geometry

Current systems for automatic chromosome classification are interactive and require human intervention for correct separation between touching and overlapping chromosomes. Special separation methods are required to segregate chromosomes because they are non-rigid objects. This study develops a new technique to separate overlapping chromosomes based on computational geometry. This technique requires the identification of all possible cut points from the contour line of overlapping chromosomes, using Voronoi diagrams and Delaunay triangulations to select the four target cut points and cut overlapping chromosomes into two chromosomes. We test our algorithm on 35 overlapping chromosome images and find that 28 out of 35 overlapping chromosomes images can be separated correctly (i.e. 80.0 %). Three out of the 35 images are separate incorrectly (i.e. 8.6 %) and four out of 35 images are not separable by our algorithm (i.e. 11.4 %).
Cip/Kip cyclin‐dependent kinase inhibitors: brakes of the cell cycle engine during development

Precise control of cell‐cycle progression is believed to be critical for normal development, while oncogenesis may be a direct result of its disturbance. Cell‐cycle progression is regulated predominantly by a series of serine/threonine kinases, the cyclin‐dependent kinases (CDKs). The activities of the CDKs are controlled by a variety of mechanisms, and a group of molecules that inhibit CDK activity, CDK inhibitors (CKIs), has recently become the focus of interest, particularly in the fields of development and tumorigenesis. To date, seven CKIs have been identified in mammals and categorized into two families, the Cip/Kip and Ink4 families. The Cip/Kip family is well conserved phylogenetically, suggesting that it is biologically important. Despite the structural and biochemical similarities among the Cip/Kip members, the phenotypes of knockout mice of each Cip/Kip member are surprisingly different, which suggests that the Cip/Kip CKIs have a variety of physiological functions. In this review, the biological roles of Cip/Kip CKIs in development and tumor suppression are discussed. BioEssays 20:1020–1029, 1998. © 1998 John Wiley & Sons, Inc.
Should Instructors Require Discussion in Online Courses? Effects of Online Discussion on Community of Inquiry, Learner Time, Satisfaction, and Achievement.

Online discussion is a commonly used means to promote student understanding of a topic and to facilitate social interaction among students or between students and instructor; however, its effects on student learning in online learning environments have rarely been investigated. The purpose of this study was to examine the role of online discussion in student learning experiences measured with community of inquiry, learner time, satisfaction, and achievement. One instructor taught the same online course for three consecutive semesters using three different conditions. During one semester enrolled students engaged in no discussion, during another semester they engaged in discussion without instructor participation, and in the remaining semester they engaged in discussion with active instructor participation. No significant differences were found among conditions in cognitive presence and the instructor’s teaching presence, whereas significant difference was found in social presence among conditions. No significant differences among conditions were found time spent on Blackboard, course satisfaction, and student achievement. Implications for online teaching and learning as well as for designing an online course conclude the paper.
Cytokines in stored red blood cell concentrates: promoters of systemic inflammation and simulators of acute transfusion reactions?

Background: The cytokine network has important implications for the systemic inflammatory and metabolic response in trauma and infection. Cytokines exogenously administered to traumatized and infected patients may have implications for the trauma response in these patients. The main objective of this study was to characterize red blood cell concentrates (RBCs) with regard to cytokine content.
Protein O-Mannosyltransferases Associate with the Translocon to Modify Translocating Polypeptide Chains*

Background: O-Mannosylation is a conserved, essential protein modification that is initiated in the endoplasmic reticulum (ER). Results: Protein O-mannosyltransferases act at the translocon complex to modify proteins entering the ER. Conclusion: Protein translocation into the ER, O-mannosylation, and N-glycosylation are coordinated processes. Significance: Defining the mechanism of O-mannosylation is crucial to understand its diverse physiological roles for ER homeostasis. O-Mannosylation and N-glycosylation are essential protein modifications that are initiated in the endoplasmic reticulum (ER). Protein translocation across the ER membrane and N-glycosylation are highly coordinated processes that take place at the translocon-oligosaccharyltransferase (OST) complex. In analogy, it was assumed that protein O-mannosyltransferases (PMTs) also act at the translocon, however, in recent years it turned out that prolonged ER residence allows O-mannosylation of un-/misfolded proteins or slow folding intermediates by Pmt1-Pmt2 complexes. Here, we reinvestigate protein O-mannosylation in the context of protein translocation. We demonstrate the association of Pmt1-Pmt2 with the OST, the trimeric Sec61, and the tetrameric Sec63 complex in vivo by co-immunoprecipitation. The coordinated interplay between PMTs and OST in vivo is further shown by a comprehensive mass spectrometry-based analysis of N-glycosylation site occupancy in pmtΔ mutants. In addition, we established a microsomal translation/translocation/O-mannosylation system. Using the serine/threonine-rich cell wall protein Ccw5 as a model, we show that PMTs efficiently mannosylate proteins during their translocation into microsomes. This in vitro system will help to unravel mechanistic differences between co- and post-translocational O-mannosylation.
Protection of bone marrow mesenchymal stem cells from acute lung injury induced by paraquat poisoning

Objective. To examine the protective effect of bone marrow mesenchymal stem cell (BMSC) transplantation against lung injury induced by paraquat (PQ) poisoning. Materials and methods. Fifty-four female SD rats were randomly divided into four groups: a PQ group, a BMSC treatment group, a BMSC control group, and a normal control group. BMSC, isolated and cultured in vitro, were injected into the tail veins of the rats. The mortality rate, the ratio of lung wet/dry weight, plasma levels of IL-1β, tumor necrosis factor-α (TNF-α), malonaldehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), and NF-κBp65 expression in the lung tissues were examined during 14 days after injection. Results. Survival in the PQ group ranged from 8 to 12 days, with an average of 9.6 days. All the rats in the BMSC treatment group survived for more than 14 days. In the BMSC treatment group, the ratio of lung wet /dry weight (P = 0.02 < 0.05), plasma IL-1β and TNF-α levels (P = 0.00 < 0.01), MDA levels (P = 0.03 < 0.05), and expression of NF-κBp65 in the lung tissues (P = 0.00 < 0.01) were significantly lower than those in the PQ group by day 7 post-injection. However, the SOD and GSH-PX levels began to increase (P = 0.00 < 0.01) compared with the PQ group. There was no significant difference between the BMSC control group and the normal control group (P > 0.01). Discussion and conclusion. BMSC transplantation may have the potential to protect against PQ-induced lung injury, by reducing lung edema and lipid peroxidation, inhibiting the release of inflammatory mediators. However, the protective effects require time to develop, and early BMSC transplantation may be more evident during the middle and late stages of therapy.
UFO: Unified convex optimization algorithms for fixed-outline floorplanning

In this paper, we apply two convex optimization methods, named UFO, for fixed-outline floorplanning. Our approach consists of two stages which are a global distribution stage and a local legalization stage. In the first stage, we first transform modules into circles and use a pull-push model to distribute modules among a fixed outline under the wirelength consideration. Because good results can be obtained after the first stage, we do not need to consider wirelegnth in the second stage; thus, we can devote to legalize modules. To keep the good results of the first stage, we propose a procedure to extract the geometric relations of modules from a layout and record them by constraint graphs. Then, a quadratic function as well as non-overlap and boundary constraints are formulated to determine the locations and shapes of modules. We have implemented the two convex functions on Matlab, and experimental results have demonstrated that UFO clearly outperforms the results reported in the literature on the GSRC benchmark.
Experimenter audience effects on young adults' facial expressions during pain.

Facial expression has been used as a measure of pain in clinical and experimental studies. The Sociocommunications Model of Pain (T. Hadjistavropoulos, K. Craig, & S. Fuchs-Lacelle, 2004) characterizes facial movements during pain as both expressions of inner experience and communications to other people that must be considered in the social contexts in which they occur. While research demonstrates that specific facial movements may be outward manifestations of pain states, less attention has been paid to the extent to which contextual factors influence facial movements during pain. Experimenters are an inevitable feature of research studies on facial expression during pain and study of their social impact is merited. The purpose of the present study was to investigate the effect of experimenter presence on participants’ facial expressions during pain. Healthy young adults (60 males, 60 females) underwent painful stimulation induced by a cold pressor in three social contexts: alone; alone with knowledge of an experimenter watching through a one-way mirror; and face-to-face with an experimenter. Participants provided verbal self-report ratings of pain. Facial behaviours during pain were coded with the Facial Action Coding System (P. Ekman, W. Friesen, & J. Hager, 2002) and rated by naïve judges. Participants’ facial expressions of pain varied with the context of the pain experience condition but not with verbally self-reported levels of pain. Participants who were alone were more likely to display facial actions typically associated with pain than participants who were being observed by an experimenter who was in another room or sitting across from them. Naïve judges appeared to be influenced by these facial expressions as, on average, they rated the participants who were alone as experiencing more pain than those who were observed. Facial expressions shown by people experiencing pain can communicate the fact that they are feeling pain. However, facial expressions can be influenced by factors in the social
Regulatory T Cells Dampen Pulmonary Inflammation and Lung Injury in an Animal Model of Pneumocystis Pneumonia1

CD4+CD25+FoxP3+ regulatory T cells are decreased in patients infected with HIV and have been shown to be critical in mediating Ag tolerance in the lung. Because a subset of Pneumocystis-infected individuals develop substantial lung injury, which can be modeled in immune reconstituted scid mice, we used mouse models of Pneumocystis carinii to investigate the role of regulatory T cells in opportunistic infection and immune reconstitution. In this study, we show that CD4+CD25+FoxP3+ cells are part of the host response to Pneumocystis in CD4+ T cell-intact mice. Moreover, lung injury and proinflammatory Th1 and Th2 cytokine levels in the bronchoalveolar lavage fluid and lung homogenate were increased following CD4+CD25− immune reconstitution in Pneumocystis-infected SCID mice but not in CD4+CD25+ T cell-reconstituted animals. The ability of CD4+CD25+ T cells to control inflammation and injury during the course of Pneumocystis was confirmed by treatment of wild-type C57BL/6 mice with anti-CD25 mAb. These data show that CD4+CD25+ T cells control pulmonary inflammation and lung injury associated with Pneumocystis infection both in the setting of immune reconstitution as well as new acquisition of infection.
Similarity in Semantic Graphs: Combining Structural, Literal, and Ontology-based Measures

Semantic graphs provide a valuable way to represent data while preserving real world meaning. As these graphs become more popular for storing large quantities of data, it is important to have methods of determining similarity between nodes in the graph. This paper extends previous structural similarity algorithms by taking advantage of meaning contained in a graph’s literals and the graph’s ontology and allowing users to control how much each type of similarity effects overall scores. Preliminary tests indicate that including these sources of similarity increases scores in way that is better aligned with human intuition.
Men1-dependent Increase in RPeD1 Excitability is Required for Long Term Memory Consolidation after Aversive Operant Conditioning in Lymnaea stagnalis.

Long term memory (LTM) formation is a complex process involving signalling cascades, new protein synthesis and gene regulation. Increasing evidence demonstrates a role of intrinsic plasticity in memory formation, but the underlying molecular mechanisms remain relatively unknown. LTM was established using an aversive operant conditioning model in Lymnaea stagnalis. Using intracellular electrophysiology in an isolated preparation, increased gain of firing frequency was observed in the RPeD1 neuron after LTM. This provides the first demonstration of intrinsic plasticity after operant conditioning in RPeD1, a neuron required for the conditioned behaviour and LTM. I also determined the contribution of the transcription factor men1 to plasticity. Using in vivo RNAi silencing, I found that men1 is required for LTM and increasing RPeD1 excitability during consolidation, demonstrating men1-mediated intrinsic plasticity is critical for LTM. I propose a new model of memory formation in which men1dependent increase of excitability during consolidation is required for LTM.
Cyanidin-3-O-Glucoside Enhanced the Function of Syngeneic Mouse Islets Transplanted Under the Kidney Capsule or Into the Portal Vein

Background It was previously shown that islets are susceptible to oxidative stress due to their inherent low antioxidant capacity. Therefore, in this study, we determined whether treatment of mouse islets with an antioxidant cyanidin-3-O-glucoside (C3G) could enhance their function after transplantation under the kidney capsule or into the portal vein. Methods B6 mouse islets were treated with various concentrations of C3G, their viability, and the expression of antioxidant (HO-1) and antiapoptotic (Bcl-2 and Survivin) genes were determined. The C3G-treated (1.0 &mgr;M) or untreated B6 mouse islets (100, 200, and 400 IEQ) were transplanted under the kidney capsule or into the portal vein of diabetic B6 mice, and their blood glucose levels were monitored for more than 100 days after transplantation. Results The C3G-treated islets showed higher cell viability compared to untreated control and the expression of HO-1; Bcl-2 and Survivin genes were enhanced in a concentration-dependent manner. All mice that were transplanted with C3G-treated islets achieved normoglycemia faster than recipients of untreated islets. Mice that received 400, 200, or 100 treated islets transplanted under the kidney capsule achieved normoglycemia, whereas only mice that were transplanted with 400 and 200 treated islets into the portal vein achieved normoglycemia. The mean blood glucose levels of mice that received C3G-treated islets were lower compared to those observed in mouse recipients of untreated islets transplanted under the kidney capsule or into the portal vein. Conclusions Our results show that C3G could enhance the viability of mouse islets and improve their function after transplantation.
Random replicators with asymmetric couplings

Systems of interacting random replicators are studied using generating functional techniques. While replica analyses of such models are limited to systems with symmetric couplings, dynamical approaches as presented here allow us specifically to address cases with asymmetric interactions where there is no Lyapunov function governing the dynamics. We focus on replicator models with Gaussian couplings of general symmetry between p ≥ 2 species, and discuss how an effective description of the dynamics can be derived in terms of a single-species process. Upon making a fixed point ansatz persistent order parameters in the ergodic stationary states can be extracted from this process, and different types of phase transitions can be identified and related to each other. We discuss the effects of asymmetry in the couplings on the order parameters and the phase behaviour for p = 2 and p = 3. Numerical simulations verify our theory. For the case of cubic interactions, numerical experiments indicate regimes in which only a finite number of species survives, even when the thermodynamic limit is considered.
Life events and senile dementia. I. Admission, deterioration and social environment change

Synopsis This study examines the frequency of life events before admission and before deterioration in 70 dementia patients, in comparison with 50 dementia controls living in the community and 50 fit elderly people matched for age and sex. We hypothesized that there would be an excess of events connoting changes in routine and the social environment. Specific scales were developed to measure these aspects of events. Our results supported the initial hypothesis, confirming that it is the social disruptiveness of change rather than the threat implied by life events that is associated with deterioration. The findings are discussed in the light of current models of the dementia process.
The Snow Must Go On: Ground Ice Encasement, Snow Compaction and Absence of Snow Differently Cause Soil Hypoxia, CO2 Accumulation and Tree Seedling Damage in Boreal Forest

At high latitudes, the climate has warmed at twice the rate of the global average with most changes observed in autumn, winter and spring. Increasing winter temperatures and wide temperature fluctuations are leading to more frequent rain-on-snow events and freeze-thaw cycles causing snow compaction and formation of ice layers in the snowpack, thus creating ice encasement (IE). By decreasing the snowpack insulation capacity and restricting soil-atmosphere gas exchange, modification of the snow properties may lead to colder soil but also to hypoxia and accumulation of trace gases in the subnivean environment. To test the effects of these overwintering conditions changes on plant winter survival and growth, we established a snow manipulation experiment in a coniferous forest in Northern Finland with Norway spruce and Scots pine seedlings. In addition to ambient conditions and prevention of IE, we applied three snow manipulation levels: IE created by artificial rain-on-snow events, snow compaction and complete snow removal. Snow removal led to deeper soil frost during winter, but no clear effect of IE or snow compaction done in early winter was observed on soil temperature. Hypoxia and accumulation of CO2 were highest in the IE plots but, more importantly, the duration of CO2 concentration above 5% was 17 days in IE plots compared to 0 days in ambient plots. IE was the most damaging winter condition for both species, decreasing the proportion of healthy seedlings by 47% for spruce and 76% for pine compared to ambient conditions. Seedlings in all three treatments tended to grow less than seedlings in ambient conditions but only IE had a significant effect on spruce growth. Our results demonstrate a negative impact of winter climate change on boreal forest regeneration and productivity. Changing snow conditions may thus partially mitigate the positive effect of increasing growing season temperatures on boreal forest productivity.
The systematic position and structure of the genus Leyogonimus Ginetsinskaya, 1948 (Platyhelminthes: Digenea) with comments on the taxonomy of the superfamily Microphalloidea Ward, 1901

The systematic position, phylogenetic relationships and composition of the genus Leyogonimus Ginetsinskaya, 1948 have always been uncertain. In the present study, we investigate the taxonomic position and phylogenetic relationships between the type-species L. polyoon (Linstow, 1887) and L. postgonoporus (Neiland, 1951) (previously classified as Macyella), based on newly obtained partial sequences of the nuclear large ribosomal subunit DNA. To test some of the previously proposed systematic arrangements, we have also sequenced specimens of Stomylotrema vicarium Braun, 1901 and Phaneropsolus sp. Our results clearly demonstrate that both L. polyoon and L. postgonoporus belong to the family Pleurogenidae Looss, 1899 within the superfamily Microphalloidea. Thus, the Leyogonimidae Dollfus, 1951 should be recognized as a synonym of the Pleurogenidae. Leyogonimus polyoon clearly constitutes a separate, sister branch to the clade consisting of Collyricloides massanae Vaucher, 1969 and L. postgonoporus. Based on these results, we resurrect the genus Macyella Neiland, 1951 with type-species M. postgonoporus. Besides, Collyricloides Vaucher, 1968 is synonymized with Macyella resulting in new combination Macyella massanae (Vaucher, 1968) comb. nov. Molecular phylogenetic analysis has demonstrated the lack of a close phylogenetic relationships between Stomylotema vicarium and Leyogonimus previously placed by several authors into the family Stomylotrematidae Poche, 1925. The status of the Phaneropsolidae Mehra, 1935 as independent family was confirmed with the addition of the newly sequenced Phaneropsolus sp. from China.
Community-based participatory research with Mexican migrants in a new rural destination: A good fit?

In this article, we offer our reflections on our community-based participatory research (CBPR) project in partnership with Mexican migrants in a new rural destination of the Rocky Mountain West. To set the stage for our work, we first present the Montana migration context – a unique context in which the migrant community is hard to define, locate, and engage. Next, we present who we are and how we forged a partnership with Mexican migrants in Montana. We then provide the details of our project – Salud y Comunidad: Latinos en Montana – and reflect on the pragmatic and ethical challenges of using a CBPR approach in this context. Finally, we attempt to reframe some of the tensions and paradoxes inherent in community-based work with vulnerable communities and reflect on the question, ‘is CBPR a good fit? ’ We aim for our analysis to contribute a unique perspective to the rich discussions underway about using CBPR to ameliorate health disparities and promote justice in marginalized communities.