Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat-Specific Locomotor Variation among Chinese Hook Snout Carp (Opsariichthys bidens) along a River

The Wujiang River is a tributary of the upper Yangtze River that shows great variations in its flow regime and habitat condition. Dams have been built along the Wujiang River and have altered the habitats profoundly enough that they may give rise to reproductive isolation. To test whether the swimming performance and morphology of the Chinese hook snout carp (Opsariichthys bidens), varied among habitats and whether the possible differences had a genetic basis, we measured the steady and unsteady swimming performance, external body shape and genetic distance among fish collected from both the main and tributary streams of the upper, middle and lower reaches along the river. We also measured the routine energy expenditure (RMR), maximum metabolic rate (MMR), cost of transport (COT) and calculated the optimal swimming speed. The steady swimming capacity, RMR, MMR and optimal swimming speed were all higher and the COT was lower in the upper reach or tributary streams compared with the lower reach or main stream. However, unsteady swimming performance showed no variation among collecting sites. Flow regimes as suggested by river slope and water velocity were positively correlated with steady swimming performance but not with unsteady swimming performance. Predation stress were significantly related with body morphology and hence energy cost during swimming but not U crit value. The fish from only one population (Hao-Kou) showed relatively high genetic differentiation compared with the other populations. Fish from the upper reach or tributary streams exhibited improved steady swimming performance through improved respiratory capacity and lower energy expenditure during swimming at the cost of higher maintenance metabolism. There was no correlation between the steady and unsteady swimming performance at either the population or the individual levels. These results suggest that a trade-off between steady and unsteady swimming does not occur in O. bidens.
Hsl7p, the yeast homologue of human JBP1, is a protein methyltransferase.

The yeast protein Hsl7p is a homologue of Janus kinase binding protein 1, JBP1, a newly characterized protein methyltransferase. In this report, Hsl7p also is shown to be a methyltransferase. It can be crosslinked to [(3)H]S-adenosylmethionine and exhibits in vitro protein methylation activity. Calf histones H2A and H4 and bovine myelin basic protein were methylated by Hsl7p, whereas histones H1, H2B, and H3 and bovine cytochrome c were not. We demonstrated that JBP1 can complement Saccharomyces cerevisiae with a disrupted HSL7 gene as judged by a reduction of the elongated bud phenotype, and a point mutation in the JBP1 S-adenosylmethionine consensus binding sequence eliminated all complementation by JBP1. Therefore, we conclude the yeast protein Hsl7p is a sequence and functional homologue of JBP1. These data provide evidence for an intricate link between protein methylation and macroscopic changes in yeast morphology.
Parvalbumin is expressed in glutamatergic and GABAergic corticostriatal pathway in mice

The connections between the cortex and the striatum are critically involved in control and execution of voluntary movements. Here we focused on the expression of calcium binding protein parvalbumin (PV) in the corticostriatal pathway. Injections of Fluorogold into the striatum gave rise to retrograde labeling of PV‐positive neurons in the retrosplenial cortex and somatosensory cortex. The PV‐positive corticostriatal projection neurons were mainly found in layer V, but occasionally seen in layers II, III, and VI. The PV immunoreactivity of retrogradely labeled cells was weaker than that of nonlabeled cells. Although it was rather difficult to analyze the morphology of Fluorogold‐labeled neurons that exhibited PV immunoreactivity, some of them showed distinct apical dendrites and were considered pyramidal cells. The main target of PV‐positive cortical afferents was the caudal striatum on the ipsilateral side. Next, we tested whether PV‐positive corticostriatal projection neurons were GABAergic or not, because previous studies emphasized that PV was an important marker for cortical GABAergic neurons. Unexpectedly, we found that the majority of PV‐positive corticostriatal projection neurons were glutamic acid decarboxylase (GAD)‐negative, while some of them were GAD‐positive. Finally, an anterograde tracer Phaseolus vulgaris leucoagglutinin (PHA‐L) injection into the somatosensory cortex resulted in many PV‐positive corticostriatal terminals that were vesicular glutamate transporter 1‐positive, whereas some of the PV‐positive PHA‐L‐labeled terminals were GAD‐positive. Our results provide anatomical evidence for expression of PV in glutamatergic and GABAergic corticostriatal pathway in mice and suggest that a subset of cortical afferents may exert some inhibitory influence on striatal activity. J. Comp. Neurol. 477:188–201, 2004. © 2004 Wiley‐Liss, Inc.
Sampling and learning the Mallows and Generalized Mallows models under the Cayley distance

The Mallows and Generalized Mallows models are compact yet powerful and natural ways of representing a probability distribution over the space of permutations. In this paper we deal with the problems of sampling and learning (estimating) such distributions when the metric on permutations is the Cayley distance. We propose new methods for both operations, whose performance is shown through several experiments. We also introduce novel procedures to count and randomly generate permutations at a given Cayley distance both with and without certain structural restrictions. An application in the ﬁeld of biology is given to motivate the interest of this model
Structures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment*

Inhibitor of apoptosis (IAP) proteins are key negative regulators of cell death that are highly expressed in many cancers. Cell death caused by antagonists that bind to IAP proteins is associated with their ubiquitylation and degradation. The RING domain at the C terminus of IAP proteins is pivotal. Here we report the crystal structures of the cIAP2 RING domain homodimer alone, and bound to the ubiquitin-conjugating (E2) enzyme UbcH5b. These structures show that small changes in the RING domain accompany E2 binding. By mutating residues at the E2-binding surface, we show that autoubiquitylation is required for regulation of IAP abundance. Dimer formation is also critical, and mutation of a single C-terminal residue abrogated dimer formation and E3 ligase activity was diminished. We further demonstrate that disruption of E2 binding, or dimerization, stabilizes IAP proteins against IAP antagonists in vivo.
Heparan sulfate: a key regulator of embryonic stem cell fate

Abstract Heparan sulfate (HS) belongs to a class of glycosaminoglycans and is a highly sulfated, linear polysaccharide. HS biosynthesis and modification involves numerous enzymes. HS exists as part of glycoproteins named HS proteoglycans, which are expressed abundantly on the cell surface and in the extracellular matrix. HS interacts with numerous proteins, including growth factors, morphogens, and adhesion molecules, and thereby regulates important developmental processes in invertebrates and vertebrates. Embryonic stem cells (ESCs) are distinguished by their characteristics of self-renewal and pluripotency. Self-renewal allows ESCs to proliferate indefinitely in their undifferentiated state, whereas pluripotency implies their capacity to differentiate into the three germ layers and ultimately all cell types of the adult body. Both traits are tightly regulated by numerous cell signaling pathways. Recent studies have highlighted the importance of HS in the modulation of ESC functions, specifically their lineage fate. Here, we review the current advances that have been made in understanding the structural changes of HS during ESC differentiation and in deciphering the molecular mechanisms by which HS modulates cell fate. Finally, we discuss the applications of heparinoids and chemical inhibitors of HS biosynthesis for the manipulation of ESC culture and directed differentiation.
Toward an Empirical Multidimensional Structure of Anhedonia, Reward Sensitivity, and Positive Emotionality: An Exploratory Factor Analytic Study

Positive emotionality, anhedonia, and reward sensitivity share motivational and experiential elements of approach motivation and pleasure. Earlier work has examined the interrelationships among these constructs from measures of extraversion. More recently, the Research Domain Criteria introduced the Positive Valence Systems as a primary dimension to better understand psychopathology. However, the suggested measures tapping this construct have not yet been integrated within the structural framework of personality, even at the level of self-report. Thus, this study conducted exploratory factor and exploratory bifactor analyses on 17 different dimensions relevant to approach motivation, spanning anhedonia, behavioral activation system functioning, and positive emotionality. Convergent validity of these dimensions is tested by examining associations with depressive symptoms. Relying on multiple indices of fit, our preferred model included a general factor along with specific factors of affiliation, positive emotion, assertiveness, and pleasure seeking. These factors demonstrated different patterns of association with depressive symptoms. We discuss the plausibility of this model and highlight important future directions for work on the structure of a broad Positive Valence Systems construct.
Integrated care for diabetes: clinical, psychosocial, and economic evaluation

Abstract Objectives : To evaluate integrated care for diabetes in clinical, psychosocial, and economic terms. Design : Pragmatic randomised trial. Setting : Hospital diabetic clinic and three general practice groups in Grampian. Patients : 274 adult diabetic patients attending a hospital clinic and registered with one of three general practices. Intervention - Random allocation to conventional hospital clinic care or integrated care. Integrated care patients seen in general practice every three or four months and in the hospital clinic annually. General practitioners were given written guidelines for integrated care. Main outcome measures : Metabolic control, psychosocial status,knowledge of diabetes, beliefs about control of diabetes, satisfaction with treatment, disruption of normal activities, numbers of consultations and admissions, frequency of metabolic monitoring, costs to patients and NHS. Results - A higher proportion of patients defaulted from conventional care (14 (10%)) than from integrated care (4 (3%), 95% confidence interval of difference 2% to 13%). After two years no significant differences were found between the groups in metabolic control, psychosocial status, knowledge, beliefs about control, satisfaction with treatment, unscheduled admissions, or disruption of normal activities. Integrated care was as effective for insulin dependent as non-insulin dependent patients. Patients in integrated care had more visits and higher frequencies of examination. Costs to patients were lower in integrated care (mean pounds sterling 1.70) than in conventional care (pounds sterling 8). 88% of patients who experienced integrated care wished to continue with it. Conclusions : This model of integrated care for diabetes was at least as effective as conventional hospital clinic care.
Attention bias to faces in Asperger Syndrome: a pictorial emotion Stroop study

Background. Emotional Stroop tasks have shown attention biases of clinical populations towards stimuli related to their condition. Asperger Syndrome (AS) is a neuropsychiatric condition with social and communication deficits, repetitive behaviours and narrow interests. Social deficits are particularly striking, including difficulties in understanding others. Method. We investigated colour-naming latencies of adults with and without AS to name colours of pictures containing angry facial expressions, neutral expressions or non-social objects. We tested three hypotheses: whether (1) controls show longer colour-naming latencies for angry versus neutral facial expressions with male actors, (2) people with AS show differential latencies across picture types, and (3) differential response latencies persist when photographs contain females. Results. Controls had longer latencies to pictures of male faces with angry compared to neutral expressions. The AS group did not show longer latencies to angry versus neutral expressions in male faces, instead showing slower latencies to pictures containing any facial expression compared to objects. When pictures contained females, controls no longer showed longer latencies for angry versus neutral expressions. However, the AS group still showed longer latencies to all facial picture types, compared to objects, providing further evidence that faces produce interference effects for this clinical group. Conclusions. The pictorial emotional Stroop paradigm reveals normal attention biases towards threatening emotional faces. The AS group showed Stroop interference effects to all facial stimuli regardless of expression or sex, suggesting that faces cause disproportionate interference in AS.
An Optimal Partitioning Algorithm for Combinational CMOS Circuits Using Particle Swarm Optimization

This paper presents a swarm intelligence based approach to optimally partition combinational CMOS circuits for pseudoexhaustive testing. The partitioning algorithm ensures reduction in the number of test vectors required to detect faults in VLSI circuits. The algorithm is based on the circuit’s primary input cone (N) and fanout (F) values to decide the location and number of partitions. Particle Swarm Optimization (PSO) is used to determine the optimal values of N and F to minimize the number of test vectors as well as the number of partitions. The proposed algorithm has been applied to the ISCAS’85 benchmark circuits and the results obtained are compared with those from the I-PIFAN partitioning approach.
Psycholinguistic mechanisms supporting school-age children's comprehension of spoken directions: A preliminary study

The contribution of two working memory mechanisms to school-age children's comprehension of spoken directions was examined. Sixty typically developing school-age children completed the CELF-4 (Clinical Evaluation of Language Fundamentals-4, Semel, Wiig, & Secord, 2003) concepts and following oral directions subtest and four predictor measures. Predictors included global measures of lexical and syntactic knowledge, verbal short-term memory (STM) capacity, and the updating mechanism in WM. Correlation and regression analyses were conducted. Regression analysis indicated that lexical knowledge, STM capacity, and updating accuracy jointly accounted for 27% variance in the comprehension of spoken directions as measured by the CELF-4, with receptive vocabulary contributing the most. STM capacity and updating accuracy were comparably robust in their contribution and shared mechanisms that accounted for significant variance in the criterion. The importance of understanding the relation between cognitive and language processes is highlighted. The limitations of the study and methodological considerations for research in children with developmental language impairment are discussed.
Optical and thermal response of laser irradiated tissue

A Java Simulation Application was developed to simulate optical and thermal response of laser irradiated tissue by using Monte Carlo and Finite Difference Methods. For light propagation Monte Carlo was preferred according to its high accuracy because a number of photon packets can be launched to increase efficiency. Also Finite Difference Method was used for heat diffusion because of its simplicity. The results taken from Monte Carlo Model are used as a source term in heat conduction equation. Thus, in small time steps by doing iterations of Finite Difference Method thermal gradients are measured inside a tissue. At 1064 nm fluence and thermal contours of brain and liver tissues are obtained with same laser parameters. Also at different wavelengths, 1064 nm and 630 nm, fluence and thermal contours of liver tissue are calculated in the same conditions. The thermal gradients of laser irradiated tissue were plotted with 2D colored surface plotting.
Ergodic Sum-Rate Maximization for Fading Cognitive Multiple-Access Channels Without Successive Interference Cancelation

In this paper, the ergodic sum rate of a fading cognitive multiple-access channel (C-MAC) is studied, where a secondary network (SN) with multiple secondary users (SUs) transmitting to a secondary base station shares the spectrum band with a primary user (PU). An interference power constraint (IPC) is imposed on the SN to protect the PU. Under such a constraint and the individual transmit power constraint (TPC) imposed on each SU, we investigate the power allocation strategies to maximize the ergodic sum rate of a fading C-MAC without successive interference cancelation (SIC). In particular, this paper considers two types of constraints: 1) average TPC and average IPC and 2) peak TPC and peak IPC. For the first case, it is proved that the optimal power allocation is dynamic time-division multiple access (D-TDMA), which is exactly the same as the optimal power allocation to maximize the ergodic sum rate of the fading C-MAC with SIC under the same constraints. For the second case, it is proved that the optimal solution must be at the extreme points of the feasible region. It is shown that D-TDMA is optimal with high probability when the number of SUs is large. Moreover, we show that when the SUs can be sorted in a certain order, an algorithm with linear complexity can be used to find the optimal power allocation.
Emotions in tweets: From instantaneity to preconstruction

This article deals with the expression of emotions in tweets. The aim is to observe the way users formulate their feelings in a technologically constrained yet expressively free communicative environment, in a context of written instantaneity which leaves place for the selection of context-adapted linguistic formulae. Comparison between emotional expressions involved in hashtags and the emotional lexicon used in the body of the messages shows some topical discrepancies and, more particularly, different degrees of denotational power. It also reveals a constructivist dimension of emotional expressions.
Cardiovascular risk factors underestimate atherosclerotic burden in chronic kidney disease: usefulness of non-invasive tests in cardiovascular assessment.

BACKGROUND Cardiovascular risk scoring (Score) does not specifically address chronic kidney disease (CKD) patients. The aim of our study is to quantify atherosclerosis using carotid ultrasound and ankle-brachial index (ABI) and to assess its additional value in risk scoring. METHODS In this cross-sectional, observational study, patients were studied according to a standardized protocol including carotid ultrasound and ABI to determine the atherosclerosis score (AS), ranging from absence of to severe atherosclerosis (AS 0 to AS 3). RESULTS We included 409 CKD-affected patients (231 on dialysis, 99 in CKD Stages IV-V and 79 in CKD Stages I-III) and 851 subjects with normal renal function. The presence and severity of atherosclerosis was significantly higher in the CKD group than in the controls at every decade of age studied. Among the CKD-affected subjects, the prevalence of carotid plaques was significantly higher in the dialysis group (78.3%) than in the group in CKD Stages I-III (55.6%, P < 0.001). We identified 174 patients at low-intermediate risk. Among them, 110 (63.2%) presented either moderate (AS 2) or severe (AS 3) atherosclerosis. Variables significantly (P < 0.05) and positively related to atherosclerosis were being on dialysis [OR = 3.40, 95% CI (1.73, 6.78) vs CKD Stages I-III], age [OR = 1.08, 95% CI (1.06-1.11)] and C-reactive protein [OR = 1.04, 95% CI (1.01-1.08)]. Conversely, female sex was negatively related to atherosclerosis [OR = 0.40, 95% CI (0.23-0.71), P = 0.002]. CONCLUSION The use of carotid ultrasound and ABI identifies atherosclerosis in a population of CKD patients in which risk scoring underestimates atherosclerosis burden.
The Emergence of Predators in Early Life: There was No Garden of Eden

Background Eukaryote cells are suggested to arise somewhere between 0.85∼2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85∼2.7 billion years ago, leads to an unexpected prediction of a long period (∼1–3 billion years) with no phagocytotes – a veritable Garden of Eden. Methodology We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms - given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. Conclusions Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.