Miracle-dz/UniFAR-FTUs huggingface dataset:
The Song Sparrow, Melospiza melodia, as a ring species: Patterns of geographic variation, a revision of subspecies, and implications for speciation

Abstract Identification and analysis of ring species are important to our understanding of evolution and speciation. We review geographic variation in the Song Sparrow (Melospiza melodia) in the context of a ring species, one of few known from the highly vagile class Aves. Although 52 subspecies have been named, our reassessment of morphological variation across the entire species reveals that 25 subspecies are diagnosable throughout the species’ range, which includes much of the North American continent. We include an analysis of plumage variation in M. m. heermanni of coastal California and M. m. fallax of the Sonoran Desert and a description of the contact zone between these subspecies, which forms the contact points of a ring centred around the Sierra Nevada and Mojave Desert. These two subspecies come into contact in a narrow hybrid zone, where interbreeding is limited. In addition to substantial differences in plumage, songs of these subspecies vary concomitantly with differences in the structure of occupied habitat. Females tend to exhibit assort‐ative preferences for plumage and song and males exhibit assortative recognition (and associated agonistic behaviour) of song. Plumage variation across the Song Sparrow varies according to climate and habitat, suggesting both geographical and ecological components to the species’ diversification.
Reprogramming movements: extraction of motor intentions from cortical ensemble activity when movement goals change

The ability to inhibit unwanted movements and change motor plans is essential for behaviors of advanced organisms. The neural mechanisms by which the primate motor system rejects undesired actions have received much attention during the last decade, but it is not well understood how this neural function could be utilized to improve the efficiency of brain-machine interfaces (BMIs). Here we employed linear discriminant analysis (LDA) and a Wiener filter to extract motor plan transitions from the activity of ensembles of sensorimotor cortex neurons. Two rhesus monkeys, chronically implanted with multielectrode arrays in primary motor (M1) and primary sensory (S1) cortices, were overtrained to produce reaching movements with a joystick toward visual targets upon their presentation. Then, the behavioral task was modified to include a distracting target that flashed for 50, 150, or 250 ms (25% of trials each) followed by the true target that appeared at a different screen location. In the remaining 25% of trials, the initial target stayed on the screen and was the target to be approached. M1 and S1 neuronal activity represented both the true and distracting targets, even for the shortest duration of the distracting event. This dual representation persisted both when the monkey initiated movements toward the distracting target and then made corrections and when they moved directly toward the second, true target. The Wiener filter effectively decoded the location of the true target, whereas the LDA classifier extracted the location of both targets from ensembles of 50–250 neurons. Based on these results, we suggest developing real-time BMIs that inhibit unwanted movements represented by brain activity while enacting the desired motor outcome concomitantly.
Rapid gist perception of meaningful real-life scenes: Exploring individual and gender differences in multiple categorization tasks

In everyday life, we are generally able to dynamically understand and adapt to socially (ir)elevant encounters, and to make appropriate decisions about these. All of this requires an impressive ability to directly filter and obtain the most informative aspects of a complex visual scene. Such rapid gist perception can be assessed in multiple ways. In the ultrafast categorization paradigm developed by Simon Thorpe et al. (1996), participants get a clear categorization task in advance and succeed at detecting the target object of interest (animal) almost perfectly (even with 20 ms exposures). Since this pioneering work, follow-up studies consistently reported population-level reaction time differences on different categorization tasks, indicating a superordinate advantage (animal versus dog) and effects of perceptual similarity (animals versus vehicles) and object category size (natural versus animal versus dog). In this study, we replicated and extended these separate findings by using a systematic collection of different categorization tasks (varying in presentation time, task demands, and stimuli) and focusing on individual differences in terms of e.g., gender and intelligence. In addition to replicating the main findings from the literature, we find subtle, yet consistent gender differences (women faster than men).
Temperament, childhood environment and psychopathology as risk factors for avoidant and borderline personality disorders

Objective: To evaluate childhood experiences (neglect and abuse), temperament and childhood and adolescent psychopathology as risk factors for avoidant and borderline personality disorders in depressed outpatients. Method: One hundred and eighty depressed outpatients were evaluated for personality disorders. Risk factors of childhood abuse, parental care, temperament, conduct disorder symptoms, childhood and adolescent anxiety disorders, depressive episodes, hypomania and alcohol and drug dependence were obtained by questionnaires and interviews. Results: Avoidant personality disorder can be conceptualized as arising from a combination of high harm avoidance (shy, anxious), childhood and adolescent anxiety disorders and parental neglect. Borderline personality disorder can be formulated as arising from a combination of childhood abuse and/or neglect, a borderline temperament (high novelty seeking and high harm avoidance), and childhood and adolescent depression, hypomania, conduct disorder and alcohol and drug dependence. Conclusions: Combinations of risk factors from the three domains of temperament, childhood experiences and childhood and adolescent psychopathology make major contributions to the development of avoidant and borderline personality disorders.
A VLP Library of C-Terminally Truncated Hepatitis B Core Proteins: Correlation of RNA Encapsidation with a Th1/Th2 Switch in the Immune Responses of Mice

An efficient pBR327- and Ptrp-based E. coli expression system was used to generate a large-scale library of virus like particles (VLP) formed by recombinant hepatitis B virus (HBV) core (HBc) protein derivatives. To construct the library, the gene of HBc protein of the genotype D/subtype ayw2 virus was gradually truncated from the 3`-end and twenty-two HBc variants (with truncation up to 139 aa) were expressed at high levels. The proteins were purified by salt precipitation and gel filtration. Background RNA binding was observed for VLPs formed by HBc1-149, which lacked all C-terminal Arg blocks, and the addition of three Arg residues (HBc1-152) only slightly increased RNA binding. The presence of two Arg blocks (proteins HBc1-162 and HBc1-163) resulted in approximately half of the typical level of RNA binding, and the presence of three blocks (protein HBc1-171) led to approximately 85% of the typical level of binding. Only a small increase in the level of RNA binding was found for the HBc1-175 VLPs, which contained all four Arg blocks but lacked the last 8 aa of the full-length HBc protein. VLPs containing high levels of RNA had higher antigenicity according to an ELISA with anti-HBc mAbs than the VLPs formed by HBc variants without C-terminal Arg blocks and lacking RNA. The results indicate that the VLPs were stabilised by nucleic acids. The immunogenicity in BALB/c mice was comparable for VLPs formed by different HBc proteins, but a clear switch from a Th1 response to a Th2 response occurred after the loss of encapsidated RNA. We did not observe significant differences in lymphocyte proliferation in vitro for the tested VLP variants; however, the loss of RNA encapsidation correlated with a decreased level of IFN-γ induction, which is a measure of the potential CTL activity of immunogens.
Impact of Covid-19 on Investors Herding Behavior: Evidence from Stock Market

The purpose of this research was to use a descriptive and causal-comparative approach to analyze herding behavior in the Nepalese stock market during the COVID-19 epidemic. The study employed a regression model and a cross-sectional standard deviation (CSSD) index to evaluate the herding tendency. The investigation covers a significant time period from January 1, 2018, to February 28, 2023, and involves a substantial number of observation sessions totaling 1103. It appears that there is currently no evidence to suggest that herding behavior has occurred before, during, or after the COVID-19 pandemic. This study indicates that market participants were making independent decisions based on their own analysis and assessment of the situation during the pandemic, rather than relying on the actions or decisions of others.
Polymorphic Type Inference for the Relational Algebra

We give a polymorphic account of the relational algebra. We introduce a formalism of “type formulas” specifically tuned for relational algebra expressions, and present an algorithm that computes the “principal” type for a given expression. The principal type of an expression is a formula that specifies, in a clear and concise manner, all assignments of types (sets of attributes) to relation names, under which a given relational algebra expression is well-typed, as well as the output type that expression will have under each of these assignments. Topics discussed include complexity and polymorphic expressive power.
Piecewise linear quadratic optimal control

A technique for computation of piecewise quadratic Lyapunov functions is further developed for performance analysis and controller synthesis for nonlinear systems. In this way, degree of observability is estimated, L/sub 2/ induced gain is computed and optimal control problems are solved. The computations are based on convex optimization in terms of linear matrix inequalities.
Energy expenditure, insulin, and VLDL-triglyceride production in humans Published, JLR Papers in Press, July 18, 2006.

Hypertriglyceridemia is considered a cardiovascular risk factor in diabetic and nondiabetic subjects. In this study, we aimed to determine potential regulators of very low density lipoprotein-triglyceride (TG) production. VLDL-TG kinetics were measured in 13 men and 12 women {body mass index [mean (range)]: 24.8 (20.2–35.6) kg/m2}. VLDL-TG production was assessed from the plasma decay of a bolus injection of ex vivo labeled VLDL particles ([1-14C]triolein-VLDL-TG). Similar VLDL-TG production (μmol/min) was found in men and women. VLDL-TG production was not significantly correlated with palmitate flux ([9,10-3H]palmitate) (r = 0.09, P = 0.67) or palmitate concentration (r = −0.29, P = 0.2) but was correlated significantly with fasting insulin concentration (r = 0.46, P < 0.05) and resting energy expenditure (REE) (r = 0.45, P < 0.05). The latter correlation improved when adjusted for sex. The best multivariate model with VLDL-TG production as the dependent variable and REE, body composition, hormones, and substrate levels as independent variables included fasting insulin (P = 0.02) and REE (P = 0.02) (r2 = 0.32, P < 0.001). We conclude that VLDL kinetics are similar in men and women and that REE and plasma insulin are significant independent predictors of VLDL-TG production. FFA availability and body fat distribution are unrelated to VLDL production. We suggest that REE plays a greater role in VLDL-TG production than previously anticipated. REE and insulin should be taken into account when VLDL-TG production comparisons between groups are made.
Self-Supervised Multi-Modal Learning for Collaborative Robotic Grasp-Throw

Accurate throwing skills can expand the pick-and-place ability of a manipulator, which is significant but challenging in the field of robotics. Most existing robotic throwing methods neglect the mass of an object and air drag, not to mention the effect of a grasp on the subsequent throw, resulting in inaccurate throws. In this regard, we propose collaborative grasping and throwing learning (CGTL). It consists of a grasp agent with a grasping network (G-Net), a throw agent with a learning-based throw reference (LTR), and a multi-modal throw compensator network (MTC-Net). First, G-Net generates multi-channel grasp affordances for inferring grasps. Subsequently, LTR predicts a throw velocity reference by exploiting an air resistance estimation network (ARE-Net) and a projectile equation considering air drag. Meanwhile, MTC-Net uses multi-modal data to predict the compensation for the throwing velocity reference. Moreover, CGTL takes throwing performances into the reward of the grasp agent and the grasp affordances into the throw agent's observation to facilitate more accurate throwing. Finally, extensive experiments show that our CGTL outperforms its peers regarding throwing accuracy, especially when throwing different objects into new positions.
Characterisation of Hawkes Bay rivers based on biotic communities : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University

Environmental data, aquatic macroinvertebrates and periphyton were sampled in 52 rivers throughout Hawkes Bay primarily between January and March, 1995. The 97 invertebrate taxa collected comprised predominantly Trichoptera (27), Ephemeroptera (17), Diptera (11) and Coleoptera (10). 49 periphyton taxa were collected which comprised of 30 diatoms, 10 Green algae and 9 Blue-Green algae. An ordination of sites by macroinvertebrate data using Detrended Correspondence Analysis (DECORANA) produced two interpretable axes. Axis 1 was correlated with measures reflecting terrain, land use and nutrient levels. Axis 2 was correlated with measures of periphyton abundance. DECORANA analysis of periphyton indicated pH had most influence over community structure, with measures of periphyton abundance, leaf litter, and water colour (absorbance at 440nm) having a secondary influence. Classification of macroinvertebrate communities usmg Two-Way Indicator Species Analysis (TWINSP AN) produced six groups. Sites within each group were generally found to fall into restricted areas of Hawkes Bay and these are suggested as bioregions. Each bioregion is described and could be used as a management unit by appropriate organisations. Analysis of periphyton with TWINSP AN classified sites into seven groups, but no geographical pattern was evident. Direct analysis of environmental variables and macroinvertebrate taxa using Canonical Correspondence Analysis (CANOCO) indicated that gradient, altitude, substrate size, conductivity, S04 and K had most influence over macroinvertebrate communities. Two widely used biotic indices of water quality (MCI and EPT) were strongly positively correlated with several chemical variables and negatively correlated with substrate related factors so it was difficult to know if macroinvertebrates were responding to water quality or physical features . Ranking taxa by their CANOCO axis scores is suggested as a way of recalibrating taxa MCI scores for a region and assigning appropriate MCI scores to new taxa. iii The bioregions generated from the TWIN SP AN analysis of macroinvertebrates are compared to an existing New Zealand-wide ecoregion classification and also to ecoregions developed from a cluster analysis of six climatic and geomorphological factors of the 52 sites in Hawkes Bay. Little correlation was found between the bioregions and the cluster analysis, however some similarity between bioregions and the existing ecoregion classification was found, and the bioregions are suggested as possible "subecoregions". Environmental data and macroinvertebrates were also sampled in nine sites on each of two major Hawkes Bay rivers to look at longitudinal patterns in macroinvertebrate communities. Both rivers exhibited a zonation pattern rather than a continuum, and the zonation is related to degree of human disturbance.
Assessing physicians' accuracy in diagnosing paediatric patients with acute abdominal pain: measuring accuracy for multiple diseases

In evaluating the accuracy of diagnostic tests there are many situations where the true disease status can be one of multiple disorders. For example, when paediatric patients suffer acute abdominal pain, the underlying diagnosis could be appendicitis, intestinal obstruction, gastroenteritis, urinary tract infection, etc. In this paper we describe a format for collecting data for the case of multiple truth states. This new format allows one to make pairwise comparisons of the diagnostic accuracy between all of the different truth states. We propose a summary measure of accuracy which is a weighted average of the pairwise estimates of accuracy. Estimators are derived for the variance and covariance of the estimated summary accuracy. The small sample properties of the estimators are evaluated in a Monte Carlo simulation study. The new data collection format and summary measure were used in a paediatric acute abdominal pain study; data from this study are used to illustrate the methods. Copyright © 2001 John Wiley & Sons, Ltd.
Centrosomes Enhance the Fidelity of Cytokinesis in Vertebrates and Are Required for Cell Cycle Progression

When centrosomes are destroyed during prophase by laser microsurgery, vertebrate somatic cells form bipolar acentrosomal mitotic spindles (Khodjakov, A., R.W. Cole, B.R. Oakley, and C.L. Rieder. 2000. Curr. Biol. 10:59–67), but the fate of these cells is unknown. Here, we show that, although these cells lack the radial arrays of astral microtubules normally associated with each spindle pole, they undergo a normal anaphase and usually produce two acentrosomal daughter cells. Relative to controls, however, these cells exhibit a significantly higher (30–50%) failure rate in cytokinesis. This failure correlates with the inability of the spindle to properly reposition itself as the cell changes shape. Also, we destroyed just one centrosome during metaphase and followed the fate of the resultant acentrosomal and centrosomal daughter cells. Within 72 h, 100% of the centrosome-containing cells had either entered DNA synthesis or divided. By contrast, during this period, none of the acentrosomal cells had entered S phase. These data reveal that the primary role of the centrosome in somatic cells is not to form the spindle but instead to ensure cytokinesis and subsequent cell cycle progression.
Water Governance in Cities: Current Trends and Future Challenges

Adapting water governance to changing needs, while coping with the uncertainties caused by climate change and the consequences of urbanisation and demographic growth, is key for inclusive, safe and resilient cities. The urgency of the challenges calls for innovative practices to enhance water security and provide better services to citizens, as foreseen by the Sustainable Development Goal (SDG) 6. The key question is: how to accomplish these objectives? While there is no doubt that technical solutions are available and play a fundamental role, they represent only part of the solution. Cities must ensure that the institutional frameworks in place are “fit to fix the pipes”, from accessible information to adequate capacity, from sufficient funding to transparency and integrity, and from meaningful stakeholder engagement to coherence across sectoral policies. Building mainly on recent studies on water governance carried out by The Organisation for Economic Co-operation and Development (OECD) and specifically on urban water governance, this paper will discuss current trends and provide a set of tools for policy solutions based on OECD’s 3Ps framework: people, policies and places. It will conclude by highlighting the importance of improving monitoring and evaluation for better design and implementation of urban water governance.
Relationship between cyclic AMP‐dependent protein tyrosine phosphorylation and extracellular calcium during hyperactivation of boar spermatozoa

In mammalian spermatozoa, the state of protein tyrosine phosphorylation is modulated by protein tyrosine kinases and protein tyrosine phosphatases that are controlled via cyclic AMP (cAMP)‐protein kinase A (PKA) signaling cascades. The aims of this study were to examine the involvement of cAMP‐induced protein tyrosine phosphorylation in response to extracellular calcium and to characterize effects of pharmacological modulation of the cAMP‐induced protein phosphorylation state and calmodulin activity during hyperactivation in boar spermatozoa. Ejaculated spermatozoa were incubated with cBiMPS (a cell‐permeable cAMP analog) and CaCl2 at 38.5°C to induce hyperactivation, and then used for Western blotting and indirect immunofluorescence of phosphorylated proteins and for the assessment of motility. Both cBiMPS and CaCl2 were necessary for hyperactivation. The increase in hyperactivated spermatozoa exhibited a dependence on the state of cBiMPS‐induced protein tyrosine phosphorylation in the connecting and principal pieces. The addition of calyculin A (an inhibitor for protein phosphatases 1/2A (PP1/PP2A), 50–100 nM) coincidently promoted hyperactivation and cAMP‐induced protein tyrosine phosphorylation in the presence of cBiMPS and CaCl2. Moreover, the addition of W‐7 (a calmodulin antagonist, 2–4 µM) enhanced the percentages of hyperactivated spermatozoa after incubation with cBiMPS and CaCl2, independently of protein tyrosine phosphorylation. These findings indicate that cAMP‐induced protein tyrosine phosphorylation in the connecting and principal pieces is involved in hyperactivation in response to extracellular calcium, and that calmodulin may suppress hyperactivation via the signaling cascades that are independent of cAMP‐induced protein tyrosine phosphorylation. Mol. Reprod. Dev. 79: 727–739, 2012. © 2012 Wiley Periodicals, Inc.
The effect of gamma on perceived image quality

The effect of gamma, the exponent of the power function that characterizes luminance transfer, on perceptual image quality and on the strength of its underlying dimensions, brightness contrast and sharpness have been studied for complex black-and-white scenes, displayed on a TV monitor. Gamma was found to have a scene-independent optimum value that is higher than expected. This optimum was found to be uniquely determined by (subjective) brightness contrast. Although (subjected) sharpness is influenced by gamma, experiments show that no interaction is to be expected in the range of interest. The results also show that luminance contrast ratio is an adequate measure of brightness contrast. <<ETX>>
Cellular Automata and Lattice Boltzmann Techniques: an Approach to Model and Simulate Complex Systems

We discuss the cellular automata approach and its extensions, the lattice Boltzmann and multiparticle methods. The potential of these techniques is demonstrated in the case of modeling complex systems. In particular, we consider applications taken from various fields of physics, such as reaction-diffusion systems, pattern formation phenomena, fluid flows, fracture processes and road traffic models.