Miracle-dz/UniFAR-FTUs huggingface dataset:
Demographic history of a recent invasion of house mice on the isolated Island of Gough

Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behaviour. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution.
Rapamycin Inhibits Formation of Urethral Stricture in Rabbits

Rapamycin has been reported to inhibit hepatic fibrosis, lung fibrosis, renal fibrosis, and subglottic stenosis. Fibrosis is also involved in urethral stricture. Therefore, we investigated the effect of rapamycin on the inhibition of urethral stricture formation in a rabbit model. First, models of urethral stricture were successfully established by electrocoagulation of the bulbar urethra in adult New Zealand male rabbits. Forty-six model rabbits were randomly assigned to four groups: high-dose rapamycin (RH, 1.0 mg/day), low-dose rapamycin (RL, 0.1 mg/day), dimethyl sulfoxide (DMSO) alone (DMSO, solvent control), and normal saline (NS). Urethral stricture was assessed by a retrograde urethrogram and video-urethroscopy. Urethra pathology was evaluated by hematoxylin and eosin and Sirius red staining. After 28 days of treatment, lumen reduction in the RH, RL, DMSO, and NS groups was 36.0, 56.5, 69.1, and 82.9, respectively. Comparison of the rapamycin groups (RH and RL) and control groups (DMSO and NS) indicated significantly less restriction in the rapamycin groups. Histopathological analysis confirmed the presence of fibroblasts and an increase in collagen at the stricture site in the two control groups but not in the RH or RL groups. These results indicate that rapamycin inhibits experimentally induced urethral stricture formation in rabbits. This effect may be due to its inhibition of fibroblast proliferation and collagen expression.
Modeling Destructive Group Dynamics in On-Line Gaming Communities

Social groups often exhibit a high degree of dynamism. Some groups thrive, while many others die over time. Modeling destructive dynamics and understanding whether/why/when a person will depart from a group can be important in a number of social domains. In this paper, we take the World of Warcraft game as an exemplar platform for studying destructive group dynamics. We build models to predict if and when an individual is going to quit his/her guild, and whether this quitting event will inflict substantial damage on the guild. Our predictors start from in-game census data and extract features from multiple perspectives such as individual-level, guild-level, game activity, and social interaction features. Our study shows that destructive group dynamics can often be predicted with modest to high accuracy, and feature diversity is critical to prediction performance.
Pitch and stimulus fine structure.

It has often been suggested that the pitch of a complex tone is given by the inverse of the time between peaks in the fine structure of the stimulus waveform. This paper argues that in view of recent empirical evidence such a position is untenable. Fine‐structure models of pitch such as the “peak‐picker” are phase sensitive; they predict that changes in stimulus fine structure will be accompanied by changes in pitch. Results from several pitch‐matching experiments do not support this prediction. Two experiments are described in which pitch matches were made to complex‐tone stimuli presented in several different phase configurations. In both experiments the distributions of pitch matches appeared to be the same for all phase configurations. Stimulus fine structure, of course, changed dramatically with phase. Of course, the fact that pitch is insensitive to the relative phases of the stimulus components does not mean that listeners cannot hear the phase changes. In many cases stimuli with the same pitch are perfectly discriminable. It is only pitch that appears to be insensitive to details of wave form fine structure. This leads us to reject the simple fine‐structure theories of pitch.
Estimation of Anonymous Email Network Characteristics through Statistical Disclosure Attacks

Social network analysis aims to obtain relational data from social systems to identify leaders, roles, and communities in order to model profiles or predict a specific behavior in users’ network. Preserving anonymity in social networks is a subject of major concern. Anonymity can be compromised by disclosing senders’ or receivers’ identity, message content, or sender-receiver relationships. Under strongly incomplete information, a statistical disclosure attack is used to estimate the network and node characteristics such as centrality and clustering measures, degree distribution, and small-world-ness. A database of email networks in 29 university faculties is used to study the method. A research on the small-world-ness and Power law characteristics of these email networks is also developed, helping to understand the behavior of small email networks.
Total cerebral volume is reduced in patients with localization-related epilepsy and a history of complex febrile seizures.

CONTEXT Febrile seizures may lead to later epilepsy. They have been associated with hippocampal atrophy but their effect on total cerebral volume is unknown. OBJECTIVE To compare total cerebral volume in patients with mesial temporal lobe epilepsy with and without a history of complex febrile seizures (CFS). DESIGN Survey. SETTING Epilepsy monitoring center. SUBJECTS Forty patients with localization-related epilepsy and temporal lobe onset determined by video electroencephalogram and 20 controls. INTERVENTION Magnetic resonance imaging measurement of cerebral volume. MAIN OUTCOME MEASURE Total cerebral volume. RESULTS Patients with a history of CFS had significantly reduced total cerebral volume compared with patients without CFS. In addition, male patients with CFS had significantly lower total cerebral volume than male normal controls. There was no significant difference between patients without CFS, or all patients, and controls. CONCLUSION Complex febrile seizures may have a global effect on brain development.
CXCL12-CXCR7 axis contributes to the invasive phenotype of pancreatic cancer

Chemokine (C-X-C motif) receptor 7 (CXCR7) and its ligand, chemokine (C-X-C motif) ligand 12 (CXCL12), were established to be involved in biological behaviors and associated with prognosis in many cancers. However, effects, underlying mechanisms of CXCL12-CXCR7 axis in invasive phenotype of pancreatic cancer (PC) and its clinicopathologic significances have not been comprehensively explored. In the present study, it was first found by tissue microarray-based immunohistochemistry that CXCL12 and CXCR7 staining scores were significantly associated with vessel invasion and overall survival in two independent cohorts of PC. Besides, co-expression of these proteins was an independent prognosticator in multivariate analysis in both cohorts. Then, migration and invasion, but not proliferation, were decreased in CXCR7-stably silenced PC cells, whereas opposite changes were observed in CXCR7-stably overexpressed cells, accompanied by alterations of mTOR and Rho/ROCK pathways. CXCL12 stimulated migration, invasion, CXCR7 expression and phosphorylation of key mTOR proteins. AMD3100 did not influence effects of CXCL12. Two mTOR inhibitors, rapamycin and Torin1, reversed enhanced invasive phenotypes and mTOR phosphorylation in CXCR7-overexpressed cells. Moreover, CXCR7 directly interacts with mTOR. Finally, liver metastasis, but not growth, was affected by CXCR7 status in orthotopically-implanted PC models in nude mice. Collectively, CXCL12-CXCR7 axis accelerates migration and invasion of PC cells through mTOR and Rho/ROCK pathways, and predicts poor prognosis of PC.
Identification of genes specifically methylated in Epstein–Barr virus‐associated gastric carcinomas

We studied the comprehensive DNA methylation status in the naturally derived gastric adenocarcinoma cell line SNU‐719, which was infected with the Epstein–Barr virus (EBV) by methylated CpG island recovery on chip assay. To identify genes specifically methylated in EBV‐associated gastric carcinomas (EBVaGC), we focused on seven genes, TP73, BLU, FSD1, BCL7A, MARK1, SCRN1, and NKX3.1, based on the results of methylated CpG island recovery on chip assay. We confirmed DNA methylation of the genes by methylation‐specific PCR and bisulfite sequencing in SNU‐719. The expression of the genes, except for BCL7A, was upregulated by a combination of 5‐Aza‐2′‐deoxycytidine and trichostatin A treatment in SNU‐719. After the treatment, unmethylated DNA became detectable in all seven genes by methylation‐specific PCR. We verified DNA methylation of the genes in 75 primary gastric cancer tissues from 25 patients with EBVaGC and 50 EBV‐negative patients who were controls. The methylation frequencies of TP73, BLU, FSD1, BCL7A, MARK1, SCRN1, and NKX3.1 were significantly higher in EBVaGC than in EBV‐negative gastric carcinoma. We identified seven genes with promoter regions that were specifically methylated in EBVaGC. Inactivation of these genes may suppress their function as tumor suppressor genes or tumor‐associated antigens and help to develop and maintain EBVaGC.
Bootstrapped Named Entity Recognition for Product Attribute Extraction

We present a named entity recognition (NER) system for extracting product attributes and values from listing titles. Information extraction from short listing titles present a unique challenge, with the lack of informative context and grammatical structure. In this work, we combine supervised NER with bootstrapping to expand the seed list, and output normalized results. Focusing on listings from eBay's clothing and shoes categories, our bootstrapped NER system is able to identify new brands corresponding to spelling variants and typographical errors of the known brands, as well as identifying novel brands. Among the top 300 new brands predicted, our system achieves 90.33% precision. To output normalized attribute values, we explore several string comparison algorithms and found n-gram substring matching to work well in practice.
Purification and Characterization of a Soluble and a Particulate Glutamate Dehydrogenase from Rat Brain

Glutamate dehydrogenase (GDH) activity was determined in high‐speed fractions (100,000 g for 60 min) obtained from whole rat brain homogenates after removal of a low‐speed pellet (480 g for 10 min). Approximately 60% of the high‐speed GDH activity was particulate (associated with membrane) and the remaining was soluble (probably of mitochondrial matrix origin). Most of the particulate GDH activity resisted extraction by several commonly used detergents, high concentration of salt, and sonication; however, it was largely extractable with the cationic detergent cetyltrimethylammonium bromide (CTAB) in hypotonic buffer solution. The two GDH activities were purified using a combination of hydrophobic interaction, ion exchange, and hydroxyapatite chromatography. Throughout these purification steps the two activities showed similar behavior. Kinetic studies indicated similar Km values for the two GDH fractions for the substrates μ‐ketoglutarate, ammonia, and glutamate; however, there were small but significant differences in Km values for NADH and NADPH. Although the allosteric stimulation by ADP and L‐leucine and inhibition by diethylstilbestrol was comparable, the two GDH components differed significantly in their susceptibility to GTP inhibition in the presence of 1 mM ADP, with apparent Ki values of 18.5 and 9.0 μM GTP for the soluble and particulate fractions, respectively. The HIll plot coefficient, binding constant, and cooperativity index for the GTP inhibition were also significantly different, indicating that the two GDH activities differ in their allosteric sites. In addition, enzyme activities of the two purified proteins exhibited a significant difference in thermal stability when inactivated at 45°C and pH 7.4 in 50 mM phosphate buffer.
Optimal Randomization of Signal Constellations on the Downlink of a Multiuser DS-CDMA System

In this study, the jointly optimal power control with signal constellation randomization is proposed for the downlink of a multiuser communications system. Unlike a conventional system in which a fixed signal constellation is employed for all the bits of a user (for given channel conditions and noise power), power control with signal constellation randomization involves randomization/time-sharing among different signal constellations for each user. A formulation is obtained for the problem of optimal power control with signal constellation randomization, and it is shown that the optimal solution can be represented by a randomization among (K+1) or fewer distinct signal constellations for each user, where K denotes the number of users. In addition to the original nonconvex formulation, an approximate solution based on convex relaxation is derived. Then, detailed performance analysis is presented when the receivers employ symmetric signaling and sign detectors. Specifically, the maximum asymptotical improvement ratio is shown to be equal to the number of users, and the conditions under which the maximum and minimum asymptotical improvement ratios are achieved are derived. Numerical examples are presented to investigate the theoretical results, and to illustrate performance improvements achieved via the proposed approach.
Outcome after temporal lobectomy in bilateral temporal lobe epilepsy

We determined how noninvasive presurgical data relate to prognosis after temporal lobectomy in patients with independent bilateral temporal lobe (IBTL) complex partial seizures on the intracranial electroencephalogram (EEG). Between 1986 and 1994, 28 patients had IBTL seizures on intracranial EEG. Fifteen of these 28 patients underwent temporal lobectomy and 13 were not offered surgery. Of the 15 patients who had surgery, 10 patients became seizure‐free. Magnetic resonance imaging (MRI) and the Wada test were the only variables associated with a seizure‐free outcome. Seven of 10 seizure‐free patients had a lateralized Wada result or the presence of unilateral hippocampal sclerosis, whereas none of the patients with persistent seizures had either of these findings. Variables not found to be predictive of a seizure‐free outcome included location of scalp interictal spikes, degree of seizure‐onset laterality, presence of early epilepsy risk factor, duration of epilepsy, and full‐scale intelligence quotient. We conclude that MRI and the Wada test provide information of prognostic value in patients with bilateral temporal seizures independent of intracranial EEG data.
A Multi-Agent Intelligent Design System Integrating Manufacturing and Shop-Floor Control

A multi-agnnt architectnre has been developed for the integration of design, riming, and shop floor control activities. This is based on cooperating intellismt entities in the sub-domain~ which make decisions through negotiation, using domain-specific knowledge both distributed among the entities and ao~ssible to them. Using this archRecmral framework, an Agent Based Coty~’rent Design Environment system has been developed for featarebased design, manufacturability evaluation, and dypnmlc process planning. This is a multi-agent prototype system involving the following types of agent: design agent; geometric interface agent; feature agent; part agem; machine agent; tool agent; environment manager; and shop floor manager. A new technique for evaluating manufacturability is introduced, based on interacting intelligent features of the part being designed. This proof-of-concept system was developed for three-dimensional prismatic parts, with twenty-five different feature types, but can be extended to other geometries. The system has been completed and tested, and is being integrated into a larger multi-agent environment incorporating muting, sehecbding, and overall production control.
Robust Price of Anarchy Bounds via LP and Fenchel Duality

Bounding the price of anarchy (PoA), which quantifies the degradation in the quality of outcomes in a (pure) Nash equilibrium of a game, is one of the fundamental questions in computational game theory. However, for a large class of games, a pure NE may not always exist and hence a natural question to pursue is to quantify the inefficiency for weaker notions of equilibrium such as mixed Nash equilibrium, correlated equilibrium or coarse correlated equilibrium, all of which are known to exist for finite games. Several techniques have been developed for bounding the price of anarchy, yet, only a handful of them are applicable for proving the PoA bounds for general equilibrium concepts. Most notable among such techniques is Roughgarden's elegant smoothness framework, which led to the concept of robust price of anarchy. The term refers to the inefficiency bounds applicable to general equilibrium notions such as coarse correlated equilibrium. In this paper, we develop a new framework based on LP and Fenchel duality for bounding the robust price of anarchy for a large class of games. We use our framework to give the first PoA bounds for temporal routing games on graphs and energy minimization games in machine scheduling. Most notably, we present the first coordination mechanisms with bounded PoA for temporal routing over general graphs, show a related lowerbound result, and an improved bound on the price of stability for this game. Previously, coordination mechanisms with bounded PoA were only known for restricted classes of graphs such as trees or parallel edges. Furthermore, we demonstrate the wide applicability of our framework by giving new proofs of the PoA bounds for three classical games - weighted affine congestion games, competitive facility location games and simultaneous second price auctions. Our price anarchy bounds for these games match the ones known in the literature or obtained using the smoothness framework. All our proofs use the following technique: we first show that for a wide class of games, one can formulate the underlying optimization problem as a linear (or convex) program such that the (Fenchel) dual of the relaxation encodes the equilibrium condition. Further, the dual program has a specific structure with variables for players and resources, which can be naturally interpreted as the cost incurred by the players and the congestion of the resource in an equilibrium outcome. This lets us argue that our definition of dual variables satisfy the dual constraints and using the weak duality theorem we establish the PoA bounds.
Brain training in progress: a review of trainability in healthy seniors

The cognitive deterioration associated with aging is accompanied by structural alterations and loss of functionality of the frontostriatal dopamine system. The question arises how such deleterious cognitive effects could be countered. Brain training, currently highly popular among young and old alike, promises that users will improve on certain neurocognitive skills, and this has indeed been confirmed in a number of studies. Based on these results, it seems reasonable to expect beneficial effects of brain training in the elderly as well. A selective review of the existing literature suggests, however, that the results are neither robust nor consistent, and that transfer and sustained effects thus far appear limited. Based on this review, we argue for a series of elements that hold potential for progress in successful types of brain training: (1) including flexibility and novelty as features of the training, (2) focusing on a number of promising, yet largely unexplored domains, such as decision-making and memory strategy training, and (3) tailoring the training adaptively to the level and progress of the individual. We also emphasize the need for covariance-based MRI methods in linking structural and functional changes in the aging brain to individual differences in neurocognitive efficiency and trainability in order to further uncover the underlying mechanisms.
A Validation and Reliability Study of the Physical Activity and Healthy Food Efficacy Scale for Children (PAHFE)

The purpose of this study was to obtain validity evidence for the Physical Activity and Healthy Food Efficacy Scale for Children (PAHFE). Construct validity evidence identifies four subscales: Goal-Setting for Physical Activity, Goal-Setting for Healthy Food Choices, Decision-Making for Physical Activity, and Decision-Making for Healthy Food Choices. The scores on each of these subscales show a moderate to high degree of internal consistency (0.59 ≤ α ≤ 0.87). The Decision-Making for Healthy Food Choice subscale and the Decision-Making for Physical Activity subscale scores show significant convergent validity evidence. These results provide support for using this self-efficacy scale to measure children's perceived confidence to make decisions about healthy eating and physical activity. The PAHFE may be considered to be a useful predictor of both physical activity and eating behaviors.
myo-Inositol Oxygenase is Required for Responses to Low Energy Conditions in Arabidopsis thaliana

myo-Inositol is a precursor for cell wall components, is used as a backbone of myo-inositol trisphosphate (Ins(1,4,5)P3) and phosphatidylinositol phosphate signaling molecules, and is debated about whether it is also a precursor in an alternate ascorbic acid synthesis pathway. Plants control inositol homeostasis by regulation of key enzymes involved in myo-inositol synthesis and catabolism. Recent transcriptional profiling data indicate up-regulation of the myo-inositol oxygenase (MIOX) genes under conditions in which energy or nutrients are limited. To test whether the MIOX genes are required for responses to low energy, we first examined MIOX2 and MIOX4 gene expression regulation by energy/nutrient conditions. We found that both MIOX2 and MIOX4 expression are suppressed by exogenous glucose addition in the shoot, but not in the root. Both genes were abundantly expressed during low energy/nutrient conditions. Loss-of-function mutants in MIOX genes contain alterations in myo-inositol levels and growth changes in the root. Miox2 mutants can be complemented with a MIOX2:green fluorescent protein fusion. Further we show here that MIOX2 is a cytoplasmic protein, while MIOX4 is present mostly in the cytoplasm, but also occasionally in the nucleus. Together, these data suggest that MIOX catabolism in the shoot may influence root growth responses during low energy/nutrient conditions.