Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphism in the couch potato gene clines in eastern Australia but is not associated with ovarian dormancy in Drosophila melanogaster

Natural selection can generate parallel latitudinal clines in traits and gene frequencies across continents, but these have rarely been linked. An amino acid (isoleucine to lysine, or I462K) polymorphism of the couch potato (cpo) gene in Drosophila melanogaster is thought to control female reproductive diapause cline in North America ( Schmidt et al. 2008 , Proc Natl Acad Sci USA, 105, 16207–16211). Here, we show that under standard diapause‐inducing conditions (12 °C and short photoperiod) ( Saunders et al. 1989 , Proc Natl Acad Sci USA, 86, 3748–3752), egg maturation in Australian flies is delayed, but not arrested at previtellogenic stages. At 12 °C, the phenotypic distribution in egg development was bimodal at stages 8 and 14 and showed a strong nonlinear pattern on the east coast of Australia, with incidence of egg maturation delay (ovarian dormancy) increasing both toward tropical and temperate climates. Furthermore, we found no evidence for an association between the cpo I462K polymorphism and ovarian dormancy at either 12 or 10 °C (when egg maturation was often delayed at stage 7). Owing to strong linkage disequilibrium, the latitudinal cline in cpo allele frequencies was no longer evident once variation in the In(3R)P inversion polymorphism was taken into account. Our results suggest that the standard diapause‐inducing conditions (12 °C and short photoperiod) were not sufficient to cause the typical previtellogenic developmental arrest in Australian flies and that the cpo I462K polymorphism does not explain the observed delay in egg development. In conclusion, ovarian dormancy does not show a simple latitudinal cline, and the lack of cpo‐dormancy association suggests a different genetic basis to reproductive dormancy in North America and Australia.
An easily-configurable robot audition system using Histogram-based Recursive Level Estimation

This paper presents an easily-configurable robot audition system using the Histogram-based Recursive Level Estimation (HRLE) method. In order to achieve natural human-robot interaction, a robot should recognize human speeches even if there are some noises and reverberations. Since the precision of automatic speech recognizers (ASR) have been degraded by such interference, many systems applying speech enhancement processes have been reported. However, performance of most reported systems suffer from acoustical environmental changes. For example, an enhancement process optimized for steady-state noise, such as fan noise, yields low performance when the process is used for non-steady-state noises, such as background music. The primary reason is mismatches of parameters because the appropriate parameters change according to the acoustical environments. To solve this problem, we propose a robot audition system that optimizes parameters adaptively and automatically. Our system applies linear and non-linear enhancement sub-processes. For the linear sub-process, we used Geometric Source Separation with the Adaptive Step-size method (GSS-AS). This adjusts the parameters adaptively and does not have any manual parameters. For the non-linear sub-process, we applied a spectral subtraction-based enhancement method with the HRLE method that is newly introduced in this paper. Since HRLE controls the threshold level parameter implicitly based on the statistical characteristics of noise and speech levels, our system has high robustness against acoustical environmental changes. For robot audition systems, all processes should be performed in real-time. We also propose implementation techniques to make HRLE run in real-time and show the effectiveness. We evaluate performance of our system and compare it to conventional systems based on the Minima Controlled Recursive Average (MCRA) method and Minimum Mean Square Error (MMSE) method. The experimental results show that our system achieves better performance than the conventional systems.
Energy-efficient statistical delay guarantee for duty-cycled wireless sensor networks

Radio duty cycling is a commonly employed mechanism to support long-term sustainable operations of WSNs. Combined with the effect of unreliable wireless links, many challenges arise for ensuring delay bounded data delivery with reliability constraint. However, research on energy-efficient data forwarding with statistical delay bound in duty-cycled WSNs still remains unaddressed. This paper proposes EDGE, a novel opportunistic forwarding technique tailored for duty-cycled WSNs with unreliable wireless links. The key idea is to exploit the available path diversity to minimize the transmission cost while providing statistical delay guarantees. Delay quantiles are derived at each node in a distributed manner and are used as the guidelines in forwarding decision making, so that an early arriving packet will be opportunistically switched to the energy-optimal path for communication cost minimization. Comprehensive evaluation results show that EDGE effectively reduces the transmission cost with statistical delay guarantees under various network settings.
MINIMAL ENERGIES OF BIPARTITE BICYCLIC GRAPHS

The energy of a graph is defined as the sum of the absolute values of all the eigenvalues of the graph. Let B(n) be the class of bipartite bicyclic graphs on n vertices containing a cycle with length congruent to 2 modulo 4. We determine respectively the graphs with minimal energies in the class of graphs in B(n )w ith exactly three cycles, in the class of graphs in B(n) with exactly two cycles of a common vertex, and in the class of graphs in B(n) with exactly two vertex-disjoint cycles.
Identification and Estimation of a Nonparametric Panel Data Model with Unobserved Heterogeneity ∗

This paper considers a nonparametric panel data model with nonadditive unobserved heterogeneity. As in the standard linear panel data model, two types of unobservables are present in the model: individual-specific effects and idiosyncratic disturbances. The individual-specific effects enter the structural function nonseparably and are allowed to be correlated with the covariates in an arbitrary manner. The idiosyncratic disturbance term is additively separable from the structural function. Nonparametric identification of all the structural elements of the model is established. No parametric distributional or functional form assumptions are needed for identification. The identification result is constructive and only requires panel data with two time periods. Thus, the model permits nonparametric distributional and counterfactual analysis of heterogeneous marginal effects using short panels. The paper also develops a nonparametric estimation procedure and derives its rate of convergence. As a by-product the rates of convergence for the problem of conditional deconvolution are obtained. The proposed estimator is easy to compute and does not require numeric optimization. A Monte-Carlo study indicates that the estimator performs very well in finite samples. ∗This paper is a revision of the first chapter of my thesis. I am very grateful to Donald Andrews, Xiaohong Chen, Yuichi Kitamura, Peter Phillips, and Edward Vytlacil for their advice, support, and enthusiasm. I am especially thankful to my advisor Yuichi Kitamura for all the effort and time he spent nurturing me intellectually. I have also benefited from discussions with Joseph Altonji, Stephane Bonhomme, Martin Browning, Victor Chernozhukov, Flavio Cunha, Bryan Graham, Jerry Hausman, James Heckman, Stefan Hoderlein, Joel Horowitz, Ilze Kalnina, Lung-Fei Lee, Simon Lee, Yoonseok Lee, Taisuke Otsu, James Powell, Pavel Stetsenko, and Quang Vuong. I also thank seminar participants at Yale, Brown, Chicago Booth, Chicago Economics, Duke, EUI, MIT/Harvard, Northwestern, Princeton, Toulouse, UC Berkeley, UCLA, Warwick, North American Summer Meeting of the Econometric Society 2009, SITE 2009 Summer Workshop on Advances in Nonparametric Econometrics, and Stats in the Chateau Summer School for very helpful comments. All errors are mine. Financial support of Cowles Foundation via Carl Arvid Anderson Prize is gratefully acknowledged. †E-mail: kevdokim@princeton.edu.
Positive effect of radiotherapy and surgery on hormonally active pulmonary metastases of primary parathyroid carcinoma.

OBJECTIVE Parathyroid carcinoma is a rare cause of primary hyperparathyroidism. Surgery is the primary treatment in recurrent or metastatic disease. Radiotherapy has been used as an adjuvant to control subclinical local disease but is otherwise considered ineffective. DESIGN We report on a patient with parathyroid carcinoma with hypercalcaemia and pulmonary metastases, treated with pamidronate and radiotherapy and later with surgery. METHODS The treatment was evaluated using serial analysis of serum parathyroid hormone (PTH) and calcium, clinical evaluation and chest radiographs. RESULTS Intravenous pamidronate alone had limited effect on hypercalcaemia. Following irradiation of the pulmonary lesions (34 Gy in ten fractions), serum levels of calcium and PTH decreased and pamidronate could be discontinued. The patient's general condition improved parallel to a radiological response. At clinical relapse 18 months following radiotherapy, the pulmonary metastases were resected and serum PTH was normalised. CONCLUSIONS The results indicate that parathyroid carcinoma can be radiosensitive. Thus radiotherapy may be an alternative to palliate symptoms of hypercalcaemia in patients not suited for surgery.
Gossip-based resource management for cloud environments

We address the problem of resource management for a large-scale cloud environment that hosts sites. Our contribution centers around outlining a distributed middleware architecture and presenting one of its key elements, a gossip protocol that meets our design goals: fairness of resource allocation with respect to hosted sites, efficient adaptation to load changes and scalability in terms of both the number of machines and sites. We formalize the resource allocation problem as that of dynamically maximizing the cloud utility under CPU and memory constraints. While we can show that an optimal solution without considering memory constraints is straightforward (but not useful), we provide an efficient heuristic solution for the complete problem instead. We evaluate the protocol through simulation and find its performance to be well-aligned with our design goals.
Towards Detecting Wikipedia Task Contexts

Wikipedia is a resource used by many people for many different purposes. We posit that it might be benecial to alter the content or the way content is presented depending on the task context. Here we describe a small pilot lab study to investigate features of interaction that might help to infer the contextual situation surrounding wikipedia search tasks. We describe our eort to collect data and analyse relationships between the features and the assigned task context.
Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells

The termination of the proliferation of Drosophila neural stem cells, also known as neuroblasts (NBs), requires a ‘decommissioning’ phase that is controlled in a lineage-specific manner. Most NBs, with the exception of those of the mushroom body (MB), are decommissioned by the ecdysone receptor and mediator complex, causing them to shrink during metamorphosis, followed by nuclear accumulation of Prospero and cell cycle exit. Here, we demonstrate that the levels of Imp and Syp RNA-binding proteins regulate NB decommissioning. Descending Imp and ascending Syp expression have been shown to regulate neuronal temporal fate. We show that Imp levels decline slower in the MB than in other central brain NBs. MB NBs continue to express Imp into pupation, and the presence of Imp prevents decommissioning partly by inhibiting the mediator complex. Late-larval induction of transgenic Imp prevents many non-MB NBs from decommissioning in early pupae. Moreover, the presence of abundant Syp in aged NBs permits Prospero accumulation that, in turn, promotes cell cycle exit. Together, our results reveal that progeny temporal fate and progenitor decommissioning are co-regulated in protracted neuronal lineages. Highlighted Article: Temporal progression of Imp/Syp gradients determines the timing of neuroblast decommissioning and cell cycle exit in addition to progeny temporal fate, allowing proper completion of a neuronal lineage.
Ankyrin binds to the 15th repetitive unit of erythroid and nonerythroid beta-spectrin

Ankyrin mediates the attachment of spectrin to transmembrane integral proteins in both erythroid and nonerythroid cells by binding to the beta-subunit of spectrin. Previous studies using enzymatic digestion, 2- nitro-5-thiocyanobenzoic acid cleavage, and rotary shadowing techniques have placed the spectrin-ankyrin binding site in the COOH-terminal third of beta-spectrin, but the precise site is not known. We have used a glutathione S-transferase prokaryotic expression system to prepare recombinant erythroid and nonerythroid beta-spectrin from cDNA encoding approximately the carboxy-terminal half of these proteins. Recombinant spectrin competed on an equimolar basis with 125I-labeled native spectrin for binding to erythrocyte membrane vesicles (IOVs), and also bound ankyrin in vitro as measured by sedimentation velocity experiments. Although full length beta-spectrin could inhibit all spectrin binding to IOVs, recombinant beta-spectrin encompassing the complete ankyrin binding domain but lacking the amino-terminal half of the molecule failed to inhibit about 25% of the binding capacity of the IOVs, suggesting that the ankyrin-independent spectrin membrane binding site must lie in the amino-terminal half of beta-spectrin. A nested set of shortened recombinants was generated by nuclease digestion of beta- spectrin cDNAs from ankyrin binding constructs. These defined the ankyrin binding domain as encompassing the 15th repeat unit in both erythroid and nonerythroid beta-spectrin, amino acid residues 1,768- 1,898 in erythroid beta-spectrin. The ankyrin binding repeat unit is atypical in that it lacks the conserved tryptophan at position 45 (1,811) within the repeat and contains a nonhomologous 43 residue segment in the terminal third of the repeat. It also appears that the first 30 residues of this repeat, which are highly conserved between the erythroid and nonerythroid beta-spectrins, are critical for ankyrin binding activity. We hypothesize that ankyrin binds directly to the nonhomologous segment in the 15th repeat unit of both erythroid and nonerythroid beta-spectrin, but that this sequence must be presented in the context of a properly folded spectrin "repeat unit" structure. Future studies will identify which residues within the repeat unit are essential for activity, and which residues determine the specificity of various spectrins for different forms of ankyrin.
Estimating parameters of sinusoids from noisy data using Bayesian inference with simulated annealing

In this paper, we consider Bayesian analysis proposed by Bretthorst for estimating parameters of the corrupted signals and incorporate it with a simulated annealing algorithm to obtain a global maximum of the posterior probability density of the parameters. Thus, this analysis offers different approach to find parameter values through a directed, but random, search of the parameter space. For this purpose, we developed a Mathematica code of this Bayesian approach and used it for recovering sinusoids corrupted by random noise. The simulation results support the effectiveness of the method.
A functional magnetic resonance imaging study of tic suppression in Tourette syndrome.

BACKGROUND The inability to inhibit unwanted behaviors and impulses produces functional debility in a broad range of neuropsychiatric disorders. A potentially important model of impulse control is volitional tic suppression in Tourette syndrome. METHODS Tic suppression was studied in 22 adult subjects with Tourette syndrome by using functional magnetic resonance imaging. Images acquired during periods of voluntary tic suppression were compared with images acquired when subjects allowed the spontaneous expression of their tics. The magnitudes of signal change in the images were then correlated with measures of the severity of tic symptoms. CONCLUSIONS Significant changes in signal intensity were seen in the basal ganglia and thalamus and in anatomically connected cortical regions believed to subserve attention-demanding tasks. The magnitudes of regional signal change in the basal ganglia and thalamus correlated inversely with the severity of tic symptoms. These findings suggest that the pathogenesis of tics involves an impaired modulation of neuronal activity in subcortical neural circuits.
Plantar pressure assessment.

Measurements of plantar pressure provide an indication of foot and ankle functions during gait and other functional activities, because the foot and ankle provide both the necessary support and flexibility for weight bearing and weight shifting while performing these activities.1–3 Although plantar pressure data have been recognized as an important element in the assessment of clients with diabetes and peripheral neuropathy, information derived from plantar pressure data also can assist in determining and managing the impairments associated with various musculoskeletal, integumentary, and neurological disorders. The use of force platforms is the method most commonly used to assess the interaction of the foot and supporting surface. Although the force platform provides valuable information regarding both the vertical and shear components of the ground reaction force, it provides little information on how the planter surface of the foot is loaded with respect to the supporting surface. When evaluating patients, atypical amounts of loading or patterns of loading may be reflective of a systemic or localized lower-extremity pathology and may be indicators (risk factors) for or predictors of further pathology or worsening of the existing pathology.4 In addition, force platforms have very specific requirements for attachment to the supporting surface on which data collection will occur. Such is not the case with numerous commercially available systems for measuring plantar pressure (eg, Emed sensor platform, * Pedar insole system, * F-Scan system,† Musgrave footprint system‡). Thus, plantar pressure measurement systems offer the clinician a high degree of portability, permitting utilization among multiple clinic sites. Pressure (p) (also called “stress”) is defined as force (f) per unit area (a) (ie, p=f/a). 5 Force , when measured using a force platform, is the net result of the 3 components of the ground reaction or resultant force acting on the foot. …
Three-Year Longitudinal Study of Genotypes of Mycobacterium tuberculosis Isolates in Tuscany, Italy

ABSTRACT The genetic diversity of 829 strains of Mycobacterium tuberculosis isolated during a 3-year period in Tuscany, Italy, a country with a low prevalence of tuberculosis, from 480 Italian-born and 349 foreign-born patients was determined by spoligotyping. The predominant spoligotype families were T (30.2% of isolates), Haarlem (19.9%), and the Latino-American and Mediterranean family (LAM) (11.2%); the remaining isolates were distributed among the Beijing (6.5%), S (4.2%), East Africa-India (EAI) (3.0%), Bovis (2.3%), Central Asia (CAS) (2.1%), Africanum (1.3%), and X (1.2%) families or were undefined (2.7%) or orphan (14.1%) isolates. Isolates of the families T, Haarlem, Bovis, and X were distributed among Italian- and foreign-born patients almost proportionally to the patients' numbers. Isolates of the LAM family were prevalent in foreign-born people (13.5%, versus 9.6% in Italian-born patients). Isolates of the S family were found almost exclusively in Italian-born patients, while strains of families EAI and CAS were isolated almost exclusively from foreign-born patients; Africanum isolates were all from African-born patients. The isolates of the Beijing family showed a trend to a steady increase during the survey. The prevalence of Beijing strains was 11.7% among foreign-born people and 2.7% among Italian-born patients. The Beijing strains were typed by the standardized IS6110 restriction fragment length polymorphism assay, which yielded a total of 38 distinct IS6110 patterns; 21 isolates (39.6%) occurred in six distinct clusters; of these, three contained two isolates and the other three contained four, five and six isolates, thus demonstrating that Beijing strains caused several tuberculosis outbreaks in the region. These findings indicate that transmission of Beijing strains between immigrants and the autochthonous population has occurred frequently and suggests an ongoing active transmission of the Beijing genotype in the region.
Metabolic and hormonal parameters in post-menopausal women 10 years after transdermal oestradiol treatment, alone or combined to micronised oral progesterone

Background. In the post-Women's Health Initiative Study era few post-menopausal women complete long term hormonal treatment (HT). Objective. To analyse metabolic/hormonal parameters and frequency of the metabolic syndrome (METS) in post-menopausal women after 10 years of HT. Methods. Retrospective data from parallel cohorts of post-menopausal women receiving HT for 10 years was analysed. Regimens included: transdermal oestradiol (50 μg) (n = 22), sequential cyclic HT with transdermal oestradiol (50 μg) plus 200 mg/day micronised oral progesterone (cycle days 12–25) (n = 83), or continuous combined HT with transdermal oestradiol (50 μg) plus 100 mg/day micronised oral progesterone (n = 46). A group of women who elected not to use HT served as a control group (n = 35). Results. Frequency of the METS did not significantly increase after 10 years of HT. Oestradiol and sex hormone binding globulin (SHBG) levels displayed a significant increase compared to baseline after 10 years of HT (all regimens). These values were significant higher when compared to the control group. Glucose levels were significantly higher after 10 years in women receiving the sequential cyclic regimen. Although not reaching statistical significance, there was a trend for transdermal oestradiol alone to increase HDL-C and decrease triglyceride levels. Conclusion. Serum oestradiol and SHBG levels were significantly higher after 10 years of transdermal oestradiol, alone or combined with micronised oral progesterone, without differences observed in serum metabolic parameters. More research through randomised clinical trials is required.