Miracle-dz/UniFAR-FTUs huggingface dataset:
High genetic variation in resting‐stage production in a metapopulation: Is there evidence for local adaptation?

Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting‐stage production is locally adapted—that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life‐history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within‐ and between‐population variation for all dormancy‐related traits, but no evidence for the hypothesized higher resting‐stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation.
Ubiquitination of the yeast a-factor receptor

The a-factor receptor (Ste3p) is one of two pheromone receptors in the yeast Saccharomyces cerevisiae that enable the cell-cell communication of mating. In this report, we show that this receptor is subject to two distinct covalent modifications-phosphorylation and ubiquitination. Phosphorylation, evident on the unstimulated receptor, increases upon challenge by the receptor's ligand, a-factor. We suggest that this phosphorylation likely functions in the adaptive, negative regulation of receptor activity. Removal of phosphorylation by phosphatase treatment uncovered two phosphatase-resistant modifications identified as ubiquitination using a myc-epitope-tagged ubiquitin construct. Ste3p undergoes rapid, ligand-independent turnover that depends on vacuolar proteases and also on transport of the receptor from surface to vacuole (i.e., endocytosis) (Davis, N.G., J.L.Horecka, and G.F. Sprague, Jr., 1993 J. Cell Biol. 122:53-65). An end4 mutation, isolated for its defect in the endocytic uptake of alpha-factor pheromone (Raths, S., J. Rohrer, F. Crausaz, and H. Riezman. 1993. J. Cell Biol. 120:55-65), blocks constitutive endocytosis of the a-factor receptor, yet fails to block ubiquitination of the receptor. In fact, both phosphorylation and ubiquitination of the surfacebound receptor were found to increase, suggesting that these modifications may occur normally while the receptor is at the cell surface. In a mutant strain constructed to allow for depletion of ubiquitin, the level of receptor ubiquitination was found to be substantially decreased. Correlated with this was an impairment of receptor degradative turnover-receptor half-life that is normally approximately 20 min at 30 degrees C was increased to approximately 2 h under these ubiquitin-depletion conditions. Furthermore, surface residency, normally of short duration in wild-type cells (terminated by endocytosis to the vacuole), was found to be prolonged; the majority of the receptor protein remained surface localized fully 2 h after biosynthesis. Thus, the rates of a-factor receptor endocytosis and consequent vacuolar turnover depend on the available level of ubiquitin in the cell. In cells mutant for two E2 activities, i.e., ubc4 delta ubc5 delta cells, the receptor was found to be substantially less ubiquitinated, and in addition, receptor turnover was slowed, suggesting that Ubc4p and Ubc5p may play a role in the recognition of the receptor protein as substrate for the ubiquitin system. In addition to ligand-independent uptake, the a-factor receptor also undergoes a ligand-dependent form of endocytosis (Davis, N.G., J.L. Horecka, and G.F. Sprague, Jr. 1993. J. Cell. Biol. 122:53-65). Concurrent with ligand-dependent uptake, we now show that the receptor undergoes ligand-induced ubiquitination, suggesting that receptor ubiquitination may function in the ligand-dependent endocytosis of the a-factor receptor as well as in its constitutive endocytosis. To account for these findings, we propose a model wherein the covalent attachment of ubiquitin to surface receptor triggers endocytic uptake.
A Three-Generational Study of Transmission of Risk for Sexual Abuse

This intergenerational study investigates histories of both attachment relationships and abusive experiences and domains of current functioning that distinguish families of sexually abused children from families of nonabused children. The participants included (a) 199 nonoffending African American mothers of whom approximately half had children with documented sexual abuse histories and half had children with no documented abuse histories and (b) 106 maternal grandmothers of these children; approximately half had sexually abused grandchildren and half had grandchildren with no documented abuse. The children were 4 to 12 years old. Histories of abuse and attachment experiences and current functioning of the grandmother and mother were evaluated. Logistic regression analyses revealed that sexual abuse in a child was best predicted by 3 factors: maternal problems in adult functioning, a currently negative relationship between the grandmother and mother, and a disrupted pattern of caregiving during the mother's childhood. The findings underscore that troubled intergenerational attachment relationships in families can significantly heighten the risk of a child being sexually abused.
Operational Definitions for the NINDS-AIREN Criteria for Vascular Dementia: An Interobserver Study

Background and Purpose— Vascular dementia (VaD) is thought to be the most common cause of dementia after Alzheimer’s disease. The commonly used International Workshop of the National Institute of Neurological Disorders and Stroke (NINDS) and the Association Internationale pour la Recherche et l’Enseignement en Neurosciences (AIREN) criteria for VaD necessitate evidence of vascular disease on CT or MRI of the brain. The purposes of our study were to operationalize the radiological part of the NINDS-AIREN criteria and to assess the effect of this operationalization on interobserver agreement. Methods— Six experienced and 4 inexperienced observers rated a set of 40 MRI studies of patients with clinically suspected VaD twice using the NINDS-AIREN set of radiological criteria. After the first reading session, operational definitions were conceived, which were subsequently used in the second reading session. Interobserver reproducibility was measured by Cohen’s &kgr;. Results— Overall agreement at the first reading session was poor (&kgr;=0.29) and improved slightly after application of the additional definitions (&kgr;=0.38). Raters in the experienced group improved their agreement from almost moderate (&kgr;=0.39) to good (0.62). The inexperienced group started out with poor agreement (&kgr;=0.17) and did not improve (&kgr;=0.18). The experienced group improved in both the large- and small-vessel categories, whereas the inexperienced group improved generally in the extensive white matter hyperintensities categories. Conclusions— Considerable interobserver variability exists for the assessment of the radiological part of the NINDS-AIREN criteria. Use of operational definitions improves agreement but only for already experienced observers.
Computed tomography diagnosed cachexia and sarcopenia in 725 oncology patients: is nutritional screening capturing hidden malnutrition?

Nutrition screening on admission to hospital is mandated in many countries, but to date, there is no consensus on which tool is optimal in the oncology setting. Wasting conditions such as cancer cachexia (CC) and sarcopenia are common in cancer patients and negatively impact on outcomes; however, they are often masked by excessive adiposity. This study aimed to inform the application of screening in cancer populations by investigating whether commonly used nutritional screening tools are adequately capturing nutritionally vulnerable patients, including those with abnormal body composition phenotypes (CC, sarcopenia, and myosteatosis).
MicroRNA-92b promotes cell proliferation and invasion in osteosarcoma by directly targeting Dickkopf-related protein 3

Deregulation of microRNA-92b (miR-92b) has been implicated in osteosarcoma. However, the underlying regulatory mechanism of miR-92b in osteosarcoma growth and metastasis remains largely unclear. In the present study, reverse transcription-quantitative polymerase chain reaction and western blotting were used to measure mRNA and protein expression. MTT and Transwell assays were conducted to determine cell proliferation and invasion, and a luciferase reporter assay was performed to confirm the association between miR-92b and Dickkopf3-related protein (DKK3). The results demonstrated that miR-92b was significantly upregulated in osteosarcoma tissues compared with matched adjacent non-tumor tissues. Additionally, high miR-92b levels were significantly associated with lung metastasis and advanced tumor, node, metastasis stage (P<0.05) but not with age, sex, tumor size, location, serum lactate dehydrogenase or serum alkaline phosphatase. miR-92b expression was also significantly upregulated in osteosarcoma cell lines compared with normal osteoblast cells. Knockdown of miR-92b significantly inhibited the proliferation and invasion of osteosarcoma U2OS cells (P<0.01). By contrast, overexpression of miR-92b significantly increased U2OS cell proliferation and invasion (P<0.01). DKK3 was identified as a target gene of miR-92b and it was demonstrated that DKK3 expression was negatively regulated by miR-92b in U2OS cells. Restoration of DKK3 expression abrogated the increased proliferation and invasion of U2OS cells induced by miR-92b overexpression. Notably, DKK3 was significantly downregulated in osteosarcoma tissues compared with adjacent non-tumor tissues and its expression was inversely correlated to miR-92b levels in osteosarcoma tissues. Taken together, these data indicate that miR-92b promotes cell proliferation and invasion in osteosarcoma by targeting DKK3. Therefore, miR-92b may become a potential therapeutic target for osteosarcoma.
Prevalence, hematology and treatment of Balantidium coli among small ruminants in and around Lahore, Pakistan.

Sheep and goats of Lahore district were examined for the prevalence, hematology and treatment of Balantidium coli. A total of 752 sheep and goats were examined (n=376 sheep; n=376 goats). Sheep had a somewhat greater prevalence (3.99%) than goats (3.46%). In both species, decrease in hemoglobin (Hb) and increased packed cell volume (PCV) was observed in infected animals. Efficacy of Secnidazole was higher as compared to Oxytetracycline and Metronidazole in all experimental animals. Balantidiasis is rarely studied infection in small ruminants and this is the first report published on the disease from Pakistan. It is still unclear whether this is an emerging infection, or whether it is a newly reported endemic in the studied area.
VERITAS‐PRN: a new measure of adherence to episodic treatment regimens in haemophilia

Summary. Episodic treatment of bleeding disorders is defined as utilization of clotting factor concentrates in response to acute bleeding episodes to achieve haemostasis. Non‐adherence to prescribed episodic regimens can limit treatment effectiveness and result in target joint formation, pain and disability. Evaluation of and interventions to promote adherence may improve health outcomes. The purpose of this study was to validate a new adherence scale developed for individuals with bleeding disorders treated on episodic infusion regimens, entitled VERITAS‐PRN [Validated Hemophilia Regimen Treatment Adherence Scale – PRN]. Participants were recruited from the Indiana Hemophilia and Thrombosis Center patient population. Participants completed the scale for psychometric development and analysis. Subjective ratings of adherence from participants and providers were used for validation. The study sample included 51 male and three female patients. Twenty‐seven participants (50.0%) were diagnosed with FVIII deficiency, 21 (38.9%) with FIX deficiency and six (11.1%) with von Willebrand’s disease (VWD). Internal consistency reliability for the total VERITAS‐PRN score and the majority of subscales was good‐to‐excellent, with the one exception being the ‘Plan’ subscale. Test‐retest reliability correlations were good‐to‐excellent for the total scale and all subscales. The VERITAS‐PRN total scale had moderate‐to‐strong and statistically significant correlations with validity measures. The VERITAS‐PRN is a reliable and valid measure of adherence to episodic treatment regimens for bleeding disorders. This tool may be utilized as a standard measure of adherence to increase sensitivity to adherence problems and promote targeted interventions to enhance adherence and health outcomes
A biologically plausible learning rule for the Infomax on recurrent neural networks

A fundamental issue in neuroscience is to understand how neuronal circuits in the cerebral cortex play their functional roles through their characteristic firing activity. Several characteristics of spontaneous and sensory-evoked cortical activity have been reproduced by Infomax learning of neural networks in computational studies. There are, however, still few models of the underlying learning mechanisms that allow cortical circuits to maximize information and produce the characteristics of spontaneous and sensory-evoked cortical activity. In the present article, we derive a biologically plausible learning rule for the maximization of information retained through time in dynamics of simple recurrent neural networks. Applying the derived learning rule in a numerical simulation, we reproduce the characteristics of spontaneous and sensory-evoked cortical activity: cell-assembly-like repeats of precise firing sequences, neuronal avalanches, spontaneous replays of learned firing sequences and orientation selectivity observed in the primary visual cortex. We further discuss the similarity between the derived learning rule and the spike timing-dependent plasticity of cortical neurons.
Area Distribution and Scaling Function for Punctured Polygons

Punctured polygons are polygons with internal holes which are also polygons. The external and internal polygons are of the same type, and they are mutually as well as self-avoiding. Based on an assumption about the limiting area distribution for unpunctured polygons, we rigorously analyse the effect of a finite number of punctures on the limiting area distribution in a uniform ensemble, where punctured polygons with equal perimeter have the same probability of occurrence. Our analysis leads to conjectures about the scaling behaviour of the models. We also analyse exact enumeration data. For staircase polygons with punctures of fixed size, this yields explicit expressions for the generating functions of the first few area moments. For staircase polygons with punctures of arbitrary size, a careful numerical analysis yields very accurate estimates for the area moments. Interestingly, we find that the leading correction term for each area moment is proportional to the corresponding area moment with one less puncture. We finally analyse corresponding quantities for punctured self-avoiding polygons and find agreement with the conjectured formulas to at least 3–4 significant digits.
Permian tetrapod biochronology, correlation and evolutionary events

Abstract The most extensive Permian tetrapod (amphibian and reptile) fossil records from the western USA (New Mexico to Texas) and South Africa have been used to define 11 land vertebrate faunachrons (LVFs). These are, in ascending order, the Coyotean, Seymouran, Mitchellcreekian, Redtankian, Littlecrotonian, Kapteinskraalian, Gamkan, Hoedemakeran, Steilkransian, Platbergian and Lootsbergian. These faunachrons provide a biochronological framework with which to assign ages to, and correlate, Permian tetrapod fossil assemblages. Intercalated marine strata, radioisotopic ages and magnetostratigraphy were used to correlate the Permian LVFs to the standard global chronostratigraphic scale with varying degrees of precision. Such correlations identified the following significant events in Permian tetrapod evolution: a Coyotean chronofaunal event (end Coyotean); Redtankian events (Mitchellcreekian–Littlecrotonian); Olson's gap (late Littlecrotonian); a therapsid event (Kapteinskraalian); a dinocephalian extinction event (end Gamkan); and a latest Permian extinction event (Platbergian–Lootsbergian boundary). Problems of incompleteness, endemism and taxonomy, and the relative lack of non-biochronological age control continue to hinder the refinement and correlation of a Permian timescale based on tetrapod biochronology. Nevertheless, the global Permian timescale based on tetrapod biochronology is a robust tool for both global and regional age assignment and correlation. Advances in Permian tetrapod biochronology will come from new fossil discoveries, more detailed biostratigraphy and additional alpha taxonomic studies based on sound evolutionary taxonomic principles.
Functional capacity and activity level before and after renal transplantation.

Functional capacity and activity level were measured among 9 renal transplant recipients prior to transplantation (T1), 6 weeks (T2), and 16 weeks (T3) after transplantation. Functional capacity was measured by a symptom-limited treadmill test. The Human Activity Profile was used to obtain self-reported activity level. A 24% improvement in functional capacity was found from T1 to T2 with only a 5% improvement from T2 to T3 (p less than .001). In contrast, significant improvement in activity level was not present until after T2. Although activity level increased from T1 to T3 (p less than .01), it continued to be low in comparison with age/gender matched normative data.
Scientific and Pragmatic Challenges for Bridging Education and Neuroscience

Educational neuroscience is an emerging effort to integrate neuroscience methods, particularly functional neuroimaging, with behavioral methods to address issues of learning and instruction. This article consolidates common concerns about connecting education and neuroscience. One set of concerns is scientific: in-principle differences in methods, data, theory, and philosophy. The other set of concerns is pragmatic: considerations of costs, timing, locus of control, and likely payoffs. The authors first articulate the concerns and then revisit them, reinterpreting them as potential opportunities. They also provide instances of neuroscience findings and methods that are relevant to education. The goal is to offer education researchers a window into contemporary neuroscience to prepare them to think more specifically about the prospects of educational neuroscience.
Disability and difference: balancing social and physical constructions

The world of disability theory is currently divided between those who insist it reflects a physical fact affecting life quality and those who believe disability is defined by social prejudice. Despite a dialogue spanning bioethical, medical and social scientific literatures the differences between opposing views remains persistent. The result is similar to a figure-ground paradox in which one can see only part of a picture at any moment. This paper attempts to find areas of commonality between the opposing camps, and thus to rearrange the figures of the paradox at a fundamental level. The purpose is first to identify areas in which common ground can be achieved, and secondarily, to clarify the areas in which disagreement continues. While a general and unified theory of physical difference/disability is beyond the scope of this paper the result may advance that general goal.
Recursive Camera-Motion Estimation With the Trifocal Tensor

In this paper, an innovative extended Kalman filter (EKF) algorithm for pose tracking using the trifocal tensor is proposed. In the EKF, a constant-velocity motion model is used as the dynamic system, and the trifocal-tensor constraint is incorporated into the measurement model. The proposed method has the advantages of those structure- and-motion-based approaches in that the pose sequence can be computed with no prior information on the scene structure. It also has the strengths of those model-based algorithms in which no updating of the three-dimensional (3-D) structure is necessary in the computation. This results in a stable, accurate, and efficient algorithm. Experimental results show that the proposed approach outperformed other existing EKFs that tackle the same problem. An extension to the pose-tracking algorithm has been made to demonstrate the application of the trifocal constraint to fast recursive 3-D structure recovery
Exercise-induced Mitochondrial Biogenesis Begins before the Increase in Muscle PGC-1α Expression*

Exercise results in rapid increases in expression of the transcription coactivator peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) and in mitochondrial biogenesis in skeletal muscle. PGC-1α regulates and coordinates mitochondrial biogenesis, and overexpression of PGC-1α in muscle cells results in increases in mitochondrial content. In this context, it has been proposed that the increase in PGC-1α protein expression mediates the exercise-induced increase in mitochondrial biogenesis. However, we found that mitochondrial proteins with a short half-life increase as rapidly as, or more rapidly than, PGC-1α protein. This finding led us to hypothesize that activation, rather than increased expression, of PGC-1α mediates the initial phase of the exercise-induced increase in mitochondria. In this study, we found that most of the PGC-1α in resting skeletal muscle is in the cytosol. Exercise resulted in activation of p38 MAPK and movement of PGC-1α into the nucleus. In support of our hypothesis, binding of the transcription factor nuclear respiratory factor 1 (NRF-1) to the cytochrome c promoter and NRF-2 to the cytochrome oxidase subunit 4 promoter increased in response to exercise prior to an increase in PGC-1α protein. Furthermore, exercise-induced increases in the mRNAs of cytochrome c, δ-aminolevulinate synthase, and citrate synthase also occurred before an increase in PGC-1 protein. Thus, it appears that activation of PGC-1α may mediate the initial phase of the exercise-induced adaptive increase in muscle mitochondria, whereas the subsequent increase in PGC-1α protein sustains and enhances the increase in mitochondrial biogenesis.