Miracle-dz/UniFAR-FTUs huggingface dataset:
Bill Shape and Sexual Shape Dimorphism between Two Species of Temperate Hummingbirds: Black-Chinned Hummingbird (Archilochus alexandri) and Ruby-Throated Hummingbird (A. Colubris)

ABSTRACT. Sexual size dimorphism occurs throughout the animal kingdom, and its ecological and evolutionary causes and implications have been intensively studied. Sex-specific differences in bill curvature are known in several species of birds, including some tropical hummingbirds. Despite the importance of bill shape for foraging, comparative studies of sexual dimorphism of bill shape are few. We quantified bill shape in two temperate hummingbird species, Black-chinned Hummingbird (Archilocus alexandri) and Ruby-throated Hummingbird (A. colubris) and compared patterns of sexual shape dimorphism. Several commonly used bill-curvature indices yielded contrasting results; one found differences between species and sexes, a second identified no differences in curvature, and a circle-curvature approach revealed shape differences between species and between the sexes. By contrast, landmark-based geometric morphometric methods identified significant differences in sexual shape dimorphism and also revealed that Ruby-throated Hummingbirds exhibited significant sexual differences in shape, whereas Black-chinned Hummingbirds did not. Female Ruby-throated Hummingbirds exhibited relatively greater bill curvature than males, a pattern consistent with observations of some tropical hummingbirds. Although the causes of differences in bill-shape dimorphism between Black-chinned and Ruby-throated hummingbirds remain unclear, we hypothesize that it may be attributable to differences in the structure of the community in which each species breeds and the interplay between inter- and intraspecific competition for resources in these communities. Finally, we recommend that future studies of bill shape include geometric morphometric approaches because they are better suited than univariate approaches for identifying more complex shape differences within and among species.
Mitotic Accumulation of Dimethylated Lysine 79 of Histone H3 Is Important for Maintaining Genome Integrity During Mitosis in Human Cells

The loss of genome stability is an early event that drives the development and progression of virtually all tumor types. Recent studies have revealed that certain histone post-translational modifications exhibit dynamic and global increases in abundance that coincide with mitosis and exhibit essential roles in maintaining genomic stability. Histone H2B ubiquitination at lysine 120 (H2Bub1) is regulated by RNF20, an E3 ubiquitin ligase that is altered in many tumor types. Through an evolutionarily conserved trans-histone pathway, H2Bub1 is an essential prerequisite for subsequent downstream dimethylation events at lysines 4 (H3K4me2) and 79 (H3K79me2) of histone H3. Although the role that RNF20 plays in tumorigenesis has garnered much attention, the downstream components of the trans-histone pathway, H3K4me2 and H3K79me2, and their potential contributions to genome stability remain largely overlooked. In this study, we employ single-cell imaging and biochemical approaches to investigate the spatial and temporal patterning of RNF20, H2Bub1, H3K4me2, and H3K79me2 throughout the cell cycle, with a particular focus on mitosis. We show that H2Bub1, H3K4me2, and H3K79me2 exhibit distinct temporal progression patterns throughout the cell cycle. Most notably, we demonstrate that H3K79me2 is a highly dynamic histone post-translational modification that reaches maximal abundance during mitosis in an H2Bub1-independent manner. Using RNAi and chemical genetic approaches, we identify DOT1L as a histone methyltransferase required for the mitotic-associated increases in H3K79me2. We also demonstrate that the loss of mitotic H3K79me2 levels correlates with increases in chromosome numbers and increases in mitotic defects. Collectively, these data suggest that H3K79me2 dynamics during mitosis are normally required to maintain genome stability and further implicate the loss of H3K79me2 during mitosis as a pathogenic event that contributes to the development and progression of tumors.
Predictors of Immunosuppressive Regulatory T Lymphocytes in Healthy Women

Immunosuppressive regulatory T (Treg) cells play an important role in antitumor immunity, self-tolerance, transplantation tolerance, and attenuation of allergic response. Higher proportion of Treg cells has been observed in peripheral blood of cancer cases compared to controls. Little is known about potential epidemiological predictors of Treg cell levels in healthy individuals. We conducted a cross-sectional study including 75 healthy women, between 20 and 80 years of age, who participated in the Data Bank and BioRepository (DBBR) program at Roswell Park Cancer Institute (RPCI), Buffalo, NY, USA. Peripheral blood levels of CD4+CD25+FOXP3+ Treg cells were measured using flow cytometric analysis. A range of risk factors was evaluated using Wilcoxon Rank-Sum test, Kruskal-Wallis test, and linear regression. Age, smoking, medications for treatment of osteoporosis, postmenopausal status, body mass index (BMI), and hormone replacement therapy (HRT) were found to be significant positive predictors of Treg cell levels in peripheral blood (P ≤ 0.05). Higher education, exercise, age at first birth, oral contraceptives, and use of Ibuprofen were found be significant (P < 0.05) negative predictors of Treg levels. Thus, various epidemiological risk factors might explain interindividual variation in immune response to pathological conditions, including cancer.
Functional Dissection of Reelin Signaling by Site-Directed Disruption of Disabled-1 Adaptor Binding to Apolipoprotein E Receptor 2: Distinct Roles in Development and Synaptic Plasticity

The Reelin signaling pathway controls neuronal positioning in human and mouse brain during development as well as modulation of long-term potentiation (LTP) and behavior in the adult. Reelin signals by binding to two transmembrane receptors, apolipoprotein E receptor 2 (Apoer2) and very-low-density lipoprotein receptor. After Reelin binds to the receptors, Disabled-1 (Dab1), an intracellular adaptor protein that binds to the cytoplasmic tails of the receptors, becomes phosphorylated on tyrosine residues, initiating a signaling cascade that includes activation of Src-family kinases and Akt. Here, we have created a line of mutant mice (Apoer2 EIG) in which the Apoer2 NFDNPVY motif has been altered to EIGNPVY to disrupt the Apoer2–Dab1 interaction to further study Reelin signaling in development and adult brain. Using primary neuronal cultures stimulated with recombinant Reelin, we find that normal Reelin signaling requires the wild-type NFDNPVY sequence and likely the interaction of Apoer2 with Dab1. Furthermore, examination of hippocampal, cortical, and cerebellar layering reveals that the NFDNPVY sequence of Apoer2 is indispensable for normal neuronal positioning during development of the brain. Adult Apoer2 EIG mice display severe abnormalities in LTP and behavior that are distinct from those observed for mice lacking Apoer2. In Apoer2 EIG slices, LTP degraded to baseline within 30 min, and this was prevented in the presence of Reelin. Together, these findings emphasize the complexity of Reelin signaling in the adult brain, which likely requires multiple adaptor protein interactions with the intracellular domain of Apoer2.
A dominant negative bone morphogenetic protein 4 receptor causes neuralization in Xenopus ectoderm.

Injection of DN-BR mRNA encoding a dominant negative type I receptor for bone morphogenetic protein 4 (BMP4) converted prospective ectoderm into neural tissue in Xenopus animal cap explants, in the absence of expression of mesodermal marker genes. The injected caps expressed a general neural marker NCAM and the forebrain marker opsin. Coinjection of wild-type BMP4 receptor mRNA completely reversed the neuralization by DN-BR. No expression of known neuralizing factors, i.e., noggin and follistatin, was detected in the DN-BR-injected animal caps. Furthermore, neuralization elicited by noggin or 3m, a LIM domain mutant of Xlim-1, was substantially inhibited by co-injection of BMP4 mRNA. Since BMP4 is expressed in the prospective ectoderm during gastrulation, our results suggest that the ventralizing factor BMP4 acts also as a physiological inhibitor of neuralization in the development of Xenopus ectoderm.
Employment outcome and predictors of competitive employment at 2-year follow-up of a vocational rehabilitation programme for individuals with schizophrenia in a high-income welfare society

Abstract Background: Employment is an important part of recovery for individuals with schizophrenia. The employment rate for this group is as low as 10% in Norway, and major system related barriers to employment are evident. Aims: This study reports the competitive employment outcome at 2-year follow-up of a vocational rehabilitation study augmented with cognitive remediation (CR) or elements from cognitive behaviour therapy (CBT) for individuals with schizophrenia spectrum disorders. It also investigates if global functioning, self-esteem, and depression at baseline predicts employment outcome, and if change in these variables during the intervention period is associated with employment outcome. Method: One hundred and forty-eight participants with schizophrenia spectrum disorders in six Norwegian counties received 10 months vocational rehabilitation augmented with either CBT (n = 84) or CR (n = 64). Both competitive and sheltered workplaces were used. Participants were assessed at baseline, at the end of the intervention period, and at 2-year follow-up. Results: At 2-year follow-up, 21.2% had obtained competitive employment. A further 25.3% had work placements in competitive workplaces. Significant improvements were found in global functioning, self-esteem, and depression during the intervention period, but no significant differences between the two intervention groups. High baseline global functioning and self-esteem, as well as positive change in these variables during the intervention period, were significantly associated with higher competitive employment outcome at 2-year follow-up. Conclusion: The results add to existing evidence that competitive employment is attainable for individuals with schizophrenia. High global functioning and self-esteem were strongly associated with competitive employment outcome.
The Influence of Goal-Directed and Experiential Activities on Online Flow Experiences

Recently, it has been proposed that creatingcompellingexperiencesin the distinctiveconsumption environmentdefined by the Internet depends on facilitating a state of flow. Although it has been establishedthat consumersdo, in fact, experienceflow while using the Web, consumer researchers do not as yet have a comprehensive understanding of the specific activities during which consumers actually have these experiences. One fruitful focus of research on online consumer experiencehas been on two distinct categories of consumptionbehavior—goal directed and experientialconsumptionbehavior.Drawing distinctionsbetween these behaviors for the Web may be particularlyimportant becausethe experiential process is, for many individuals, as or even more important than the final instrumental result. However, the general and broad nature of flow measurement to date has precluded a precise investigation of flow during goal-directed versus experiential activities. In this article, we explore this issue, investigating whether flow occurs during both experiential and goal-directedactivities,if experientialand goal-directedflow states differ in terms of underlyingconstructs,and what the key characteristicsare—based on prior theory—that define “types” of flow experiencesreported on the Web. Our approach is to perform a series of quantitative analyses of qualitative descriptionsof flow experiencesprovided by Web users collected in conjunctionwith the 10th GVU WWW User Survey. In contrast with previous research that suggestsflow would be more likely to occur during recreationalactivitiesthan task-orientedactivities, we found more evidence of flow for task-orientedrather than experientialactivities,although there is evidence flow occurs under both scenarios. As a final note, we argue that the role that goal-directed and experiential activities may play in facilitating the creation of compelling online environments may also be important in a broader consumer policy context.
Disembodied Mind: Cortical Changes Following Brainstem Injury in Patients with Locked-in Syndrome

Locked-in syndrome (LIS) following ventral brainstem damage is the most severe form of motor disability. Patients are completely entrapped in an unresponsive body despite consciousness is preserved. Although the main feature of LIS is this extreme motor impairment, minor non-motor dysfunctions such as motor imagery defects and impaired emotional recognition have been reported suggesting an alteration of embodied cognition, defined as the effects that the body and its performances may have on cognitive domains. We investigated the presence of structural cortical changes in LIS, which may account for the reported cognitive dysfunctions. For this aim, magnetic resonance imaging scans were acquired in 11 patients with LIS (6 males and 5 females; mean age: 52.3±5.2SD years; mean time interval from injury to evaluation: 9±1.2SD months) and 44 healthy control subjects matching patients for age, sex and education. Freesurfer software was used to process data and to estimate cortical volumes in LIS patients as compared to healthy subjects. Results showed a selective cortical volume loss in patients involving the superior frontal gyrus, the pars opercularis and the insular cortex in the left hemisphere, and the superior and medium frontal gyrus, the pars opercularis, the insular cortex, and the superior parietal lobule in the right hemisphere. As these structures are typically associated with the mirror neuron system, which represents the neural substrate for embodied simulation processes, our results provide neuroanatomical support for potential disembodiment in LIS.
Prognosis of Prostate Cancer With Other Primary Malignancies

Purpose The objective was to investigate the clinicopathological characteristics and the prognosis of prostate cancer patients affected by other primary malignancies. Materials and Methods From 1990 to 2008, we retrospectively reviewed the medical records of 1,317 patients who underwent radical prostatectomy (RP) for prostate cancer. We assessed the effect of other primary malignancies on clinicopathological features, biochemical recurrence (BCR)-free survival, cancer-specific survival (CSS), and overall survival (OS). Results Of 1,317 patients, at least one additional other primary malignancy was detected in 187 patients (14.2%). A comparison of patient groups according to the presence or absence of other primary malignancies showed no significant differences in preoperative serum prostate-specific antigen concentrations, pathological Gleason scores, or pathological staging. Prostate cancer patients with other primary malignancies were older than patients without other primary malignancies (p<0.001). No significant differences in 5-year BCR-free survival (80.2% compared with 77.7%; p=0.656) or CSS (98.9% compared with 98.5%; p=0.733) were found between these groups, respectively. Five-year OS was significantly lower in prostate cancer patients with than in those without other primary malignancies (89.3% compared with 95.4%; p<0.001). Multivariate analysis showed that other primary malignancies diagnosed after RP for prostate cancer were independent predictors of OS (hazard ratio, 4.10; p<0.001) but not of BCR-free survival or CSS. Conversely, other primary malignancies diagnosed before RP for prostate cancer did not independently predict BCR-free survival, OS, or CSS. Conclusions Prostate cancer prognosis after RP is not dependent on the presence or absence of other primary malignancies. However, other primary malignancies diagnosed after RP for prostate cancer negatively affect OS.
The Management of Oral Pemphigus Vulgaris with Systemic Corticosteroid and Dapsone

Background and aims Oral pemphigus vulgaris is a chronic autoimmune mucocutaneous intraepi-thelial disease that primarily affects patients over the age of fifty, resulting in mucosal ulceration and is a potentially life-threatening disease. The purpose of this study was to investigate the efficacy of dap-sone in combination with systemic corticosteroids to treat the oral lesions of oral pemphigus. Materials and methods Twenty patients diagnosed with oral pemphigus were selected. Oral mani-festations were graded according to the severity of disease from 1 to 3. All patients were treated initially with systemic corticosteroids. Each was assigned to one of 4 groups according to their response to ther-apy. Patients who responded less than 50% healing of lesions began a trial of dapsone. After 4 weeks, signs and symptoms were recorded, and if a patient was lesion-free, the dapsone dosage was gradually tapered. Results Five patients with mild to moderate disease were treated with systemic corticosteroids alone. 15 patients with moderate to severe disease were treated with systemic corticosteroid and dapsone ther-apy. Of these, 10 patients had significant benefits, while 5 patients did not respond to dapsone adjuvant. Conclusions. The use of dapsone in combination with systemic corticosteroids is a useful method for treatment of oral pemphigus. Conclusions The use of dapsone in combination with systemic corticosteroids is a useful method for treatment of oral pemphigus.
Effects of Infarcted Myocardium on Regional Blood Flow Measurements to Ischemic Regions in Canine Heart

The present study assesses effects of acutely infarcted myocardium on apparent micro-sphere loss as a function of time, determines effects of apparent microsphere loss on blood flow measurements to ischemic regions, and determines to what extent apparent microsphere loss alters interpretation of serial measurements of collateral blood flow. Studies were performed in 35 awake mongrel dogs chronically instrumented with catheters in the aorta and left atrium and an occluder on the proximal circumflex coronary artery. Myocardial blood flow was measured before and 15 minutes after complete occlusion. Dogs were randomly divided into four groups to be killed at 6 and 24 hours, and 3 and 6 days. In the 3-day group, an additional blood flow measurement was made 24 hours postocclusion. The entire left ventricle was sectioned into 1– to 2-g samples and myocardial blood flow determined. The ratio of preocclusion blood flow in each ischemic sample to mean nonischemic flow was used to calculate apparent microsphere loss and to correct ischemic blood flow in each sample. Significant apparent microsphere loss occurred in epicardial layers at 24 hours and in epi-and endocardial layers at 3 and 6 days; maximum loss at each interval was 22.3,19.4, and 22.2% respectively. Absolute blood flow corrections for ischemic myocardium were small, range —0.035 to 0.083 ml/min per g. Changes in flow to ischemic regions between 15 minutes and 24 hours were comparable before and after correction for apparent microsphere loss. Although infarction resulted in significant apparent microsphere loss, effects on ischemic blood flow measurements were very small and consequently did not prevent interpretation of serial blood flow measurements after infarction in animals killed at 3 days. Circ Res 47: 701-709, 1980
The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

Background Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. Methodology/Principal Findings We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). Conclusions/Significance The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
Mutations in the clathrin-assembly gene Picalm are responsible for the hematopoietic and iron metabolism abnormalities in fit1 mice

Recessive N-ethyl-N-nitrosourea (ENU)-induced mutations recovered at the fitness-1 (fit1) locus in mouse chromosome 7 cause hematopoietic abnormalities, growth retardation, and shortened life span, with varying severity of the defects in different alleles. Abnormal iron distribution and metabolism and frequent scoliosis have also been associated with an allele of intermediate severity (fit14R). We report that fit14R, as well as the most severe fit15R allele, are nonsense point mutations in the mouse ortholog of the human phosphatidylinositol-binding clathrin assembly protein (PICALM) gene, whose product is involved in clathrin-mediated endocytosis. A variety of leukemias and lymphomas have been associated with translocations that fuse human PICALM with the putative transcription factor gene AF10. The Picalmfit1–5R and Picalmfit1–4R mutations are splice-donor alterations resulting in transcripts that are less abundant than normal and missing exons 4 and 17, respectively. These exon deletions introduce premature termination codons predicted to truncate the proteins near the N and C termini, respectively. No mutations in the genes encoding Picalm, clathrin, or components of the adaptor protein complex 2 (AP2) have been previously described in which the suite of disorders present in the Picalmfit1 mutant mice is apparent. These mutants thus provide unique models for exploring how the endocytic function of mouse Picalm and the transport processes mediated by clathrin and the AP2 complex contribute to normal hematopoiesis, iron metabolism, and growth.
A hybrid approach to cyber-physical systems verification

We propose a performance verification technique for cyber-physical systems that consist of multiple control loops implemented on a distributed architecture. The architectures we consider are fairly generic and arise in domains such as automotive and industrial automation; they are multiple processors or electronic control units (ECUs) communicating over buses like FlexRay and CAN. Current practice involves analyzing the architecture to estimate worst-case end-to-end message delays and using these delays to design the control applications. This involves a significant amount of pessimism since the worst-case delays often occur very rarely. We show how to combine functional analysis techniques with model checking in order to derive a delay-frequency interface that quantifies the interleavings between messages with worst-case delays and those with smaller delays. In other words, we bound the frequency with which control messages might suffer the worst-case delay. We show that such a delay-frequency interface enables us to verify much tigher control performance properties compared to what would be possible with only worst-case delay bounds.