Miracle-dz/UniFAR-FTUs huggingface dataset:
Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined SNP-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine scale sub-population differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring sub-populations had low but significant genetic differentiation (FST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two sub-populations and there were significant differences in juvenile growth rates and size-at-age after oceanic migration between individuals in the respective sub-populations. Our findings suggest that different evolutionary processes affect each sub-population and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.
DJ-1 gene deletion reveals that DJ-1 is an atypical peroxiredoxin-like peroxidase

Parkinson's disease (PD) is a common neurodegenerative movement disorder. Whereas the majority of PD cases are sporadic, rare genetic defects have been linked to this prevalent movement disorder. Mutations in DJ-1 are associated with autosomal recessive early-onset PD. The exact biochemical function of DJ-1 has remained elusive. Here we report the generation of DJ-1 knockout (KO) mice by targeted deletion of exon 2 and exon 3. There is no observable degeneration of the central dopaminergic pathways, and the mice are anatomically and behaviorally similar to WT mice. Fluorescent Amplex red measurements of H2O2 indicate that isolated mitochondria from young and old DJ-1 KO mice have a 2-fold increase in H2O2. DJ-1 KO mice of 2–3 months of age have a 60% reduction in mitochondrial aconitase activity without compromising other mitochondrial processes. At an early age there are no differences in antioxidant enzymes, but in older mice there is an up-regulation of mitochondrial manganese superoxide dismutase and glutathione peroxidase and a 2-fold increase in mitochondrial glutathione peroxidase activity. Mutational analysis and mass spectrometry reveal that DJ-1 is an atypical peroxiredoxin-like peroxidase that scavenges H2O2 through oxidation of Cys-106. In vivo there is an increase of DJ-1 oxidized at Cys-106 after 1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine intoxication of WT mice. Taken together these data indicate that the DJ-1 KO mice have a deficit in scavenging mitochondrial H2O2 due to the physiological function of DJ-1 as an atypical peroxiredoxin-like peroxidase.
The Economic Impact of Sports Stadiums: Recasting the Analysis in Context

ABSTRACT: Independent empirical analyses are often used to refute assertions that sports stadiums can serve as economic catalysts. Criticisms of recent stadium investments, however, are commonly based on studies conducted with data that it out of date. Current generation stadiums typically exhibit a different character and purpose than the multi-use, utilitarian facilities built in the 1960s and 1970s. This study tests the importance of the new context within which stadiums are built by recasting a landmark study with current data. Nineteen metropolitan areas are included in a cross-section time-series analysis, representing every city that gained or lost an NFL or MLB team, or experienced a stadium construction for such a team between 1984 and 2001. These sports-related variables are found to be positively correlated with regional income share for eight of the nineteen metropolitan areas. A closer look at the findings suggests that context matters.
Simvastatin promotes cell metabolism, proliferation, and osteoblastic differentiation in human periodontal ligament cells.

BACKGROUND Simvastatin is one of the cholesterol lowering drugs. Recent studies demonstrated that it has a bone stimulatory effect. Periodontal ligament (PDL) cells are believed to play an important role in periodontal regeneration; that is, they may differentiate into specific cells which make cementum, bone, and attachment apparatus. It would be of interest whether simvastatin has a positive effect on PDL cells. Therefore, effects of simvastatin on cell proliferation and osteoblastic differentiation in PDL cells were analyzed. METHODS Human PDL cells were cultured in monolayer with simvastatin for 24 and 72 hours and cell metabolism and proliferation were determined. To analyze osteoblastic differentiation, human PDL cells were cultured in organoid culture for 7, 14, and 21 days and alkaline phosphatase (ALP) activity, osteopontin (OPN), bone morphogenetic protein (BMP) -2, osteocalcin (OCN), and calcium contents were measured. They were co-treated by simvastatin and mevalonate. RESULTS Simvastatin enhanced cell proliferation and metabolism dose-dependently after 24 hours. Simvastatin also stimulated ALP activity of human PDL cells dose-dependently, and maximum effect was obtained at the concentration of 10(8) M. In time dependent analysis, 10(8) M simvastatin stimulated ALP activity and osteopontin content after 7 days and calcium contents after 21 days. BMP-2 and OCN contents were not detected. Moreover this statin-enhanced ALP activity was abolished by mevalonate. CONCLUSION These results suggest that at low concentration, simvastatin exhibits positive effect on proliferation and osteoblastic differentiation of human PDL cells, and these effects may be caused by the inhibition of the mevalonate pathway.
Effects of Xylanase Supplementation on Growth Performance, Nutrient Digestibility and Non-starch Polysaccharide Degradation in Different Sections of the Gastrointestinal Tract of Broilers Fed Wheat-based Diets

This experiment was performed to investigate the effects of exogenous xylanase supplementation on performance, nutrient digestibility and the degradation of non-starch polysaccharides (NSP) in different sections of the gastrointestinal tract (GIT) of broilers fed wheat-based diets. A total of 120 7-day-old Arbor Acres broiler chicks were randomly allotted to two wheat-based experimental diets supplemented with 0 or 1.0 g/kg xylanase. Each treatment was composed of 6 replicates with 10 birds each. Diets were given to the birds from 7 to 21 days of age. The results showed that xylanase supplementation did not affect feed intake, but increased body weight gain of broiler at 21 day of age by 5.8% (p<0.05) and improved feed-to-gain ratio by 5.0% (p<0.05). Xylanase significantly increased (p<0.05) ileal digestibilities of crude protein (CP) by 3.5%, starch by 9.3%, soluble NSP by 43.9% and insoluble NSP by 42.2% relative to the control group, respectively. Also, compared with the control treatment, xylanase addition increased (p<0.05) total tract digestibilities of dry matter by 5.7%, CP by 4.1%, starch by 6.3%, soluble NSP by 50.8%, and had a tendency to increase (p = 0.093) insoluble NSP by 19.9%, respectively. The addition of xylanase increased the concentrations of arabinose and xylose in the digesta of gizzard, duodenum, jejunum, and ileum (p<0.05), and the order of their concentration was ileum>jejunum>duodenum>>gizzard> caecum. The supplementation of xylanse increased ileal isomaltriose concentration (p<0.05), but did not affect the concentrations of isomaltose, panose and 1-kestose in the digesta of all GIT sections. These results suggest that supplementation of xylanase to wheat-based diets cuts the arabinoxylan backbone into small fragments (mainly arabinose and xylose) in the ileum, jejunum and duodenum, and enhances digestibilites of nutrients by decreasing digesta viscosity. The release of arabinose and xylose in the small intestine may also be the important contributors to the growth-promoting effect of xylanase in broilers fed wheat-based diets.
Different behavioral effects of neurotoxic dorsal hippocampal lesions placed under either isoflurane or propofol anesthesia

Anesthetic protocols for behavioral neuroscience experiments are evolving as new anesthetics are developed and surgical procedures are refined to improve animal welfare. We tested whether neurotoxic dorsal hippocampal lesions produced under two different anesthetic protocols would have different behavioral and/or histo‐pathological effects. Rats were anesthetized with either propofol, an intravenous anesthetic, or isoflurane, a gaseous anesthetic, and multiple injections of an excitotoxin (N‐methyl‐D‐aspartate) were stereotaxically placed in the dorsal hippocampus bilaterally. Intraoperative physiological parameters were similar in the two surgical groups, as were the volumes of the lesions, although the profile of postoperative impairment in a spatial learning task differed between the lesion groups depending on the anesthetic regimen used. These results show that the choice of anesthetic protocol is a critical variable in designing behavioral neuroscience experiments using neurosurgical procedures. This factor should be considered carefully in experimental design and in cross‐study comparisons of lesion effects on behavior. © 2007 Wiley‐Liss, Inc.
CS 691 CL-Computational Linguistics : Syntax and Semantics Final Project Report Document Similarity Measures Utilizing Syntactics and Semantics as well as Embeddings

There is no shortage of online databases of documents containing valuable information, but there is a need for more tools to organize this data to provide users a more accessible interface than a standard keyword search. Providing solutions to this problem of information overload has been the focus of years of research in information retrieval, natural language processing and machine learning in general. In particular, much work has been done on defining document similarity measures, which determine the relatedness of two documents based on their text content. Typical approaches to this problem are based in word usage statistics and are not able to capture the essence of a text, as the syntactic and semantic relationships of the words are disregarded. In this project, we will make use of dependency parsing and automatic semantic role labeling to extract syntactically and semantically related phrases from text. Using these phrases, we hope to create a more robust document representation and similarity measure than the traditional approaches. We also apply our proposed document similarity measure to the problem of identifying relatedness between scientific research papers. The similarity of scientific research papers is a less studied problem than document similarity in general and a robust measure is in high demand [15]. Such a measure would be useful in both research paper recommender systems and search engines. The rest of this document is organized as follows: a review of related work done in this field; a description of our document representations and proposed similarity measures; experiments and results; and a conclusion highlighting future work.
Mortality in offspring of mothers with psychotic disorder

Background Previous studies suggest that offspring of mothers with psychotic disorders have an almost two-fold higher mortality risk from birth until early adulthood. We investigated predictors of mortality from late adolescence until middle age in offspring of mothers with psychotic disorders. Method The Helsinki High-Risk Study follows up offspring (n=337) of women treated for schizophrenia spectrum disorders in mental hospitals in Helsinki before 1975. Factors related to mortality up to 2005 among offspring of these mothers was investigated with a survival model. Hazard rate ratios (HRR) were calculated using sex, diagnosis of psychotic disorder, childhood socio-economic status, maternal diagnosis, and maternal suicide attempts and aggressive symptoms as explanatory variables. The effect of family was investigated by including a frailty term in the model. We also compared mortality between the high-risk group and the Finnish general population. Results Within the high-risk group, females had lower all-cause mortality (HRR 0.43, p=0.05) and mortality from unnatural causes (HRR 0.24, p=0.03) than males. Having themselves been diagnosed with a psychotic disorder was associated with higher mortality from unnatural causes (HRR 4.76, p=0.01), while maternal suicide attempts were associated with higher suicide mortality (HRR 8.64, p=0.03). Mortality in the high-risk group was over two-fold higher (HRR 2.44, p<0.0001) than in the general population, and remained significantly higher when high-risk offspring who later developed psychotic disorders were excluded from the study sample (HRR 2.30, p<0.0001). Conclusions Offspring of mothers with psychotic disorder are at increased risk of several adverse outcomes, including premature death.
Energy and Spectral Efficiency Tradeoff for Massive MIMO Systems With Transmit Antenna Selection

This correspondence investigates the fundamental tradeoff between the spectral efficiency (SE) and energy efficiency (EE) for massive multiple-input multiple-output (MIMO) systems with linear precoding and transmit antenna selection, where both the circuit power consumption and the large-scale fading are considered. The EE and SE are optimized with respect to the number of transmit antennas and transmit power, and consequently, we formulate the EE–SE tradeoff as a mixed-integer-continuous-variable multiobjective optimization (MOO) problem. Using the derived EE–SE relations, the properties of the Pareto front for the EE–SE tradeoff are analyzed. To solve the complicated MOO problem, we develop two algorithms: the weighted-sum particle swarm optimization (WS-PSO) algorithm and the normal-boundary-intersection particle swarm optimization (NBI-PSO) algorithm. Simulation results show that the two algorithms can achieve the Pareto optimal EE-SE tradeoff, and NBI-PSO provides more evenly distributed solutions than WS-PSO.
An Evaluation of Two Bug Pattern Tools for Java

Automated static analysis is a promising technique to detect defects in software. However, although considerable effort has been spent for developing sophisticated detection possibilities, the effectiveness and efficiency has not been treated in equal detail. This paper presents the results of two industrial case studies in which two tools based on bug patterns for Java are applied and evaluated. First, the economic implications of the tools are analysed. It is estimated that only 3-4 potential field defects need to be detected for the tools to be cost-efficient. Second, the capabilities of detecting field defects are investigated. No field defects have been found that could have been detected by the tools. Third, the identification of fault-prone classes based on the results of such tools is investigated and found to be possible. Finally, methodological consequences are derived from the results and experiences in order to improve the use of bug pattern tools in practice.
Romiplostim resistance in secondary failure of platelet recovery

Romiplostim, a thrombopoietin mimetic, is FDA approved for the treatment of thrombocytopenia in patients with refractory immune thrombocytopenia. Given the success of thrombopoietin agonists in the treatment of immune thrombocytopenia, data in other clinical settings are emerging. In the bone marrow transplant setting, secondary failure of platelet recovery and persistent thrombocytopenia are associated with increased mortality. In this case, romiplostim was attempted in a chronic lymphocytic leukemia patient who underwent a matched, unrelated donor, non-myeloablative stem cell transplant. This patient experienced profound thrombocytopenia despite dose escalation. Anti-thrombopoietin or anti-romiplostim antibodies were not detected by specific assays. Furthermore, the patient remains in disease remission with full chimerism. This case demonstrates that heavily pre-treated patients with limited bone marrow reserve may not respond to thrombopoietin agonists.
Ecologically Unequal Exchange, Ecological Debt, and Climate Justice

Building on structuralist perspectives of the world economy, a small but growing group of researchers have forged a new literature on `ecologically unequal exchange' and documented that energy and materials disproportionately flow from the Global South to the Global North. These findings have begun to influence efforts to negotiate a `post-Kyoto' global climate regime. Since the extraction of resources and energy is one of the most damaging stages of the chain of commodity production, a logical next step is the mounting cry from developing countries that they are owed an `ecological debt' by the North. The G-77 and China have seized on these ideas and a movement for `climate justice' is now gaining strength in and exerting influence in international negotiations, including the UNFCCC meetings in Delhi, Bali, and Poznań. This article reviews the history of these related three ideas and examines their potential to reshape the discussion of `burden sharing' in the post-Kyoto world where development is constrained by climate change.
L'adéquation entre offre et besoins

A supply strategy corresponds to choices taken for end-user services. Usually these are developed by targeting publics and require a lot of formalizing because of the interdependency of numerous levels of reflection. They are presented here not as stages to be followed but more as decisions to be taken collectively. Additional contributions follow, including one on the Scandinavian concept of "relational marketing".
To hydrolyze or not to hydrolyze: the dilemma of platelet-activating factor acetylhydrolase

Mounting ambiguity persists around the functional role of the plasma form of platelet-activating factor acetylhydrolase (PAF-AH). Because PAF-AH hydrolyzes PAF and related oxidized phospholipids, it is widely accepted as an anti-inflammatory enzyme. On the other hand, its actions can also generate lysophosphatidylcholine (lysoPC), a component of bioactive atherogenic oxidized LDL, thus allowing the enzyme to have proinflammatory capabilities. Presence of a canonical lysoPC receptor has been seriously questioned for a multitude of reasons. Animal models of inflammation show that elevating PAF-AH levels is beneficial and not deleterious and overexpression of PAF receptor (PAF-R) also augments inflammatory responses. Further, many Asian populations have a catalytically inert PAF-AH that appears to be a severity factor in a range of inflammatory disorders. Correlation found with elevated levels of PAF-AH and CVDs has led to the design of a specific PAF-AH inhibitor, darapladib. However, in a recently concluded phase III STABILITY clinical trial, use of darapladib did not yield promising results. Presence of structurally related multiple ligands for PAF-R with varied potency, existence of multi-molecular forms of PAF-AH, broad substrate specificity of the enzyme and continuous PAF production by the so called bi-cycle of PAF makes PAF more enigmatic. This review seeks to address the above concerns.
On the capacity of tree-based P2P streaming systems

The success of P2P file sharing systems inspired the development of P2P streaming systems for delivering online multimedia service in the last few years. The capacity of P2P streaming systems, i.e., how many peers can be concurrently serviced by the system, depends on system configurations including network bandwidth, overlay network formation, QoS constraints, membership management, peer selection, subscribing/publishing scheduling, coding schemes, etc. Due to the complexity, there are not too many systematical studies on system capacity. This work is our first attempt to answer this question. Based on flow concepts, we compare the capacity of single-tree P2P streaming systems and multiple-tree P2P streaming systems. The delay issues are not considered here. We prove that finding the routing tree to maximize system capacity, no matter for either single-tree systems or multiple-tree systems, is NP-hard. Two generic network formation heuristics, one for single-tree topology and the other for multiple-tree topology, are proposed. Simulation results show that since multiple-tree topology can efficiently utilize upload bandwidth, the multiple-tree systems have potential to service more clients.
Mothers' Acculturation and Beliefs About Emotions, Mother–Child Emotion Discourse, and Children's Emotion Understanding in Latino Families

Research Findings: We examined associations among Anglo acculturation, Latino enculturation, maternal beliefs, mother–child emotion talk, and emotion understanding in 40 Latino preschool-age children and their mothers. Mothers self-reported Anglo acculturation, Latino enculturation, and beliefs about the value/danger of children's emotions and parent/child roles in emotion socialization. Mother–child emotion talk was observed during a Lego storytelling task. Children's emotion understanding was measured using 2 age-appropriate tasks. Correlations showed that mothers' Latino enculturation was associated with mothers' stronger belief in guiding children's emotions and children's lower emotion understanding. Anglo acculturation was associated with mothers' lower belief that emotions can be dangerous and children's better emotion understanding. Mothers with a stronger belief in guiding children's emotions more frequently labeled emotions. Mothers with a stronger belief that emotions can be dangerous less frequently explained emotions. Regressions controlling for child age and maternal education demonstrated that mothers with a stronger belief that children can learn about emotions on their own and mothers with greater Latino enculturation had children with lower emotion understanding, whereas mothers with greater Anglo acculturation had children with better emotion understanding. Practice or Policy: Results suggest that understanding both family acculturation and family enculturation will be helpful for early childhood researchers and educators seeking to assess and promote children's socioemotional development.
5G Multi-RAT LTE-WiFi Ultra-Dense Small Cells: Performance Dynamics, Architecture, and Trends

The ongoing densification of small cells yields an unprecedented paradigm shift in user experience and network design. The most notable change comes from cellular rates being comparable to next-generation WiFi systems. Cellular-to-WiFi offloading, the standard modus operandi of recent years, is therefore shifting towards a true integration of both technology families. Users in future 5G systems will thus likely be able to use 3GPP, IEEE, and other technologies simultaneously, so as to maximize their quality of experience. To advance this high-level vision, we perform a novel performance analysis specifically taking the system-level dynamics into account and thus giving a true account on the uplink performance gains of an integrated multi radio access technology (RAT) solution versus legacy approaches. Further, we advocate for an enabling architecture that embodies the tight interaction between the different RATs, as we lay out a standardization roadmap able to materialize the envisaged design. 3GPP-compliant simulations have also been carried out to corroborate the rigorous mathematical analysis and the superiority of the proposed approach.